Contacts of the strand formed by residues 87 - 95 (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 TYR 87 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ASN* 2.7 34.4 + - - -
66B ARG* 3.0 18.0 + - - +
67B VAL 3.9 0.2 + - - -
78B TYR* 5.3 0.9 - + + -
79B PHE* 3.7 35.6 - + + -
82B SER* 4.0 10.1 - - - +
83B PHE* 3.9 26.5 - + - -
86B GLY* 1.3 77.1 - - - +
88B SER* 1.3 71.7 + - - +
89B TRP* 4.0 20.9 - + - -
107B ILE* 3.0 47.6 + - + +
177B TYR* 4.1 8.5 - + + -
178B LYS 3.3 14.6 - - - +
179B ALA* 3.6 9.9 - - + -
180B LYS* 3.9 9.2 + - - +
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Residues in contact with SER 88 (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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87B TYR* 1.3 81.1 - - - +
89B TRP* 1.3 66.2 + - - +
90B GLU* 5.1 3.5 + - - +
105B ASN 3.2 12.6 - - - -
106B ASP* 3.9 18.2 - - - -
178B LYS* 2.9 51.6 + - - +
180B LYS* 4.9 4.4 - - - +
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Residues in contact with TRP 89 (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 40.4 - - + -
63B KZ4 2.7 29.1 + - - -
65B ASN* 5.2 0.2 - - - -
87B TYR* 4.0 20.9 - + + -
88B SER* 1.3 76.1 - - - +
90B GLU* 1.3 75.6 - - - +
91B ARG* 3.5 52.9 - - + -
103B ALA* 3.8 16.2 - - + -
104B THR* 3.2 7.0 - - - -
105B ASN* 2.9 58.2 + - + +
107B ILE* 4.2 3.8 - - + -
175B THR* 4.2 2.2 - - + -
176B THR 3.1 13.9 - - - +
177B TYR* 3.7 22.0 - + + -
178B LYS* 5.9 0.2 - - - -
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Residues in contact with GLU 90 (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* 5.1 4.3 + - - +
89B TRP* 1.3 79.9 - - - +
91B ARG* 1.3 62.3 + - - +
103B ALA 3.4 5.8 - - - -
104B THR* 4.1 12.6 - - + -
175B THR* 3.3 5.0 - - - +
176B THR* 2.9 32.2 + - - +
178B LYS* 2.8 40.8 + - + +
19E ASN* 3.2 32.7 + - - +
20E GLY* 5.5 0.4 - - - -
123E VAL* 3.9 14.8 - - + -
124E ASN* 3.0 35.0 + - - +
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Residues in contact with ARG 91 (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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59B THR* 2.8 41.6 + - - -
60B VAL* 4.1 1.8 - - - +
63B KZ4 2.7 26.3 + - - +
66B ARG* 3.6 13.9 - - - +
89B TRP* 3.5 38.7 - - + +
90B GLU* 1.3 78.4 - - - +
92B SER* 1.3 71.8 + - - +
93B MET* 3.8 24.7 - - + -
101B CYS 3.8 0.5 - - - +
102B ASN* 3.3 4.0 - - - -
103B ALA* 2.7 35.0 + - - +
173B PHE* 4.0 13.7 - - - -
174B LYS 3.2 10.1 - - - +
175B THR* 2.8 28.2 + - - +
123E VAL* 3.7 8.3 - - - +
124E ASN* 4.2 0.7 - - - +
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Residues in contact with SER 92 (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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91B ARG* 1.3 74.9 - - - +
93B MET* 1.3 62.9 + - - +
94B ASN* 4.0 4.6 + - - +
100B ILE* 3.6 14.7 - - - +
101B CYS 3.4 2.9 - - - -
102B ASN* 2.9 19.8 + - - -
172B ASP 3.5 3.5 - - - +
173B PHE* 3.6 1.9 - - - -
174B LYS* 2.9 38.2 + - - +
100E ILE* 3.8 23.8 - - - +
123E VAL* 4.2 1.8 - - - -
124E ASN* 3.7 10.6 - - - +
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Residues in contact with MET 93 (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 4.6 9.2 - - - +
59B THR* 4.0 18.2 - - - -
60B VAL* 3.9 12.1 - - + -
91B ARG* 3.8 26.9 - - + -
92B SER* 1.3 76.2 + - - +
94B ASN* 1.3 58.6 + - - +
95B TYR* 3.5 16.6 - - + -
100B ILE* 3.4 4.8 - - - -
101B CYS* 2.7 62.2 + - + +
103B ALA* 3.8 27.8 - - + +
120B PHE* 4.2 2.2 - - + -
171B CYS* 3.7 12.6 - - - -
172B ASP 3.6 4.5 - - - -
173B PHE* 3.8 19.5 - - + -
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Residues in contact with ASN 94 (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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92B SER* 5.1 3.6 - - - +
93B MET* 1.3 70.9 - - - +
95B TYR* 1.3 70.9 + - - +
96B GLU* 4.9 0.2 - - - -
98B GLY* 5.0 1.4 - - - -
100B ILE* 3.1 32.1 - - + +
170B ARG 4.9 0.2 - - - -
171B CYS* 3.6 1.8 - - - -
172B ASP* 2.9 44.9 + - + +
94E ASN* 4.2 19.4 - - - +
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Residues in contact with TYR 95 (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* 3.4 30.3 + - + +
93B MET* 3.5 19.4 - - + +
94B ASN* 1.3 84.9 - - - +
96B GLU* 1.3 66.1 + - - +
97B ASP* 3.2 2.7 - - - +
98B GLY 3.0 12.8 + - - -
99B GLY 2.8 22.7 + - - +
101B CYS* 4.1 9.4 - - - -
125B PHE* 3.7 20.6 - + - -
139B TRP* 3.4 25.3 - + - -
161B LEU* 4.1 8.5 - - + -
169B TYR* 3.2 45.8 - + + +
170B ARG 3.5 4.9 - - - -
171B CYS* 3.6 33.0 - - + +
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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