Contacts of the strand formed by residues 30 - 37 (chain E) in PDB entry 2BNQ
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 TYR 30 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ARG* 3.6 15.0 - - - -
99D SER 3.9 10.3 - - - -
100D TYR* 3.9 18.6 - - + -
101D ILE* 3.9 6.1 - - - +
102D PRO* 3.4 21.9 - - + +
28E HIS* 4.1 0.9 - - - +
29E GLU* 1.3 80.3 - - - +
31E MET* 1.3 61.3 + - - +
32E SER* 3.7 32.7 + - - -
34E TYR* 4.8 0.2 + - - -
44E LEU* 4.7 2.8 - - - +
47E TYR* 3.7 29.6 - + + +
48E SER 3.2 11.4 - - - -
49E VAL* 4.4 6.7 - - + +
91E ALA 4.2 1.6 - - - -
92E SER* 3.1 7.2 - - - -
93E SER* 2.9 57.6 + - - +
94E TYR 4.5 0.2 - - - +
95E VAL* 4.0 13.7 - - + -
101E LEU* 4.1 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 31 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E CYS* 3.6 29.4 - - - +
24E GLN* 4.0 14.4 - - + +
28E HIS 4.5 3.1 - - - +
30E TYR* 1.3 82.6 - - - +
32E SER* 1.3 63.2 + - - +
47E TYR* 3.3 2.3 - - - +
48E SER 2.9 31.4 + - - +
67E ARG* 3.6 37.7 - - - +
70E THR 3.7 9.0 - - - +
71E GLU 3.7 19.7 - - - +
73E PHE* 3.5 34.6 - - + -
90E CYS* 4.2 1.3 - - - -
91E ALA 3.4 5.8 - - - +
92E SER* 3.8 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 32 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E TYR* 3.7 20.2 - - - -
31E MET* 1.3 77.7 - - - +
33E TRP* 1.3 63.3 + - - +
34E TYR* 3.8 8.0 - - - -
44E LEU* 3.8 19.7 - - - -
46E HIS 3.5 7.4 - - - -
47E TYR* 3.9 1.6 - - - -
73E PHE* 3.6 5.3 - - - -
90E CYS* 3.1 11.3 - - - -
91E ALA* 2.8 56.0 + - - +
101E LEU* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E GLN* 3.8 24.0 - - + -
20E LEU* 3.6 36.3 - - + -
21E GLN 3.9 9.4 - - - -
22E CYS* 3.5 20.4 - - + +
32E SER* 1.3 72.7 - - - +
34E TYR* 1.3 59.0 + - - +
44E LEU* 3.4 7.6 - - - +
45E ILE* 2.8 39.2 + - + -
46E HIS 3.0 11.0 + - - +
65E VAL* 4.2 6.7 - - + -
73E PHE* 2.6 49.4 + + - -
75E LEU* 3.5 42.1 - - + +
88E TYR* 3.9 17.0 - - + -
89E PHE 3.5 18.2 - - - -
90E CYS* 3.8 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D ILE* 5.3 0.2 - - - +
102D PRO* 3.5 32.1 + - + +
104D PHE* 3.5 24.8 - + - -
30E TYR* 4.8 0.5 + - - -
32E SER* 3.8 19.1 - - - -
33E TRP* 1.3 76.4 - - - +
35E ARG* 1.3 58.8 + - - +
42E LEU* 3.9 28.9 - - + -
43E ARG 3.3 23.8 - - - -
44E LEU* 3.5 26.5 - - + +
45E ILE* 3.3 9.6 - - - -
88E TYR* 3.2 10.3 - - - +
89E PHE* 2.7 39.9 + - + +
91E ALA* 4.1 12.1 - - + -
101E LEU* 5.8 0.9 - - + -
103E PHE* 4.0 22.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E TYR* 1.3 76.4 - - - +
36E GLN* 1.3 59.9 + - - +
37E ASP* 2.8 38.4 + - - +
41E GLY 3.7 1.2 - - - +
42E LEU* 3.6 2.1 - - - -
43E ARG* 3.0 46.9 + - + +
45E ILE* 3.1 20.1 - - + +
59E VAL* 4.2 17.3 - - + -
63E TYR* 3.1 28.5 + - - -
83E SER* 2.9 30.7 + - - -
84E GLN* 4.0 2.9 - - - +
85E THR 3.4 11.5 + - - -
86E SER* 3.5 11.1 + - - +
87E VAL 3.4 5.8 - - - -
88E TYR* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 36 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D GLN* 2.9 44.1 + - - -
89D LEU* 4.9 2.3 - - - +
35E ARG* 1.3 76.0 - - - +
37E ASP* 1.3 66.5 + - - +
38E PRO* 4.8 0.7 - - - +
41E GLY* 3.6 17.1 - - - +
42E LEU* 3.8 28.7 + - + +
86E SER* 3.0 11.6 + - - -
87E VAL* 2.9 29.0 + - + +
89E PHE* 3.3 17.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 37 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E ARG* 2.8 43.1 + - - +
36E GLN* 1.3 79.5 - - - +
38E PRO* 1.3 77.3 - - + +
39E GLY 3.3 0.7 + - - -
40E MET* 2.9 29.6 + - + +
41E GLY 3.4 9.5 + - - -
43E ARG* 3.1 14.6 + - - +
85E THR 3.6 3.8 - - - +
86E SER* 2.6 24.7 + - - -
----------------------------------------------------------
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