Contacts of the strand formed by residues 20 - 30 (chain A) in PDB entry 2VXE
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 20 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU 3.8 0.5 - - - +
15A ILE* 3.6 6.0 - - - -
16A SER* 3.1 28.1 + - - -
18A ALA* 3.1 36.6 - - + +
19A ASP* 1.3 80.2 - - - +
21A ARG* 1.3 66.3 + - - +
22A TYR* 3.1 45.9 - - + +
43A SER* 4.9 4.9 - - - -
45A GLY 3.6 16.8 - - - +
46A THR* 3.3 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 4.3 17.7 - - - +
14A LEU 3.8 4.5 - - - +
15A ILE* 4.9 9.6 - - + +
19A ASP 4.1 1.2 + - - +
20A ILE* 1.3 76.2 - - - +
22A TYR* 1.3 61.8 + - - +
43A SER* 3.6 3.3 - - - -
44A PHE* 3.2 62.3 + - + -
45A GLY 4.2 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 3.8 2.8 + - - -
14A LEU* 2.9 44.2 + - + +
16A SER* 3.2 31.0 - - - -
20A ILE* 3.1 44.7 - - + +
21A ARG* 1.3 77.3 - - - +
23A GLU* 1.3 61.1 + - - +
38A LEU* 6.5 0.2 - - - -
41A VAL* 4.4 11.4 - - + -
42A ARG 3.6 4.9 - - - +
43A SER* 3.4 29.1 - - - -
44A PHE* 4.6 1.3 - - - -
46A THR* 5.3 0.3 - - - +
62A TYR* 5.8 4.5 - + - -
65A ILE* 5.1 9.6 - - + -
67A PHE* 4.5 26.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 4.9 14.7 - - + +
12A ILE 3.4 20.4 - - - +
13A SER* 4.4 10.8 + - - -
14A LEU* 5.5 0.2 - - - -
22A TYR* 1.3 76.4 - - - +
24A GLY* 1.3 61.8 + - - +
38A LEU* 6.3 0.7 - - - -
41A VAL* 2.8 18.7 - - - +
42A ARG* 3.0 41.5 + - + +
44A PHE* 3.2 34.0 - - + -
78A VAL* 5.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 3.9 3.0 - - - -
12A ILE* 3.2 31.9 + - - +
23A GLU* 1.3 77.9 - - - +
25A ARG* 1.3 66.4 + - - -
26A LEU 3.8 0.2 + - - -
38A LEU* 4.6 10.1 - - - +
40A SER 3.2 14.6 - - - -
41A VAL* 3.7 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLY* 4.4 19.3 - - - +
10A SER 3.7 5.6 - - - +
11A LYS* 4.7 5.2 - - + +
24A GLY* 1.3 74.7 - - - -
26A LEU* 1.3 64.2 + - - +
27A TYR 3.2 0.3 + - - -
38A LEU* 3.4 4.8 - - - -
39A SER* 2.9 45.0 + - - +
40A SER* 3.2 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO* 3.9 33.2 - - + +
7A GLU 4.1 12.6 - - - +
8A LEU* 4.8 10.4 - - + +
9A GLY* 3.5 23.1 + - - +
10A SER* 3.2 15.5 + - - +
12A ILE* 3.2 30.5 - - + +
24A GLY 3.8 1.4 + - - -
25A ARG* 1.3 69.9 - - - +
27A TYR* 1.3 61.6 + - - +
28A THR* 4.7 15.9 - - - +
29A VAL* 5.2 14.1 - - + -
36A ILE* 5.6 7.4 - - + -
38A LEU* 3.7 16.3 - - + +
39A SER* 4.7 0.8 + - - -
75A ILE* 5.8 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.7 13.1 - - - +
25A ARG 3.2 2.8 + - - -
26A LEU* 1.3 76.5 - - - +
28A THR* 1.3 94.7 + - + +
37A ALA 3.3 13.5 + - - +
38A LEU 4.3 0.4 - - - -
39A SER* 3.6 32.3 - - - +
64A TYR* 3.4 34.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 6.1 1.1 - - - -
26A LEU* 4.7 6.1 - - - +
27A TYR* 1.3 112.3 + - + +
29A VAL* 1.3 63.4 + - - +
36A ILE* 3.9 1.9 - - - +
37A ALA* 3.1 45.0 + - - +
64A TYR* 3.8 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO* 5.5 15.7 - - + -
26A LEU* 5.2 13.7 - - + -
28A THR* 1.3 79.8 - - - +
30A ASP* 1.3 69.2 + - - +
31A PRO* 3.8 13.1 - - + +
35A THR 4.1 3.6 - - - +
36A ILE* 3.6 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 1.3 77.1 - - - +
31A PRO* 1.3 66.7 - - - +
32A GLN* 3.5 7.3 + - - +
33A GLU* 3.0 38.5 + - - +
34A CYS* 3.2 15.2 + - - -
35A THR* 3.0 32.9 + - - +
36A ILE* 4.7 0.2 - - - +
----------------------------------------------------------
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