Contacts of the strand formed by residues 113 - 123 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9F LYS* 3.3 28.0 - - + -
10F ILE 3.9 2.2 - - - -
11F LYS* 3.8 24.0 - - - -
109F LEU* 3.3 4.3 - - - +
110F ASP* 2.9 42.0 + - + +
111F GLY 3.4 0.8 - - - -
112F ASP* 1.3 83.1 - - - +
114F TYR* 1.3 76.2 + - - +
115F ILE* 3.7 6.3 + - + +
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Residues in contact with TYR 114 (chain F).
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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4F ILE* 3.6 23.4 - - - +
8F MET* 3.4 41.0 - - + +
9F LYS 2.8 19.9 + - - +
10F ILE* 3.5 2.1 - - - +
11F LYS 2.9 27.0 + - - +
33F PRO* 4.0 2.0 - - + +
65F ASN* 3.9 5.8 - - - -
67F VAL* 3.6 19.1 - - + +
68F PHE* 3.8 26.7 - + - -
83F PHE* 3.4 47.3 - + - -
107F ILE* 4.3 1.1 - - + -
108F THR 3.4 4.9 - - - +
109F LEU* 4.0 7.4 - - + -
113F CYS* 1.3 75.7 - - - +
115F ILE* 1.3 59.2 + - - +
116F TYR* 3.7 21.3 - - + -
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Residues in contact with ILE 115 (chain F).
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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11F LYS* 3.2 19.5 - - + +
12F LEU* 5.7 0.2 - - - -
106F ASP 3.4 5.2 - - - +
107F ILE* 3.4 1.9 - - - -
108F THR* 2.9 50.0 + - - +
110F ASP* 3.5 36.6 - - + +
113F CYS* 4.1 8.1 - - + +
114F TYR* 1.3 76.7 - - - +
116F TYR* 1.3 71.6 + - - +
117F GLU* 5.2 1.1 - - + +
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Residues in contact with TYR 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ILE* 3.5 36.4 - - + +
11F LYS 2.9 8.6 + - - +
12F LEU* 3.5 31.4 - - + -
13F ARG* 3.3 21.8 + - - +
38F GLN* 4.2 1.7 + - - -
40F MET* 4.5 0.7 - - + -
61F PHE 3.5 21.8 - - - -
65F ASN* 3.0 46.0 + - + +
68F PHE* 3.7 1.9 - - - -
105F ASN* 3.2 27.6 - - - +
106F ASP 3.6 0.2 - - - -
107F ILE* 3.9 14.6 - - + -
114F TYR* 3.7 15.7 - - + -
115F ILE* 1.3 85.3 - - - +
117F GLU* 1.3 59.8 + - - +
118F ILE* 3.9 8.3 - - + -
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Residues in contact with GLU 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F ARG* 4.0 3.1 - - - -
104F THR* 3.8 2.1 + - - +
105F ASN* 3.4 2.4 - - - -
106F ASP* 2.9 53.0 + - + +
115F ILE* 5.2 1.3 - - + +
116F TYR* 1.3 72.6 - - - +
118F ILE* 1.3 62.3 + - - +
119F ARG 4.3 0.2 + - - -
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Residues in contact with ILE 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F LEU* 4.6 7.0 - - + -
13F ARG 3.1 13.9 + - - +
14F MET* 3.4 22.9 - - + -
15F GLU* 3.1 25.5 + - - +
60F VAL* 3.5 45.3 - - + +
61F PHE* 4.3 16.8 - - + -
104F THR 3.3 4.7 - - - +
105F ASN* 3.5 32.5 - - + +
116F TYR* 4.0 18.4 - - + -
117F GLU* 1.3 76.7 - - - +
119F ARG* 1.3 65.7 + - - +
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Residues in contact with ARG 119 (chain F).
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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15F GLU* 3.3 37.0 + - - +
16F GLY* 3.7 17.1 + - - +
17F ALA* 4.4 4.6 - - - +
22F PRO* 6.2 0.2 - - - +
103F ALA* 3.2 8.0 - - - +
104F THR* 3.0 45.6 + - + +
117F GLU 4.3 0.2 + - - -
118F ILE* 1.3 76.9 - - - +
120F PHE* 1.3 60.0 + - - +
121F ASP* 2.9 39.2 + - - +
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Residues in contact with PHE 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F MET* 4.0 28.0 - - + -
15F GLU 3.1 6.4 + - - +
16F GLY* 2.9 26.7 - - - -
17F ALA 2.9 9.5 + - - -
18F VAL* 3.9 15.3 - - + -
23F PHE* 3.9 7.9 - + - -
56F ILE* 3.5 27.6 - - + -
57F LEU* 3.6 24.2 - - + -
60F VAL* 3.7 27.6 - - + -
93F MET* 4.3 2.7 - - + -
101F CYS* 3.4 41.7 - - + -
102F ASN 3.5 2.7 - - - -
103F ALA* 4.0 6.3 - - + -
119F ARG* 1.3 75.2 - - - +
121F ASP* 1.3 66.7 + - - +
122F GLY 4.3 1.8 - - - -
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Residues in contact with ASP 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F ALA* 3.3 12.0 - - - +
100F ILE 3.7 1.7 - - - +
101F CYS* 3.3 1.2 - - - -
102F ASN* 2.8 45.0 + - + +
119F ARG* 2.9 49.2 + - - +
120F PHE* 1.3 78.8 - - - +
122F GLY* 1.3 59.0 - - - +
123F VAL* 4.3 6.9 + - + +
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Residues in contact with GLY 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F ALA 2.9 10.6 + - - +
18F VAL* 3.3 7.0 - - - -
19F ASN* 2.7 30.8 + - - -
20F GLY 4.5 0.3 + - - -
100F ILE 3.0 9.4 - - - -
101F CYS* 3.7 17.7 - - - -
120F PHE* 4.3 3.0 - - - -
121F ASP* 1.3 72.5 - - - +
123F VAL* 1.3 63.1 + - - +
125F PHE* 4.3 5.8 - - - -
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Residues in contact with VAL 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ASN* 3.5 10.1 - - - +
20F GLY 5.4 2.9 - - - +
99F GLY* 3.5 0.2 - - - -
100F ILE* 2.8 53.2 + - + +
121F ASP* 5.1 6.1 - - + +
122F GLY* 1.3 79.8 - - - +
124F ASN* 1.3 78.5 + - - +
125F PHE* 3.2 4.9 + - - -
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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