Contacts of the strand formed by residues 94 - 103 (chain A) in PDB entry 2BNR
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 THR 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A THR* 4.2 7.0 - - + -
11A SER 3.3 9.0 - - - +
12A VAL* 4.2 12.8 - - + +
92A SER* 5.3 0.3 + - - -
93A HIS* 1.3 79.3 + - - +
95A VAL* 1.3 73.1 + - - +
96A GLN* 4.2 8.7 - - - +
117A ALA 3.9 0.3 - - - +
118A TYR* 3.4 6.2 - - - -
119A ASP* 2.7 39.4 + - - -
120A GLY 4.6 0.3 + - - -
31B HIS* 4.1 17.6 + - - +
32B PRO* 4.7 12.3 - - - +
33B SER* 5.2 1.4 + - - +
62B PHE* 4.0 27.1 - - + -
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Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A PHE 4.6 0.2 - - - -
10A THR* 3.6 0.2 - - - -
11A SER* 2.8 44.1 + - - +
74A HIS* 3.6 21.3 + - + +
77A ASP* 5.1 1.1 - - + -
78A LEU* 3.8 18.6 - - + +
81A LEU* 3.4 31.2 - - + -
94A THR* 1.3 77.6 - - - +
96A GLN* 1.3 69.2 + - - +
116A TYR* 3.4 34.3 - - + +
117A ALA 3.4 3.8 - - - +
118A TYR* 3.7 8.1 - - + -
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Residues in contact with GLN 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A PHE 3.1 6.7 - - - +
10A THR* 4.2 3.1 - - - +
74A HIS* 5.7 0.2 - - - -
94A THR* 4.2 5.7 - - + +
95A VAL* 1.3 81.5 - - - +
97A ARG* 1.3 62.9 + - - +
116A TYR* 3.4 4.5 - - - -
117A ALA* 2.8 36.2 + - + +
120A GLY 4.1 5.9 + - - -
31B HIS* 2.9 24.1 - - - -
56B PHE* 3.3 33.6 - - + -
60B TRP* 2.8 50.0 + - + +
62B PHE* 3.3 25.1 - - + -
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Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 3.5 1.6 - - - -
9A PHE* 2.7 50.8 + - + -
70A HIS* 5.0 3.4 - - - -
73A THR* 4.3 3.8 - - - +
74A HIS* 2.8 50.2 + - + +
77A ASP* 3.9 7.9 + - - -
96A GLN* 1.3 76.4 - - - +
98A MET* 1.3 66.1 + - - +
99A TYR* 3.9 20.2 - - + -
114A HIS* 3.0 38.7 + - + +
115A GLN 3.4 11.4 - - - +
116A TYR* 3.7 21.0 - - + -
147A TRP* 4.7 5.5 - - - -
56B PHE* 3.6 3.4 - - - -
60B TRP* 4.7 0.7 - - - -
3C LEU* 5.7 0.4 - - - +
6C ILE* 3.5 32.5 - - - +
7C THR 4.7 5.3 + - - -
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Residues in contact with MET 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ARG* 3.5 34.3 - - - +
7A TYR 3.3 7.6 - - - +
8A PHE* 3.6 31.0 - - + -
9A PHE* 5.0 0.2 - - - -
97A ARG* 1.3 77.1 - - - +
99A TYR* 1.3 72.7 + - - +
113A TYR* 4.3 7.2 - - + -
114A HIS* 3.3 2.3 - - - -
115A GLN* 2.7 73.4 + - + +
56B PHE* 4.1 15.0 - - + -
60B TRP* 4.6 5.6 - - + -
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Residues in contact with TYR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ARG* 3.4 1.9 - - - -
7A TYR* 2.9 43.1 + + + -
9A PHE* 3.4 21.1 - + - -
70A HIS* 2.9 27.8 + - - -
97A ARG* 3.9 14.6 - - - -
98A MET* 1.3 84.8 - - - +
100A GLY* 1.3 62.4 + - - +
113A TYR 3.2 16.8 - - - +
114A HIS* 3.8 26.0 - + + -
156A LEU* 5.5 0.7 - - + -
159A TYR* 3.5 35.4 - + - -
160A LEU* 4.8 2.9 - - + -
2C LEU* 3.5 10.2 - - - +
3C LEU* 2.9 31.7 + - + -
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Residues in contact with GLY 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A MET 3.1 14.1 - - - -
6A ARG* 3.6 10.7 - - - +
7A TYR* 5.9 1.1 - - - -
99A TYR* 1.3 82.7 - - - +
101A CYS* 1.3 62.0 + - - -
112A GLY* 3.5 0.2 - - - -
113A TYR* 2.9 27.8 + - - -
160A LEU* 3.3 9.9 - - - +
164A CYS* 3.8 11.2 - - - -
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Residues in contact with CYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A SER* 3.2 3.8 - - - -
5A MET* 3.0 33.1 + - - -
6A ARG* 3.8 1.1 - - - +
100A GLY* 1.3 74.8 - - - +
102A ASP* 1.3 67.3 + - - +
103A VAL* 5.4 0.2 - - - -
109A PHE* 4.5 1.1 - - + -
111A ARG 3.3 10.5 - - - +
112A GLY* 4.7 0.7 - - - -
113A TYR* 4.7 0.2 - - - -
160A LEU 3.7 16.2 - - - +
164A CYS* 2.1 59.2 - - - -
165A VAL* 3.6 13.0 - - + -
168A LEU* 4.1 10.9 - - - +
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Residues in contact with ASP 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 4.8 2.7 - - - +
3A HIS 3.2 7.2 - - - +
4A SER* 3.1 13.1 - - - -
6A ARG* 2.9 23.9 + - - -
101A CYS* 1.3 71.7 - - - +
103A VAL* 1.3 65.4 + - - +
109A PHE* 3.8 2.4 - - - -
110A LEU* 2.8 39.7 + - + +
111A ARG* 2.9 15.1 + - + +
113A TYR* 2.5 32.9 + - - -
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Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 2.5 29.6 + - - -
3A HIS* 2.8 35.8 + - + +
102A ASP* 1.3 78.9 - - - +
104A GLY* 1.3 56.8 + - - +
107A TRP* 3.5 37.0 - - + +
108A ARG 3.2 15.5 - - - +
109A PHE 4.2 0.7 - - - +
110A LEU* 4.1 3.8 - - - +
165A VAL* 4.2 22.7 - - + +
168A LEU* 3.8 28.0 - - + -
169A ARG* 5.5 0.9 - - + -
172A LEU* 4.6 1.6 - - + -
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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