Contacts of the helix formed by residues 628 - 643 (chain A) in PDB entry 4G34
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 ARG 628 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A PRO* 3.3 2.5 - - + +
627A ASN* 1.3 82.1 - - + +
629A GLU* 1.3 64.0 + - - +
630A LEU* 3.6 1.6 - - + +
631A ALA* 3.7 16.7 + - + +
632A ARG* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 629 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A ASN 3.7 1.8 + - - -
628A ARG* 1.3 72.7 - - - +
630A LEU* 1.3 65.7 - - + +
632A ARG* 3.4 8.5 + - - +
633A GLU* 3.1 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 630 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A ARG* 4.8 1.2 - - + +
629A GLU* 1.3 81.1 - - + +
631A ALA* 1.3 64.9 + - - +
633A GLU* 3.5 20.8 + - + +
634A LYS* 3.2 28.8 + - + +
637A ARG* 4.9 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 631 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A PRO* 3.8 25.1 - - + -
628A ARG* 3.7 13.9 + - + +
629A GLU 3.4 0.6 - - - -
630A LEU* 1.3 76.2 - - - +
632A ARG* 1.3 62.8 + - - +
634A LYS* 3.6 9.0 - - - +
635A VAL* 3.4 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 632 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A LEU* 3.4 29.3 + - + +
626A PRO* 3.6 28.1 + - - +
627A ASN* 4.6 13.5 + - - +
628A ARG 3.2 18.0 + - - +
629A GLU* 3.6 7.5 - - - +
630A LEU 3.3 0.2 - - - -
631A ALA* 1.3 75.6 - - - +
633A GLU* 1.3 60.4 + - + +
635A VAL* 3.3 6.6 + - - +
636A MET* 3.0 35.8 + - + +
658A LEU* 6.3 0.9 - - - -
880A LYS* 5.5 2.6 - - - +
881A VAL* 3.7 33.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 633 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A GLU* 3.1 44.8 + - + +
630A LEU* 3.8 21.4 - - + +
631A ALA 3.4 0.2 - - - -
632A ARG* 1.3 75.0 - - + +
634A LYS* 1.3 65.2 + - - +
636A MET* 3.4 7.2 + - - +
637A ARG* 3.0 49.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 634 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A LEU* 3.2 17.4 + - + +
631A ALA* 3.6 11.0 - - - +
632A ARG 3.3 0.2 - - - -
633A GLU* 1.3 76.6 - - - +
635A VAL* 1.3 57.6 + - + +
637A ARG* 3.3 26.4 + - - +
638A GLU* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 635 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A ILE* 5.8 4.0 - - + -
625A LEU* 3.7 26.7 - - + -
626A PRO* 4.5 15.5 - - + -
631A ALA 3.4 13.9 + - - +
632A ARG* 3.3 8.6 + - - +
634A LYS* 1.3 80.7 - - + +
636A MET* 1.3 64.8 + - + +
638A GLU* 3.2 9.1 + - - +
639A VAL* 3.0 28.1 + - - +
883A LEU* 3.9 5.8 - - + -
957A LEU* 3.6 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 636 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A LEU* 3.9 13.7 - - + -
632A ARG* 3.0 29.6 + - + +
633A GLU* 3.8 7.6 - - - +
635A VAL* 1.3 95.3 - - + +
637A ARG* 1.3 61.0 + - + +
639A VAL* 3.7 9.6 + - + +
640A LYS* 3.3 40.6 + - - +
658A LEU* 4.0 30.1 - - + -
883A LEU* 3.9 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 637 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A LEU* 4.9 2.8 + - - +
633A GLU* 3.0 43.4 + - - +
634A LYS* 3.6 33.9 - - - +
635A VAL 3.2 0.2 - - - -
636A MET* 1.3 73.9 - - + +
638A GLU* 1.3 66.0 + - - +
640A LYS* 3.3 12.7 + - + +
641A ALA* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 638 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A LYS 3.0 13.9 + - - +
635A VAL* 3.3 10.5 - - - +
637A ARG* 1.3 76.8 - - - +
639A VAL* 1.3 61.7 + - - +
641A ALA* 3.3 8.4 + - - +
642A LEU* 3.0 38.5 + - + +
932A LEU* 5.5 6.2 - - - +
935A ARG* 5.7 2.6 + - - -
956A GLY* 2.9 36.7 - - - +
957A LEU* 3.6 22.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 639 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A VAL 3.0 20.7 + - - +
636A MET* 3.8 15.3 - - + +
637A ARG 3.3 0.2 - - - -
638A GLU* 1.3 76.3 - - - +
640A LYS* 1.3 59.3 + - + +
642A LEU* 3.3 8.8 + - - +
643A ALA* 3.0 30.7 + - + +
653A TYR* 5.3 4.0 - - + +
656A ALA* 4.0 27.1 - - + -
883A LEU* 3.6 31.4 - - + -
885A ILE* 4.7 6.5 - - + -
957A LEU* 4.2 10.8 - - + -
1101A 924 5.7 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 640 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A MET* 3.3 30.8 + - - +
637A ARG* 3.3 13.8 + - + +
638A GLU 3.3 0.8 - - - -
639A VAL* 1.3 79.4 - - + +
641A ALA* 1.3 61.9 + - - +
643A ALA* 4.0 6.0 + - - +
644A LYS* 3.6 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 641 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A ARG 3.1 12.9 + - - +
638A GLU* 3.6 11.0 - - - +
640A LYS* 1.3 77.6 - - - +
642A LEU* 1.3 67.4 + - + +
644A LYS* 3.3 25.1 + - - +
645A LEU* 3.8 10.4 - - - +
932A LEU* 5.2 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 642 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A GLU* 3.0 39.2 + - + +
639A VAL* 3.3 5.8 + - - +
641A ALA* 1.3 76.4 - - + +
643A ALA* 1.3 57.7 + - - +
645A LEU* 2.9 37.0 + - + +
885A ILE* 5.5 0.7 - - + -
932A LEU* 4.9 7.2 - - + -
955A PHE* 3.5 46.7 - - + +
956A GLY* 4.4 0.9 - - - -
957A LEU* 4.1 25.1 - - + -
1101A 924 3.2 40.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 643 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A VAL* 3.0 19.1 + - + +
640A LYS* 4.2 7.4 - - - +
641A ALA 3.3 0.4 - - - -
642A LEU* 1.3 75.7 - - - +
644A LYS* 1.3 60.1 + - + +
645A LEU 3.2 4.2 + - - +
653A TYR* 3.8 45.9 - - + +
1101A 924 4.1 3.7 - - - -
----------------------------------------------------------
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