Contacts of the strand formed by residues 37 - 41 (chain B) in PDB entry 2VES
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 ILE 37 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B THR 4.8 0.3 - - - +
36B GLY* 1.3 71.4 - - - -
38B VAL* 1.3 63.9 + - - +
39B PHE* 4.2 13.5 - - + -
51B PRO* 3.8 0.9 - - - +
52B ALA* 2.8 32.1 + - + +
53B ARG* 6.0 0.2 - - - -
80B LEU* 3.8 27.6 - - + -
83B MET* 4.0 25.6 - - + -
88B ILE* 3.7 20.4 - - + +
89B ASP 3.7 9.2 - - - +
90B ASN 4.4 0.2 - - - -
91B ALA* 3.5 18.8 - - + +
93B VAL* 4.3 16.4 - - + -
247B TYR* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B THR* 3.6 37.0 - - + +
37B ILE* 1.3 80.9 - - - +
39B PHE* 1.3 69.1 + - - +
49B GLU* 3.8 24.2 - - + +
50B ILE 3.9 9.9 - - - +
51B PRO* 4.3 15.5 - - + -
91B ALA 3.0 7.0 + - - +
92B TYR* 3.2 27.4 - - + +
93B VAL* 2.7 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 4.2 3.4 - - + -
38B VAL* 1.3 75.1 - - - +
40B SER* 1.3 60.1 + - - +
48B VAL 3.9 0.5 - - - +
49B GLU* 3.3 3.1 - - - -
50B ILE* 2.8 42.5 + - + +
52B ALA* 3.9 19.1 - - + -
66B LEU* 3.4 30.1 - - + -
73B VAL* 4.1 31.4 - - + -
76B VAL* 3.8 22.4 - - + -
79B LEU* 4.3 7.4 - - + -
80B LEU* 4.0 18.2 - - + -
93B VAL* 3.3 40.2 - - + -
95B LEU* 4.1 3.6 - - + -
100B VAL* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL 4.3 0.9 + - - -
39B PHE* 1.3 76.8 + - - +
41B ARG* 1.3 62.7 + - - +
42B THR* 3.1 16.8 + - - -
47B VAL* 4.1 11.9 - - - -
48B VAL 3.4 4.3 - - - -
49B GLU* 3.7 15.3 + - - +
73B VAL* 5.5 0.7 - - - -
92B TYR* 4.1 18.2 - - - +
93B VAL 2.8 13.5 + - - +
94B GLU* 3.5 10.4 - - - +
95B LEU* 2.8 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE 4.3 0.2 - - - -
40B SER* 1.3 68.7 - - - +
42B THR* 1.3 57.1 + - - +
43B ASP* 2.9 42.0 + - - +
44B LEU* 3.2 43.4 + - + +
47B VAL* 3.6 4.1 - - - +
48B VAL* 2.7 30.3 + - + +
50B ILE* 5.2 0.9 - - + -
71B VAL* 3.7 25.7 - - + +
72B LYS* 2.9 22.8 + - - +
73B VAL* 3.8 24.0 - - + -
95B LEU* 3.9 2.0 - - - -
97B ALA* 3.3 22.8 + - - +
98B SER* 3.4 21.5 - - - +
----------------------------------------------------------
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