Contacts of the strand formed by residues 100 - 110 (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 ILE 100 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B SER* 3.6 22.9 - - - +
93B MET 3.4 6.1 - - - +
94B ASN* 3.1 39.7 - - + +
98B GLY* 3.1 16.8 - - - +
99B GLY* 1.3 78.2 - - - +
101B CYS* 1.3 65.0 + - - +
102B ASN* 4.2 1.6 - - - +
122B GLY* 3.1 1.4 - - - -
123B VAL* 2.9 34.0 + - + +
125B PHE* 4.3 1.2 - - - -
92E SER* 3.6 32.8 - - - +
94E ASN* 6.1 0.7 - - - +
100E ILE* 4.4 4.9 - - + -
102E ASN* 3.2 16.8 + - - +
174E LYS* 6.1 4.0 - - + -
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Residues in contact with CYS 101 (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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56B ILE* 4.2 5.6 - - - +
92B SER* 3.4 2.1 - - - -
93B MET* 2.7 57.0 + - + +
95B TYR* 4.1 7.2 - - + -
100B ILE* 1.3 72.3 - - - +
102B ASN* 1.3 62.5 + - - +
120B PHE* 3.5 35.2 - - + -
121B ASP 3.5 3.6 - - - -
122B GLY* 3.8 7.9 - - - -
125B PHE* 3.4 36.3 - - - -
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Residues in contact with ASN 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ARG 3.3 2.9 - - - +
92B SER* 2.9 29.6 + - - -
93B MET* 4.7 0.2 - - - -
100B ILE* 4.2 1.9 - - - +
101B CYS* 1.3 72.4 - - - +
103B ALA* 1.3 60.6 + - - +
119B ARG 4.0 0.5 - - - +
120B PHE* 3.5 2.1 - - - -
121B ASP* 2.8 36.2 + - - +
100E ILE* 3.1 28.8 + - - +
102E ASN* 3.6 25.0 + - + +
121E ASP* 3.2 25.1 + - + +
123E VAL* 3.6 19.8 - - + +
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Residues in contact with ALA 103 (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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60B VAL* 3.8 35.9 - - + -
89B TRP* 3.8 8.5 - - + -
90B GLU* 3.4 0.3 - - - -
91B ARG 2.7 34.1 + - - +
93B MET* 3.8 10.3 - - + -
102B ASN* 1.3 76.2 - - - +
104B THR* 1.3 68.0 + - - +
119B ARG 3.2 11.2 - - - +
120B PHE* 4.1 5.2 - - + -
123E VAL* 4.1 1.1 - - - +
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Residues in contact with THR 104 (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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60B VAL* 5.0 0.2 - - - +
89B TRP* 3.2 11.7 - - - -
90B GLU* 4.1 10.1 - - + -
103B ALA* 1.3 80.6 - - - +
105B ASN* 1.3 62.8 + - - +
106B ASP 4.3 0.2 - - - -
117B GLU 4.4 1.3 + - - -
118B ILE* 3.2 8.0 - - - +
119B ARG* 3.0 46.7 + - + +
17E ALA* 6.4 0.4 - - + -
20E GLY* 4.1 31.2 + - - +
123E VAL* 3.7 21.1 - - + -
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Residues in contact with ASN 105 (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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60B VAL 4.2 0.4 + - - -
63B KZ4 3.2 23.8 + - - -
88B SER* 3.2 5.9 - - - -
89B TRP* 2.9 58.8 + - + +
104B THR* 1.3 75.6 - - - +
106B ASP* 1.3 71.7 + - - +
107B ILE* 3.5 10.5 + - - +
116B TYR* 3.2 42.1 - - - +
117B GLU 3.4 3.5 - - - +
118B ILE* 3.4 18.1 - - + +
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Residues in contact with ASP 106 (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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88B SER* 3.9 12.8 - - - -
104B THR 4.3 0.2 - - - -
105B ASN* 1.3 73.7 + - - +
107B ILE* 1.3 58.9 + - - +
108B THR* 4.0 13.5 + - - +
115B ILE 3.4 4.7 - - - +
117B GLU* 3.0 52.2 + - - +
180B LYS* 3.3 30.7 + - - -
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Residues in contact with ILE 107 (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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63B KZ4 3.7 19.7 - - - +
65B ASN* 3.7 11.4 - - + +
83B PHE* 3.7 24.0 - - + -
86B GLY* 3.7 2.8 - - - -
87B TYR* 3.0 67.2 + - + +
89B TRP* 4.2 4.5 - - + +
105B ASN* 3.5 25.6 - - - +
106B ASP* 1.3 72.3 - - - +
108B THR* 1.3 70.0 + - - +
114B TYR* 4.4 4.3 - - + -
115B ILE 3.4 2.9 - - - -
116B TYR* 3.9 19.5 - - + -
180B LYS* 3.5 9.1 + - - -
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Residues in contact with THR 108 (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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83B PHE* 4.3 4.9 - - - -
85B GLU 4.7 8.3 - - - +
106B ASP* 4.4 11.6 + - - +
107B ILE* 1.3 84.4 - - - +
109B LEU* 1.3 64.7 + - - +
114B TYR* 3.3 5.9 - - - +
115B ILE* 2.8 50.6 + - - +
180B LYS* 4.2 13.2 - - - +
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Residues in contact with LEU 109 (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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3B VAL* 3.7 39.5 - - + +
8B MET* 3.7 20.6 - - + -
83B PHE* 3.7 24.2 - - + -
84B PRO* 4.0 21.7 + - + +
108B THR* 1.3 79.5 - - - +
110B ASP* 1.3 60.4 + - - +
111B GLY 3.6 23.8 + - - +
113B CYS 3.4 23.6 - - - +
114B TYR* 3.8 9.2 - - + -
115B ILE* 5.2 0.2 - - - -
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Residues in contact with ASP 110 (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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109B LEU* 1.3 73.0 - - - +
111B GLY* 1.3 66.9 + - - +
112B ASP* 3.1 1.2 + - - +
113B CYS* 2.8 28.9 + - + +
115B ILE* 3.6 26.1 - - + +
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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