Contacts of the helix formed by residues 629 - 645 (chain A) in PDB entry 4X7J
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 629 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A PHE* 5.3 8.2 - - - -
627A PRO* 3.1 5.6 - - + +
628A ASN* 1.3 80.9 - - + +
630A GLU* 1.3 60.0 + - - +
631A LEU* 4.6 13.2 - - + +
632A ALA* 3.1 36.0 + - + +
633A ARG* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 630 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A ASN 3.6 5.2 + - - +
629A ARG* 1.3 71.2 - - - +
631A LEU* 1.3 76.1 + - + +
633A ARG* 3.4 30.7 + - - +
634A GLU* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 631 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A ARG* 3.3 14.2 - - + +
630A GLU* 1.3 92.0 - - + +
632A ALA* 1.3 61.1 + - - +
634A GLU* 3.4 15.5 + - + +
635A LYS* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 632 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A PHE* 4.6 10.5 - - + -
627A PRO* 3.6 20.0 - - + -
629A ARG* 3.1 42.2 + - + +
631A LEU* 1.3 76.6 - - - +
633A ARG* 1.3 59.3 + - - +
635A LYS* 3.3 9.0 + - - +
636A VAL* 3.0 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 633 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A LEU* 4.0 26.9 - - + -
627A PRO* 3.1 44.7 + - + +
628A ASN* 3.1 24.4 + - - +
629A ARG 2.9 8.8 + - - +
630A GLU* 3.5 32.4 + - - +
631A LEU 3.3 0.2 - - - -
632A ALA* 1.3 72.3 - - - +
634A GLU* 1.3 65.9 + - - +
636A VAL* 3.4 6.8 + - - +
637A MET* 3.0 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 634 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A GLU 2.9 15.1 + - - +
631A LEU* 3.4 20.4 - - + +
632A ALA 3.3 0.2 - - - -
633A ARG* 1.3 77.2 - - - +
635A LYS* 1.3 58.3 + - - +
637A MET* 3.5 3.3 + - - +
638A ARG* 3.0 70.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 635 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A LEU 3.1 13.8 + - - +
632A ALA* 3.6 11.9 - - - +
633A ARG 3.3 0.2 - - - -
634A GLU* 1.3 76.4 + - - +
636A VAL* 1.3 58.3 + - + +
638A ARG* 3.4 26.3 + - - +
639A GLU* 2.9 66.4 + - - +
936A ARG* 5.0 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 636 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A PHE* 4.7 17.5 - - + -
624A ILE* 4.5 25.1 - - + -
626A LEU* 3.9 16.2 - - + -
627A PRO* 4.8 5.4 - - + -
632A ALA 3.0 21.9 + - - +
633A ARG* 3.4 6.9 + - - +
635A LYS* 1.3 77.4 - - + +
637A MET* 1.3 62.7 + - - +
639A GLU* 3.2 7.5 + - - +
640A VAL* 3.1 23.6 + - - +
884A LEU* 3.5 26.5 - - + -
886A ILE* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 637 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A LEU* 4.5 18.6 - - + -
633A ARG* 3.0 25.0 + - + +
634A GLU* 4.1 3.8 - - - +
636A VAL* 1.3 73.8 - - + +
638A ARG* 1.3 62.7 + - - +
640A VAL* 3.1 26.1 - - + +
641A LYS* 3.4 34.9 + - - +
659A LEU* 4.3 28.0 - - + -
884A LEU* 4.3 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 638 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A GLU* 3.0 52.1 + - - +
635A LYS* 3.6 24.2 - - - +
637A MET* 1.3 76.7 - - - +
639A GLU* 1.3 72.6 + - - +
641A LYS* 3.4 11.4 + - - +
642A ALA* 3.1 27.2 + - + +
936A ARG* 5.7 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 639 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A LYS* 2.9 55.2 + - + +
636A VAL* 3.2 6.4 + - - +
638A ARG* 1.3 85.6 + - - +
640A VAL* 1.3 59.7 + - - +
642A ALA* 3.3 7.2 + - + +
643A LEU* 2.9 30.8 + - - +
936A ARG* 3.7 17.8 + - - -
955A ASP* 5.0 7.1 - - - +
1101A 3Z1 4.1 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 640 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A VAL 3.1 13.1 + - - +
637A MET* 3.1 32.3 - - + +
639A GLU* 1.3 75.3 - - - +
641A LYS* 1.3 59.9 + - + +
643A LEU* 3.4 8.5 + - + +
644A ALA* 3.0 29.0 + - + +
654A TYR* 4.5 10.3 - - + +
657A ALA* 3.5 32.5 - - + -
884A LEU* 4.2 18.2 - - + -
886A ILE* 4.5 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 641 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A MET* 3.4 39.1 + - - +
638A ARG* 3.6 11.2 - - + +
639A GLU 3.3 0.2 - - - -
640A VAL* 1.3 82.6 - - + +
642A ALA* 1.3 61.9 + - - +
644A ALA* 3.6 12.2 + - - +
645A LYS* 3.7 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 642 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A ARG* 3.1 18.7 + - + +
639A GLU* 3.7 7.9 - - + +
640A VAL 3.3 0.2 - - - -
641A LYS* 1.3 73.5 - - - +
643A LEU* 1.3 66.5 + - - +
645A LYS* 3.2 26.5 + - - +
646A LEU* 3.4 14.6 - - - +
933A LEU* 4.7 14.4 - - + -
1101A 3Z1 4.0 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 643 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A GLU 2.9 17.0 + - - +
640A VAL* 3.6 8.1 - - - +
642A ALA* 1.3 76.1 - - - +
644A ALA* 1.3 56.6 - - - +
646A LEU* 2.9 32.6 + - + +
651A ILE* 4.8 4.9 - - + -
652A VAL 4.7 6.1 - - - +
654A TYR* 4.1 20.0 - - + +
886A ILE* 4.2 13.5 - - + -
888A MET* 4.0 33.0 - - + -
1101A 3Z1 3.7 62.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A VAL* 3.0 18.1 + - + +
641A LYS* 3.8 9.0 - - - +
642A ALA 3.3 0.4 - - - -
643A LEU* 1.3 75.9 - - - +
645A LYS* 1.3 59.7 + - + +
646A LEU 3.3 2.6 + - - +
654A TYR* 3.6 43.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A LYS* 3.7 18.3 + - - +
642A ALA* 3.2 16.5 + - - +
643A LEU 3.0 1.6 + - - -
644A ALA* 1.3 77.6 - - + +
646A LEU* 1.3 66.0 + - + +
647A GLU* 3.8 3.3 + - - +
931A LYS* 5.4 5.7 + - - -
----------------------------------------------------------
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