Contacts of the helix formed by residues 54 - 61 (chain B) in PDB entry 7A62
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 GLN 54 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 2.8 15.7 + - + +
52B SER* 2.9 29.5 + - - +
53B GLY* 1.3 80.2 - - - +
55B LEU* 1.3 66.0 + - - +
56B ARG 3.4 2.0 - - - -
57B GLU* 3.3 24.4 + - - +
58B ARG* 3.0 55.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 3.7 21.8 - - + -
46B LEU* 3.4 28.9 - - + -
49B LEU* 3.1 30.3 + - + +
50B ILE* 4.1 7.9 - - + +
53B GLY 3.6 1.8 - - - -
54B GLN* 1.3 77.2 - - - +
56B ARG* 1.3 65.8 + - + +
58B ARG* 3.0 6.4 + - - +
59B VAL* 3.0 26.5 + - + +
86B ILE* 4.5 1.3 - - + +
89B ALA* 3.4 43.1 - - + +
90B TYR* 3.6 12.3 - - + +
502B GOL 3.9 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLN 3.4 0.2 - - - -
55B LEU* 1.3 78.2 - - + +
57B GLU* 1.3 63.3 + - - +
59B VAL* 3.3 2.1 + - - +
60B GLU* 3.0 36.9 + - - +
90B TYR* 2.9 47.6 + - + +
91B VAL 2.9 24.7 + - - -
93B GLY* 3.2 18.4 - - - +
94B LYS 5.3 0.4 - - - +
98B ASP* 2.8 48.5 + - - +
99B VAL* 3.6 4.0 - - - +
100B ARG* 3.3 27.7 - - - +
502B GOL 3.4 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLY 4.7 3.9 + - - +
54B GLN* 3.3 32.2 + - - +
55B LEU 3.2 0.8 - - - -
56B ARG* 1.3 78.9 - - - +
58B ARG* 1.3 64.1 + - + +
60B GLU* 3.2 22.0 + - - +
61B LYS* 3.3 35.7 + - - +
502B GOL 5.3 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 3.8 28.5 - - - -
42B ILE* 4.0 22.5 - - + +
49B LEU* 4.1 22.6 - - + +
54B GLN* 3.0 45.1 + - - +
55B LEU* 3.0 9.0 + - - +
57B GLU* 1.3 75.8 + - + +
59B VAL* 1.3 65.9 + - - +
60B GLU 3.4 0.2 + - - -
61B LYS* 3.4 29.8 + - - +
62B LEU* 3.5 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 4.5 7.2 - - + -
55B LEU* 3.0 25.7 + - + +
56B ARG 3.3 6.7 + - - +
58B ARG* 1.3 76.8 - - - +
60B GLU* 1.3 61.8 + - - +
62B LEU* 3.2 24.7 + - + +
86B ILE* 3.7 25.8 - - + -
90B TYR* 3.9 28.9 - - + -
103B LEU* 5.6 0.7 - - + -
104B PRO* 4.5 15.8 - - + +
106B ASN* 5.5 2.3 - - - +
107B ILE* 3.9 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ARG* 3.0 27.4 + - - +
57B GLU* 3.2 12.5 + - - +
59B VAL* 1.3 78.3 - - - +
61B LYS* 1.3 58.4 + - - +
62B LEU 3.7 4.0 + - - +
90B TYR* 2.9 32.0 + - + +
100B ARG* 4.8 5.5 + - - -
104B PRO* 4.4 13.5 - - + -
106B ASN* 5.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 3.3 32.9 + - - +
58B ARG* 3.7 26.5 - - - +
59B VAL 3.2 0.4 - - - -
60B GLU* 1.3 74.1 - - - +
62B LEU* 1.3 66.0 + - - +
63B ASN* 3.5 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