Contacts of the strand formed by residues 2 - 8 (chain B) in PDB entry 2VSH
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 2 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B HIS* 4.0 16.2 - - + +
1B MET* 1.3 77.8 - - - +
3B TYR* 1.3 65.0 + - - +
45B SER* 3.4 38.7 + - - +
46B ILE* 3.5 23.6 - - + -
47B GLU* 2.7 36.0 + - - +
107B ILE* 3.6 29.2 - - + -
109B VAL* 4.3 1.8 - - + -
127B ILE* 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 3 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.4 26.9 - - + +
2B ILE* 1.3 76.0 - - - +
4B ALA* 1.3 61.7 + - - +
46B ILE* 4.1 4.7 - - - -
47B GLU* 3.6 17.4 - - + +
48B LYS* 3.6 33.0 - - + +
50B VAL* 4.7 0.7 - - + -
96B ILE* 3.6 53.2 - - + +
99B TYR* 3.6 17.9 - + - -
100B ARG* 3.5 30.7 + - - +
106B ASP* 4.5 12.8 + - + -
107B ILE 2.9 17.6 + - - +
108B VAL* 3.4 2.6 - - + -
109B VAL* 2.8 31.1 + - - +
175B CYS* 5.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 4 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TYR* 1.3 76.0 - - - +
5B GLY* 1.3 59.7 + - - +
6B ILE* 3.9 6.3 - - + -
40B PHE* 3.4 40.6 - - + -
46B ILE* 3.7 5.7 - - + +
48B LYS 3.1 7.4 + - - +
49B ILE* 4.1 18.6 - - + -
50B VAL* 2.8 30.4 + - - +
108B VAL* 4.1 2.1 - - - +
109B VAL* 3.5 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ALA* 1.3 72.5 - - - +
6B ILE* 1.3 63.5 + - - +
7B LEU* 3.6 4.7 + - - +
50B VAL 3.4 4.5 - - - -
92B ILE* 4.0 17.7 - - - -
108B VAL* 3.7 16.7 - - - +
109B VAL 2.9 11.6 + - - -
110B THR* 3.1 7.2 - - - -
111B HIS 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ALA* 4.4 4.3 - - + -
5B GLY* 1.3 76.0 - - - +
7B LEU* 1.3 62.7 + - - +
8B ALA 3.4 0.7 - - - -
33B LEU* 4.0 16.2 - - + -
36B THR* 4.4 8.7 - - + -
37B ILE* 4.9 5.8 - - + -
40B PHE* 3.5 43.7 - - + -
49B ILE* 4.0 24.7 - - + -
50B VAL 2.8 11.9 + - - +
51B VAL* 3.6 10.3 - - + -
52B GLY 2.9 28.8 - - - -
92B ILE* 3.9 1.4 - - - -
111B HIS* 3.4 9.2 - - + +
113B SER* 3.7 32.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLY 3.6 13.7 - - - +
6B ILE* 1.3 68.5 + - - +
8B ALA* 1.3 59.5 + - - +
9B GLY 3.7 2.9 + - - +
52B GLY 4.4 0.7 - - - +
85B ARG* 4.0 31.2 - - + +
88B SER* 3.7 24.2 - - - -
89B ILE* 4.0 17.5 - - + -
92B ILE* 3.6 25.4 - - + -
110B THR* 3.8 13.5 - - - -
111B HIS 3.0 28.1 + - - +
112B ASP* 4.1 9.2 - - - +
113B SER* 2.9 25.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE 3.4 0.6 - - - -
7B LEU* 1.3 73.3 - - - +
9B GLY* 1.3 56.1 + - - +
23B GLN* 2.9 27.0 + - + +
24B PHE* 4.7 2.8 - - + -
33B LEU* 4.2 5.8 - - + -
51B VAL* 4.0 11.7 - - + -
52B GLY 2.8 20.4 + - - +
53B VAL* 3.5 25.4 - - + +
54B HIS* 4.1 1.7 + - - +
113B SER* 3.4 24.5 - - - +
----------------------------------------------------------
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