Contacts of the strand formed by residues 41 - 50 (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 GLY 41 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D ARG* 3.6 23.1 - - - +
35E ARG 3.7 0.5 - - - +
36E GLN* 3.6 28.8 - - - -
37E ASP 3.4 8.3 + - - -
39E GLY 4.7 0.4 - - - +
40E MET* 1.3 85.9 - - - +
42E LEU* 1.3 60.7 + - - -
43E ARG* 3.7 2.3 + - - +
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Residues in contact with LEU 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 3.6 27.1 - - + -
89D LEU* 4.4 10.3 - - + -
104D PHE* 4.0 42.1 - - + +
106D ARG* 5.6 0.2 - - - +
34E TYR* 3.9 34.7 - - + -
35E ARG 3.6 1.6 - - - -
36E GLN* 3.8 32.1 + - + +
40E MET 4.8 0.3 - - - +
41E GLY* 1.3 70.7 - - - -
43E ARG* 1.3 64.2 + - - +
44E LEU 4.2 0.7 + - - -
58E GLU* 4.9 1.4 - - - +
89E PHE* 4.0 15.7 - - + -
103E PHE* 4.4 3.1 - - + -
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Residues in contact with ARG 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E TYR* 3.3 3.9 - - - -
35E ARG* 3.0 36.9 + - + +
37E ASP* 3.1 28.7 + - - +
40E MET* 3.3 49.1 - - - +
41E GLY 4.4 1.5 + - - +
42E LEU* 1.3 76.6 - - - +
44E LEU* 1.3 54.8 + - - +
45E ILE* 2.8 30.0 - - - +
58E GLU* 3.7 30.7 - - - +
59E VAL* 4.0 30.3 - - + +
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Residues in contact with LEU 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ILE* 3.6 49.1 - - + -
30E TYR* 4.7 2.5 - - - +
32E SER* 3.8 18.4 - - - -
33E TRP 3.4 15.9 - - - +
34E TYR* 3.5 28.9 - - + +
42E LEU 4.2 0.2 + - - -
43E ARG* 1.3 70.2 - - - +
45E ILE* 1.3 58.0 + - - +
46E HIS 3.7 15.7 - - - +
47E TYR* 4.1 7.9 - - + -
57E GLY* 3.9 14.6 - - - -
58E GLU* 2.7 36.9 + - + +
59E VAL 3.0 8.7 + - - -
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Residues in contact with ILE 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E TRP* 2.8 17.7 + - + +
34E TYR* 3.3 9.6 - - - +
35E ARG* 3.1 33.7 - - + +
43E ARG 2.8 29.6 - - - +
44E LEU* 1.3 73.5 - - - +
46E HIS* 1.3 79.4 + - + +
57E GLY* 2.8 25.0 + - - -
59E VAL* 3.8 18.6 - - + +
60E PRO* 3.6 8.0 - - - +
63E TYR* 3.5 38.1 - - + -
75E LEU* 4.2 7.0 - - + -
88E TYR* 5.1 4.7 - - + -
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Residues in contact with HIS 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E SER* 3.5 0.5 - - - -
33E TRP* 3.0 26.1 + - + +
44E LEU* 3.7 5.4 - - - +
45E ILE* 1.3 98.8 + - + +
47E TYR* 1.3 64.8 + - - +
54E THR* 5.7 0.6 + - - -
55E ASP 3.4 17.1 + - - +
56E GLN* 3.6 13.2 - - + -
57E GLY 4.1 1.6 - - - +
60E PRO* 3.4 28.3 + - + -
63E TYR* 3.1 30.1 + - + -
64E ASN* 4.3 1.9 - - - -
65E VAL* 3.6 47.0 - - + +
73E PHE* 3.9 2.0 - - - -
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Residues in contact with TYR 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ARG* 3.4 25.2 + - - -
99D SER* 3.1 31.6 - - - -
101D ILE* 3.5 27.8 - - + +
30E TYR* 3.7 23.8 - + + +
31E MET 3.3 13.0 - - - +
32E SER* 3.9 10.3 - - - -
44E LEU* 4.1 7.4 - - + -
46E HIS* 1.3 76.1 - - - +
48E SER* 1.3 67.3 + - - +
49E VAL* 4.2 11.9 - - + -
54E THR* 3.3 5.5 - - - -
55E ASP* 2.8 66.0 + - + +
56E GLN 3.6 11.9 - - - -
73E PHE* 3.7 5.2 - - - -
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Residues in contact with SER 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E GLU 3.3 1.7 - - - +
30E TYR* 3.2 5.4 - - - -
31E MET 2.9 31.8 + - - -
47E TYR* 1.3 79.2 - - - +
49E VAL* 1.3 62.0 + - - +
50E GLY 2.9 14.8 + - - -
53E ILE 2.6 27.5 + - - -
54E THR* 4.3 0.9 - - - +
55E ASP* 4.9 1.1 - - - +
67E ARG* 3.0 18.9 + - - +
73E PHE* 3.7 21.5 - - - -
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Residues in contact with VAL 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ARG* 3.7 30.3 - - + +
68A LYS* 4.3 10.3 - - + -
69A ALA* 3.9 26.3 - - + +
72A GLN* 3.9 0.9 - - - +
98D GLY 5.1 0.2 - - - +
100D TYR* 3.7 31.6 - - + -
29E GLU* 3.1 27.4 - - - +
30E TYR* 4.4 8.5 - - + +
47E TYR* 4.2 18.4 - - + -
48E SER* 1.3 73.7 + - - +
50E GLY* 1.3 57.1 + - - +
53E ILE* 4.2 15.2 + - + +
55E ASP* 5.7 1.5 + - - +
95E VAL* 4.7 2.5 - - + -
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Residues in contact with GLY 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLN* 3.7 16.8 - - - -
29E GLU 3.3 4.2 + - - -
48E SER* 2.9 15.8 + - - -
49E VAL* 1.3 82.7 - - - +
51E ALA* 1.3 67.5 + - - -
53E ILE* 3.0 19.5 + - - +
67E ARG* 3.3 13.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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