Contacts of the strand formed by residues 113 - 123 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9E LYS* 3.3 22.7 - - + -
10E ILE 3.8 2.7 - - - -
11E LYS* 3.8 25.8 - - - -
109E LEU* 3.3 4.5 - - - +
110E ASP* 2.9 41.2 + - + +
111E GLY 3.4 1.0 - - - -
112E ASP* 1.3 84.9 - - - +
114E TYR* 1.3 76.4 + - - +
115E ILE* 3.8 5.8 + - + +
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Residues in contact with TYR 114 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4E ILE* 3.6 23.4 - - - +
8E MET* 3.5 38.1 - - + +
9E LYS 2.7 20.6 + - - +
10E ILE* 4.3 1.5 - - - +
11E LYS 2.9 27.9 + - - +
33E PRO* 4.2 1.3 - - + +
65E ASN* 3.9 5.2 - - - -
67E VAL* 3.7 19.6 - - + +
68E PHE* 3.8 26.9 - + - -
83E PHE* 3.4 46.4 - + - -
107E ILE* 4.3 1.6 - - + -
108E THR 3.4 4.7 - - - +
109E LEU* 3.9 11.4 - - + -
113E CYS* 1.3 75.8 - - - +
115E ILE* 1.3 59.7 + - - +
116E TYR* 3.7 20.9 - - + -
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Residues in contact with ILE 115 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E LYS* 3.2 25.6 - - + +
106E ASP 3.4 2.4 - - - +
107E ILE* 3.3 4.3 - - - -
108E THR* 2.9 48.5 + - - +
109E LEU 4.9 0.2 - - - -
110E ASP* 3.5 34.3 - - + +
113E CYS* 4.1 7.9 - - + +
114E TYR* 1.3 78.7 - - - +
116E TYR* 1.3 71.5 + - - +
117E GLU* 5.1 1.3 - - + +
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Residues in contact with TYR 116 (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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10E ILE* 3.6 24.5 - - + +
11E LYS 2.9 9.0 + - - -
12E LEU* 3.5 32.3 - - + -
13E ARG* 3.2 22.4 + - - +
38E GLN* 4.2 1.7 + - - -
40E MET* 4.5 1.1 - - + -
61E PHE 3.7 19.3 - - - -
65E ASN* 2.9 46.8 + - + +
68E PHE* 3.7 13.3 - - - -
105E ASN* 3.2 27.1 - - - +
106E ASP 3.6 0.2 - - - -
107E ILE* 3.8 15.0 - - + -
114E TYR* 3.7 15.5 - - + -
115E ILE* 1.3 86.2 - - - +
117E GLU* 1.3 58.9 + - - +
118E ILE* 4.0 9.4 - - + -
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Residues in contact with GLU 117 (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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13E ARG* 4.0 4.5 - - + +
104E THR* 3.8 2.1 + - - +
105E ASN* 3.4 1.6 - - - -
106E ASP* 2.9 57.1 + - + +
115E ILE* 5.1 1.5 - - + +
116E TYR* 1.3 71.3 - - - +
118E ILE* 1.3 63.5 + - - +
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Residues in contact with ILE 118 (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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12E LEU* 4.7 6.5 - - + -
13E ARG 3.1 14.1 + - - +
14E MET* 3.5 21.6 - - + -
15E GLU* 3.1 26.3 + - - +
60E VAL* 3.5 47.8 - - + +
61E PHE* 4.5 14.4 - - + -
104E THR 3.2 5.8 - - - +
105E ASN* 3.4 34.1 - - + +
116E TYR* 4.0 18.2 - - + -
117E GLU* 1.3 76.1 - - - +
119E ARG* 1.3 67.2 + - - +
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Residues in contact with ARG 119 (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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17B ALA* 5.7 3.1 - - + -
119B ARG* 3.6 43.6 - - - +
121B ASP* 3.6 10.3 - - - +
15E GLU* 3.3 28.1 + - - +
16E GLY* 3.7 23.7 + - - +
17E ALA* 4.2 4.0 - - - +
102E ASN 4.6 0.4 - - - -
103E ALA* 3.2 7.0 - - - +
104E THR* 3.0 45.5 + - + +
118E ILE* 1.3 76.7 - - - +
120E PHE* 1.3 60.3 + - - +
121E ASP* 2.8 38.6 + - - +
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Residues in contact with PHE 120 (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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14E MET* 3.9 28.3 - - + -
15E GLU 3.1 6.4 + - - +
16E GLY* 2.9 26.0 - - - -
17E ALA 2.9 5.5 + - - -
18E VAL* 3.9 17.9 - - + -
23E PHE* 4.0 7.4 - + - -
56E ILE* 3.5 28.3 - - + -
57E LEU* 3.6 26.0 - - + -
60E VAL* 3.7 27.4 - - + -
93E MET* 4.1 10.3 - - + -
101E CYS* 3.5 35.0 - - + -
102E ASN 3.5 2.5 - - - -
103E ALA* 4.0 6.5 - - + -
119E ARG* 1.3 75.3 - - - +
121E ASP* 1.3 68.3 + - - +
122E GLY 4.4 1.6 - - - -
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Residues in contact with ASP 121 (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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102B ASN* 3.2 16.8 + - + +
119B ARG* 3.7 7.6 - - - +
121B ASP* 2.9 38.6 - - + +
17E ALA* 3.3 11.8 - - - +
101E CYS* 4.1 1.1 - - - -
102E ASN* 2.8 38.4 + - + +
119E ARG* 2.8 45.0 + - - +
120E PHE* 1.3 84.1 - - - +
122E GLY* 1.3 60.0 + - - +
123E VAL* 5.2 1.8 - - + -
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Residues in contact with GLY 122 (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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17E ALA 2.9 10.3 + - - +
18E VAL* 3.4 6.9 - - - -
19E ASN* 2.8 30.1 + - - -
20E GLY 4.5 0.5 + - - -
100E ILE 3.1 9.0 - - - -
101E CYS* 3.7 17.3 - - - -
120E PHE* 4.4 3.0 - - - -
121E ASP* 1.3 73.4 - - - +
123E VAL* 1.3 64.8 + - - +
125E PHE* 4.3 5.2 - - - -
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Residues in contact with VAL 123 (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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90B GLU* 3.9 11.9 - - + -
91B ARG 3.7 17.3 - - - +
92B SER* 4.2 4.0 - - - +
102B ASN* 3.6 37.7 - - + +
103B ALA 4.1 7.6 - - - +
104B THR* 3.7 29.4 - - + -
19E ASN* 3.6 4.9 - - - +
99E GLY* 3.5 0.5 - - - -
100E ILE* 2.9 30.5 + - + +
121E ASP* 5.2 2.2 - - + -
122E GLY* 1.3 80.0 - - - +
124E ASN* 1.3 75.3 + - + +
125E PHE* 3.3 5.9 + - - -
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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