Contacts of the helix formed by residues 2729 - 2758 (chain A) in PDB entry 4ERV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER2729 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2727A VAL* 4.2 1.8 + - - +
2728A LEU* 1.3 76.6 - - - +
2730A ARG* 1.3 59.4 + - - +
2731A GLU* 3.6 14.5 + - - +
2732A LEU* 3.0 36.6 + - - +
2733A GLN* 3.0 22.9 + - - +
2792A GLN* 4.7 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2730 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2728A LEU 3.8 0.2 + - - -
2729A SER* 1.3 72.6 - - - +
2731A GLU* 1.3 60.9 + - - +
2733A GLN* 3.3 17.8 + - - +
2734A GLY* 3.1 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2731 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2729A SER* 3.2 12.0 + - - +
2730A ARG* 1.3 76.0 - - - +
2732A LEU* 1.3 64.2 + - - +
2734A GLY* 3.2 4.0 + - - -
2735A MET* 3.1 36.9 + - - +
2798A VAL 5.0 2.7 - - - -
2799A SER* 3.7 12.8 - - - -
2800A ARG* 3.1 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2732 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2728A LEU* 4.2 14.4 - - + -
2729A SER* 3.0 31.5 + - - +
2731A GLU* 1.3 79.0 - - + +
2733A GLN* 1.3 57.7 + - - +
2735A MET* 3.2 11.7 + - - +
2736A VAL* 2.8 32.8 + - - +
2788A PHE* 3.7 32.2 - - + -
2792A GLN* 3.5 39.7 - - + +
2797A ILE* 5.0 6.3 - - + -
2798A VAL* 3.6 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2733 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2728A LEU* 2.7 38.1 + - + +
2729A SER 3.0 14.4 + - - +
2730A ARG* 3.6 16.3 - - - +
2731A GLU 3.2 0.2 - - - -
2732A LEU* 1.3 78.1 - - - +
2734A GLY* 1.3 61.8 + - - +
2736A VAL* 3.4 21.8 - - - +
2737A GLU* 3.4 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY2734 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2730A ARG 3.1 13.3 + - - -
2731A GLU* 3.2 4.6 + - - -
2733A GLN* 1.3 75.7 - - - +
2735A MET* 1.3 61.1 + - - +
2737A GLU* 3.2 17.7 + - - +
2738A VAL* 3.3 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET2735 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2684A TRP* 3.6 48.3 - - + -
2731A GLU* 3.1 38.8 + - - +
2732A LEU* 3.2 17.7 + - + +
2734A GLY* 1.3 74.7 - - - +
2736A VAL* 1.3 65.2 + - - +
2738A VAL* 3.1 6.4 + - + +
2739A VAL* 3.0 21.3 + - - +
2788A PHE* 3.9 11.0 - - + -
2798A VAL* 3.6 43.5 - - + +
2799A SER 4.2 4.3 - - - +
2800A ARG* 4.0 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2736 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2728A LEU* 3.8 23.8 - - + -
2732A LEU 2.8 20.1 + - - +
2733A GLN* 3.4 10.8 - - - +
2735A MET* 1.3 76.7 - - - +
2737A GLU* 1.3 70.0 + - - +
2739A VAL 3.3 0.7 + - - -
2740A ALA* 2.8 27.5 + - - +
2781A ARG* 4.1 6.3 - - - +
2784A ALA* 3.6 12.7 - - + +
2785A GLN* 3.6 31.9 - - + +
2788A PHE* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2737 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2733A GLN 3.4 11.1 + - - +
2734A GLY* 3.2 11.6 + - - +
2735A MET 3.2 0.8 - - - -
2736A VAL* 1.3 83.5 - - - +
2738A VAL* 1.3 61.1 + - + +
2740A ALA* 3.9 2.4 - - - +
2741A GLU* 2.9 31.2 + - - +
2769A TYR* 2.8 33.5 + - + -
2777A LYS* 5.2 0.3 + - - -
2781A ARG* 2.9 39.6 + - - +
2785A GLN* 5.5 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2738 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2603A ILE* 4.8 9.8 - - + +
2682A VAL* 4.7 16.4 - - + -
2684A TRP* 3.8 27.8 - - + -
2734A GLY 3.3 13.4 + - - +
2735A MET* 3.1 7.9 + - - +
2737A GLU* 1.3 76.3 - - + +
2739A VAL* 1.3 64.8 + - + +
2741A GLU* 3.8 5.8 - - - +
2742A ASN* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2739 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2603A ILE* 6.3 0.2 - - - -
2675A SER* 5.2 6.1 - - - +
2678A THR* 5.4 13.7 - - + -
2679A MET* 4.7 11.7 - - + -
2684A TRP* 3.6 30.3 - - + -
2735A MET 3.0 10.5 + - - +
2736A VAL 3.8 6.3 - - - +
2738A VAL* 1.3 76.4 - - + +
2740A ALA* 1.3 63.9 + - - +
2742A ASN* 3.1 9.5 + - + +
2743A TYR* 3.0 55.9 + - + +
2784A ALA* 3.8 11.4 - - + -
2787A LEU* 6.3 0.4 - - + -
2788A PHE* 3.8 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2740 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2736A VAL 2.8 20.5 + - - +
2737A GLU* 3.9 2.2 - - - +
2739A VAL* 1.3 73.7 - - - +
2741A GLU* 1.3 61.3 + - - +
2743A TYR* 3.3 15.6 + - - +
2744A HIS* 3.1 19.6 + - - +
2769A TYR* 3.5 25.9 - - + +
2780A ASP* 3.6 29.9 - - - +
2781A ARG* 3.8 9.4 - - + +
2784A ALA* 4.0 0.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2741 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2598A PHE* 6.1 0.7 - - - -
2737A GLU 2.9 19.0 + - - +
2738A VAL* 3.8 6.8 - - - +
2740A ALA* 1.3 77.5 - - - +
2742A ASN* 1.3 57.0 + - - +
2744A HIS* 3.2 4.2 + - - +
2745A ASN* 2.9 44.1 + - - +
2768A PRO* 5.3 3.8 - - - +
2769A TYR* 3.7 46.2 + - + +
2770A ASP* 4.6 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2742 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2601A LYS 4.5 1.2 - - - +
2602A PRO* 3.6 6.8 - - - +
2603A ILE* 2.9 49.4 + - + +
2678A THR* 3.7 25.4 + - + +
2738A VAL 3.0 14.0 + - - +
2739A VAL* 3.1 11.3 + - - +
2741A GLU* 1.3 73.8 - - - +
2743A TYR* 1.3 70.5 + - - +
2745A ASN* 3.1 9.5 + - - +
2746A ILE* 2.9 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR2743 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2675A SER* 2.6 36.2 + - - -
2678A THR* 6.2 0.4 - - - -
2739A VAL* 3.0 41.6 + - + +
2740A ALA* 3.3 5.1 + - - +
2742A ASN* 1.3 81.1 - - - +
2744A HIS* 1.3 63.0 + - - +
2746A ILE* 3.3 18.1 + - + +
2747A TRP* 3.1 21.7 + - - +
2780A ASP* 3.5 35.2 - - - +
2783A LYS* 3.5 53.9 + - + +
2784A ALA* 3.7 12.5 - - - -
2787A LEU* 4.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS2744 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2598A PHE* 4.6 2.2 - + - -
2740A ALA 3.1 6.9 + - - -
2741A GLU 3.2 7.8 + - - +
2743A TYR* 1.3 74.8 - - - +
2745A ASN* 1.3 67.9 + - - +
2747A TRP* 3.2 21.1 + + - +
2748A ALA* 2.8 30.7 + - + +
2765A LEU* 3.2 23.5 + - + -
2767A VAL 2.7 27.2 + - - -
2769A TYR* 3.6 34.3 - - + -
2772A LEU* 3.7 24.6 - - + +
2780A ASP* 3.7 18.1 + - - +
2906A GOL 4.8 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2745 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2598A PHE* 3.7 23.4 - - - -
2600A PRO* 3.6 19.0 - - + +
2601A LYS 4.3 11.1 + - - +
2602A PRO* 4.0 15.9 - - + +
2741A GLU* 2.9 40.1 + - - +
2742A ASN* 3.1 12.2 + - - +
2744A HIS* 1.3 77.6 - - - +
2746A ILE* 1.3 61.1 + - - +
2748A ALA* 4.2 0.4 - - - -
2749A LYS* 2.9 32.2 + - - +
2769A TYR 5.2 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2746 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2602A PRO* 3.8 29.2 - - + -
2603A ILE 5.9 0.9 - - - +
2678A THR* 5.7 1.3 - - - +
2742A ASN* 2.9 37.8 + - - +
2743A TYR* 3.6 17.9 - - + +
2745A ASN* 1.3 74.1 - - - +
2747A TRP* 1.3 65.1 + - - +
2749A LYS* 4.0 1.7 - - - +
2750A LYS* 3.1 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP2747 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2743A TYR 3.1 13.4 + - - +
2744A HIS* 3.2 19.0 + + - +
2746A ILE* 1.3 77.1 - - - +
2748A ALA* 1.3 85.5 + - + +
2750A LYS* 3.3 13.7 + - + +
2751A LYS* 2.9 53.0 + - + +
2763A HIS* 3.6 18.4 - + - -
2765A LEU* 3.5 44.9 - - + -
2766A LEU* 4.2 1.8 - - - -
2780A ASP* 6.1 0.4 - - - +
2901A SO4 2.9 32.0 + - - -
2906A GOL 3.1 37.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2748 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2598A PHE* 3.8 11.7 - - + -
2600A PRO* 3.8 18.6 - - + -
2744A HIS* 2.8 26.0 + - - +
2745A ASN* 3.9 2.7 - - - +
2747A TRP* 1.3 87.9 - - + +
2749A LYS* 1.3 59.8 + - - +
2751A LYS* 3.2 1.6 + - - +
2752A LYS* 2.8 30.1 + - - +
2766A LEU* 3.6 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2749 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2600A PRO* 3.6 22.3 - - + +
2602A PRO* 3.5 29.4 - - + +
2745A ASN 2.9 18.3 + - - +
2746A ILE 4.0 3.4 - - - +
2748A ALA* 1.3 72.5 - - - +
2750A LYS* 1.3 66.6 + - + +
2752A LYS* 3.3 11.5 + - + +
2753A LEU* 2.9 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2750 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2746A ILE* 3.1 38.6 + - + +
2747A TRP* 3.4 13.9 - - + +
2749A LYS* 1.3 76.6 - - - +
2751A LYS* 1.3 55.8 + - - +
2753A LEU* 3.5 8.8 + - + +
2754A GLU* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2751 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2747A TRP* 2.9 41.3 + - + +
2748A ALA* 3.2 5.1 + - - +
2750A LYS* 1.3 72.6 - - - +
2752A LYS* 1.3 60.0 + - - +
2754A GLU* 2.7 36.1 + - - +
2755A LEU* 2.8 44.3 + - + +
2763A HIS* 4.0 38.3 - - + -
2766A LEU* 4.7 4.7 - - + -
2901A SO4 3.0 37.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2752 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2598A PHE 4.4 9.6 - - - +
2599A ASP* 4.0 19.6 + - - +
2600A PRO* 4.2 20.9 - - + -
2748A ALA 2.8 15.9 + - - +
2749A LYS* 3.3 11.4 + - + +
2751A LYS* 1.3 76.8 - - - +
2753A LEU* 1.3 65.3 + - - +
2755A LEU* 3.4 3.9 + - - +
2756A GLU* 2.9 62.8 + - + +
2766A LEU* 3.9 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2753 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2749A LYS* 2.9 45.4 + - + +
2750A LYS* 3.9 6.5 - - - +
2752A LYS* 1.3 80.9 - - + +
2754A GLU* 1.3 60.6 + - - +
2756A GLU* 3.4 20.1 + - + +
2757A SER* 3.0 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2754 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2750A LYS 2.9 18.1 + - - +
2751A LYS* 2.7 41.0 + - + +
2753A LEU* 1.3 77.1 - - - +
2755A LEU* 1.3 61.5 + - + +
2757A SER* 2.5 27.6 + - - +
2758A LYS* 3.3 30.2 + - + +
2901A SO4 3.9 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2755 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2751A LYS* 2.8 31.1 + - + +
2752A LYS* 3.7 4.0 - - - +
2754A GLU* 1.3 72.4 - - + +
2756A GLU* 1.3 61.7 + - + +
2758A LYS* 3.1 20.2 + - + +
2760A GLY* 2.9 31.6 + - - +
2761A GLY* 3.5 32.1 - - - +
2762A SER* 3.7 30.1 - - - +
2763A HIS* 4.0 7.2 - - + +
2766A LEU* 3.7 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2756 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2752A LYS* 2.9 52.5 + - + +
2753A LEU* 3.8 25.1 - - + +
2755A LEU* 1.3 77.4 - - + +
2757A SER* 1.3 62.5 + - - +
2758A LYS 3.2 1.0 + - - -
2759A GLY* 3.3 12.0 + - - -
2760A GLY* 4.0 8.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER2757 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2753A LEU 3.0 13.8 + - - -
2754A GLU* 2.5 25.0 + - - +
2756A GLU* 1.3 75.4 - - - +
2758A LYS* 1.3 60.5 + - - +
2759A GLY 3.4 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2758 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2754A GLU* 3.6 37.7 - - + +
2755A LEU* 3.1 24.4 + - + +
2757A SER* 1.3 78.6 - - - +
2759A GLY* 1.3 58.6 + - - +
2760A GLY 4.1 8.0 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il