Contacts of the strand formed by residues 113 - 123 (chain B) in PDB entry 6NQN
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 CYS 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B LYS* 3.3 24.2 - - + -
10B ILE 3.9 0.2 - - - -
11B LYS* 3.6 37.0 - - - -
109B LEU* 3.4 4.3 - - - +
110B ASP* 2.8 43.7 + - + +
111B GLY 3.5 1.0 - - - -
112B ASP* 1.3 85.0 - - - +
114B TYR* 1.3 75.8 + - - +
115B ILE* 3.8 5.1 + - + +
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Residues in contact with TYR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 4.7 7.3 - - - +
8B MET* 3.3 34.7 - - + +
9B LYS 2.8 17.9 + - - +
10B ILE* 3.5 3.3 - - - +
11B LYS 2.9 26.4 + - - +
33B PRO* 4.1 7.1 - - - +
65B ASN* 4.0 6.1 - - - -
67B VAL* 3.7 25.1 - - + +
68B PHE* 3.7 33.2 - + - -
83B PHE* 3.5 46.2 - + - -
107B ILE* 4.4 0.9 - - + -
108B THR 3.3 5.4 - - - +
109B LEU* 3.8 13.6 - - + +
113B CYS* 1.3 75.6 - - - +
115B ILE* 1.3 60.6 + - - +
116B TYR* 3.7 21.1 - - + +
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Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LYS* 3.2 17.3 - - + +
12B LEU* 5.7 0.2 - - - -
106B ASP 3.4 5.5 - - - +
107B ILE* 3.4 1.9 - - - -
108B THR* 2.8 51.0 + - - +
109B LEU 5.2 0.2 - - - -
110B ASP* 3.6 33.7 - - + +
113B CYS* 4.2 11.2 - - - +
114B TYR* 1.3 76.3 - - - +
116B TYR* 1.3 70.8 + - - +
117B GLU* 6.1 1.1 - - + -
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Residues in contact with TYR 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 3.5 23.4 - - + +
11B LYS 2.9 8.6 + - - -
12B LEU* 3.5 30.5 - - + -
13B ARG* 3.3 22.9 + - - +
38B GLN* 4.3 1.7 + - - -
40B MET* 4.6 1.1 - - + -
61B PHE 3.5 22.4 - - - -
63B KZ4 4.6 0.2 - - - -
65B ASN* 2.9 45.0 + - + +
68B PHE* 3.7 13.3 - - - -
105B ASN* 3.2 28.9 - - - +
106B ASP 3.6 0.4 - - - -
107B ILE* 3.9 13.5 - - + -
114B TYR* 3.7 16.8 - - + -
115B ILE* 1.3 86.4 - - - +
117B GLU* 1.3 57.9 + - - +
118B ILE* 4.0 7.9 - - + -
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG* 4.0 3.8 - - - +
104B THR* 3.8 2.1 + - - +
105B ASN* 3.4 1.7 - - - -
106B ASP* 3.0 54.8 + - + +
115B ILE* 5.1 1.3 - - + +
116B TYR* 1.3 70.8 - - - +
118B ILE* 1.3 63.3 + - - +
119B ARG 4.3 0.2 + - - -
22E PRO* 6.1 1.4 - - - +
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 4.7 7.2 - - + -
13B ARG 3.1 12.6 + - - +
14B MET* 3.4 22.3 - - + -
15B GLU* 3.0 25.3 + - - +
60B VAL* 3.4 48.0 - - + +
61B PHE* 4.3 14.1 - - + -
104B THR 3.2 5.2 - - - +
105B ASN* 3.4 33.7 - - + +
116B TYR* 4.0 17.0 - - + -
117B GLU* 1.3 76.4 - - - +
119B ARG* 1.3 66.7 + - - +
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU* 3.2 35.3 + - - +
16B GLY* 3.7 21.7 + - - +
17B ALA* 4.0 4.0 - - - +
22B PRO* 6.0 0.8 - - - +
102B ASN 4.6 0.4 - - - -
103B ALA* 3.2 7.6 - - - +
104B THR* 3.0 45.2 + - + +
117B GLU 4.3 0.2 + - - -
118B ILE* 1.3 75.2 - - - +
120B PHE* 1.3 60.4 + - - +
121B ASP* 2.8 40.6 + - - +
17E ALA* 5.6 4.3 - - + -
119E ARG* 3.6 43.1 - - - +
121E ASP* 3.7 9.9 - - - +
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Residues in contact with PHE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B MET* 4.0 27.8 - - + -
15B GLU 3.1 6.0 + - - +
16B GLY* 2.9 29.9 - - - -
17B ALA 2.9 9.7 + - - -
18B VAL* 3.9 15.0 - - + -
23B PHE* 4.1 7.6 - + - -
56B ILE* 3.4 29.4 - - + -
57B LEU* 3.7 24.9 - - + -
60B VAL* 3.8 27.1 - - + -
93B MET* 4.2 2.7 - - + -
101B CYS* 3.5 38.4 - - + -
102B ASN 3.5 3.1 - - - -
103B ALA* 4.1 6.7 - - + -
119B ARG* 1.3 77.3 - - - +
121B ASP* 1.3 66.5 + - - +
122B GLY 4.3 2.2 - - - -
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Residues in contact with ASP 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ALA* 3.3 11.1 + - + +
101B CYS* 4.2 1.3 - - - -
102B ASN* 2.8 36.8 + - + +
119B ARG* 2.8 46.2 + - - +
120B PHE* 1.3 78.4 - - - +
122B GLY* 1.3 58.5 + - - +
123B VAL* 5.1 2.0 - - + -
102E ASN* 3.0 17.5 + - + -
119E ARG* 3.6 8.4 - - + +
121E ASP* 2.9 39.5 - - + +
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Residues in contact with GLY 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ALA 2.9 10.6 + - - +
18B VAL* 3.3 4.6 - - - -
19B ASN* 2.7 31.6 + - - -
20B GLY 4.5 0.3 + - - -
100B ILE 3.1 9.4 - - - -
101B CYS* 3.8 17.5 - - - -
120B PHE* 4.3 3.9 - - - -
121B ASP* 1.3 72.3 - - - +
123B VAL* 1.3 63.0 - - - +
125B PHE* 4.4 4.9 - - - -
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ASN* 3.5 5.6 - - - +
99B GLY* 3.5 0.5 - - - -
100B ILE* 2.9 33.5 + - + +
121B ASP* 5.1 2.0 - - + -
122B GLY* 1.3 80.0 - - - +
124B ASN* 1.3 72.7 + - - +
125B PHE* 3.2 5.6 + - - -
90E GLU* 3.9 11.2 - - + -
91E ARG 3.8 17.7 - - - +
92E SER* 4.3 3.6 - - - +
102E ASN* 3.7 39.7 - - + +
103E ALA 4.2 5.2 - - - +
104E THR* 3.7 29.6 - - + -
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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