Contacts of the strand formed by residues 86 - 93 (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 SER 86 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35E ARG* 3.5 15.0 + - - +
36E GLN 3.0 16.4 + - - -
37E ASP* 2.6 27.9 + - - -
84E GLN 3.1 8.4 + - - -
85E THR* 1.3 78.0 - - - +
87E VAL* 1.3 70.7 + - - +
88E TYR* 4.0 11.9 - - - -
107E SER 3.9 0.3 - - - +
108E ARG* 3.8 1.7 - - - +
109E LEU* 3.0 30.4 + - - +
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Residues in contact with VAL 87 (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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42D LYS 5.8 0.2 - - - +
35E ARG* 3.4 2.4 - - - -
36E GLN* 2.9 41.7 + - + +
86E SER* 1.3 80.4 + - - +
88E TYR* 1.3 64.8 + - - +
89E PHE* 3.6 32.0 + - + -
106E GLY* 4.8 1.1 - - - -
107E SER 3.4 11.7 - - - +
108E ARG* 3.9 32.5 - - + +
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Residues in contact with TYR 88 (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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5E GLN* 2.9 20.9 + - - -
20E LEU* 3.6 27.4 - - + -
33E TRP* 3.9 6.7 - - + -
34E TYR 3.2 15.0 - - - +
35E ARG* 3.9 13.5 - - + -
45E ILE* 5.1 2.9 - - + -
63E TYR* 2.8 45.6 + + - -
75E LEU* 3.9 17.3 - - + -
77E LEU* 5.0 0.9 - - + -
84E GLN* 2.5 32.7 + - - +
86E SER* 4.0 19.8 - - - -
87E VAL* 1.3 75.2 - - - +
89E PHE* 1.3 62.6 + - - +
106E GLY* 3.3 3.5 - - - -
107E SER* 2.7 31.8 + - - +
109E LEU* 4.0 20.0 - - + +
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Residues in contact with PHE 89 (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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38D GLN* 3.9 8.1 - - - -
42D LYS 4.0 4.5 - - - -
43D GLY* 3.7 32.3 - - - -
44D LEU* 4.4 4.7 - - + -
5E GLN* 3.7 0.9 - - - -
33E TRP* 3.5 5.6 - - - -
34E TYR* 2.7 46.7 + - + +
36E GLN* 3.3 25.8 - - + -
42E LEU* 4.0 17.5 - - + -
87E VAL* 3.6 26.9 - - + -
88E TYR* 1.3 74.7 - - - +
90E CYS* 1.3 60.6 + - - +
103E PHE* 3.8 25.8 - + + -
104E GLY 3.6 13.9 - - - -
105E GLU 3.8 1.3 - - - -
106E GLY* 3.4 26.7 - - - -
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Residues in contact with CYS 90 (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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3E VAL* 4.2 2.9 - - + +
5E GLN* 2.9 17.0 + - - +
22E CYS* 2.0 53.6 - - + -
31E MET* 4.2 9.9 - - - -
32E SER 3.1 17.0 - - - +
33E TRP* 3.8 17.2 - - + -
73E PHE* 4.9 0.9 - - - -
89E PHE* 1.3 74.2 - - - +
91E ALA* 1.3 63.9 + - - +
102E PHE 3.9 0.2 - - - +
103E PHE* 3.4 2.6 - - - +
104E GLY* 2.7 28.8 + - - -
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Residues in contact with ALA 91 (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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3E VAL* 5.5 0.2 - - - -
30E TYR* 4.2 1.4 - - - -
31E MET* 3.4 1.3 - - - -
32E SER* 2.8 51.6 + - - +
34E TYR* 4.1 8.1 - - + -
89E PHE 4.0 0.2 + - - -
90E CYS* 1.3 76.6 - - - +
92E SER* 1.3 60.6 + - - +
101E LEU* 4.3 13.9 - - + -
102E PHE 3.2 9.4 - - - +
103E PHE* 4.0 28.7 - - + -
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Residues in contact with SER 92 (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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3E VAL* 3.5 20.9 - - - +
24E GLN* 3.7 9.3 - - - +
28E HIS* 2.9 21.9 + - - -
30E TYR* 3.1 16.2 - - - -
31E MET* 3.8 18.6 - - - -
90E CYS* 5.7 0.4 - - - -
91E ALA* 1.3 75.5 - - - +
93E SER* 1.3 64.0 + - - +
101E LEU* 3.7 1.7 - - - -
102E PHE* 2.9 33.6 + - - +
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Residues in contact with SER 93 (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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93D ARG* 2.3 37.4 + - - -
28E HIS* 3.3 21.6 + - - +
30E TYR* 2.9 38.1 + - - -
92E SER* 1.3 75.0 - - - +
94E TYR* 1.3 67.1 + - - +
99E GLY 4.1 0.9 - - - -
100E GLU 3.0 22.9 - - - -
101E LEU* 4.2 2.2 - - - -
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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