Contacts of the strand formed by residues 26 - 33 (chain B) in PDB entry 2VN9
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 SER 26 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 3.2 3.8 - - - +
23B GLY* 2.5 41.7 + - - +
25B PHE* 1.3 81.3 - - - +
27B VAL* 1.3 65.0 + - - +
28B VAL* 4.8 2.4 - - - +
43B LYS* 3.5 37.4 - - - +
44B ILE 3.4 13.2 - - - -
45B ILE* 4.3 8.1 - - - -
1310B GVD 5.9 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU* 3.4 37.5 - - + +
21B GLY 3.8 3.1 - - - -
22B LYS* 4.3 9.4 - - + +
26B SER* 1.3 77.7 - - - +
28B VAL* 1.3 64.9 + - - +
29B ARG* 3.8 20.6 - - + -
42B ALA 3.6 0.7 - - - +
43B LYS* 3.4 2.9 - - - -
44B ILE* 2.8 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU* 3.4 3.3 - - - -
20B LEU* 2.7 42.3 + - + -
21B GLY 2.8 22.6 + - - +
22B LYS 5.0 0.2 - - - +
26B SER* 4.8 4.5 - - - +
27B VAL* 1.3 77.9 - - - +
29B ARG* 1.3 57.2 + - - +
41B ALA* 3.9 26.2 - - + -
42B ALA 3.2 9.9 - - - +
43B LYS* 4.2 19.7 - - + -
1310B GVD 3.8 47.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 4.0 26.9 + - + +
17B PHE* 2.7 30.4 + - - +
18B GLU* 3.1 12.9 - - - +
19B GLU* 3.9 7.4 - - + +
20B LEU* 4.1 3.6 - - - -
27B VAL* 3.8 15.0 - - + -
28B VAL* 1.3 77.9 - - - +
30B ARG* 1.3 64.4 + - - +
41B ALA 3.7 0.2 - - - -
42B ALA* 2.8 38.2 + - + +
44B ILE* 3.4 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.6 1.0 - - - -
17B PHE* 2.7 57.0 + - - +
18B GLU* 2.8 53.0 + - - +
20B LEU* 3.6 18.1 - - + +
29B ARG* 1.3 73.7 - - - +
31B CYS* 1.3 61.3 + - - +
32B MET* 3.8 19.6 - - - +
39B GLU* 2.7 40.5 + - - +
40B TYR 3.5 12.3 - - - +
92B LEU* 4.3 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B MET* 5.2 1.3 - - + -
14B TYR* 3.9 23.6 - - + -
15B GLN 3.0 17.5 - - - +
16B LEU* 4.2 3.8 - - + -
17B PHE* 4.0 2.7 - - - -
30B ARG* 1.3 77.8 - - - +
32B MET* 1.3 65.7 + - - +
33B LYS 4.3 0.2 - - - -
39B GLU* 3.3 6.9 - - - +
40B TYR* 2.9 55.0 + - - -
42B ALA* 3.8 28.7 - - + -
89B VAL* 4.1 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 3.3 4.7 - - - -
15B GLN* 2.8 39.6 + - + +
17B PHE* 3.5 29.8 - - + -
30B ARG* 3.8 19.7 - - - +
31B CYS* 1.3 78.0 - - - +
33B LYS* 1.3 67.6 + - - +
34B ILE* 3.5 1.1 + - + +
37B GLY* 3.8 30.3 - - - +
38B GLN 3.2 4.5 - - - +
39B GLU* 4.1 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLU* 3.5 18.9 + - - +
14B TYR* 3.5 37.5 + - + -
32B MET* 1.3 72.8 - - - +
34B ILE* 1.3 70.1 + - - +
35B PRO 3.8 0.3 - - - -
36B THR* 3.3 22.5 + - + +
37B GLY* 3.0 28.6 + - - -
38B GLN* 2.9 17.6 + - + +
40B TYR* 4.2 20.2 - - + +
78B ASP* 5.0 4.1 + - - -
----------------------------------------------------------
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