Contacts of the strand formed by residues 162 - 169 (chain B) in PDB entry 3NVN
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 THR 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B LYS* 3.6 39.8 - - - +
108B LEU* 4.6 4.3 - - + -
154B VAL* 3.8 24.2 - - + +
155B SER* 3.4 21.0 + - - -
160B GLY 4.0 0.4 + - - -
161B SER* 1.3 83.1 + - - +
163B ALA* 1.3 67.4 + - - +
179B VAL* 4.0 15.5 - - + -
180B ALA 3.3 6.7 - - - +
181B ALA* 3.5 3.5 - - + +
234B PHE 4.3 4.5 + - - +
235B VAL 5.2 1.7 - - - +
427B TYR* 5.4 3.6 + - - -
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Residues in contact with ALA 163 (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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107B LYS 5.5 0.7 - - - -
162B THR* 1.3 80.8 - - - +
164B GLY* 1.3 58.7 + - - +
178B ALA 4.0 0.2 - - - +
179B VAL* 3.7 0.6 - - - -
180B ALA* 2.9 36.2 + - + +
234B PHE* 4.4 7.9 - - + +
235B VAL 4.2 4.5 - - - +
236B ASP* 3.4 44.4 - - - +
237B ALA* 3.8 6.3 - - + +
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Residues in contact with GLY 164 (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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108B LEU* 4.7 10.6 - - - +
110B LEU* 3.2 29.5 - - - +
162B THR* 4.9 2.0 - - - +
163B ALA* 1.3 74.5 - - - +
165B VAL* 1.3 62.0 + - - +
177B LEU* 4.6 4.3 - - - -
178B ALA 3.1 12.3 - - - -
179B VAL* 4.3 3.1 - - - -
237B ALA* 3.8 9.4 + - - +
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Residues in contact with VAL 165 (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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110B LEU* 3.9 5.7 - - - +
164B GLY* 1.3 74.5 - - - +
166B VAL* 1.3 71.8 + - - +
167B TYR* 4.0 1.9 - - - -
176B TYR 4.0 0.2 - - - +
177B LEU* 3.7 2.9 - - - +
178B ALA* 3.0 31.9 + - + +
237B ALA* 3.6 27.6 - - + +
238B PHE* 4.4 4.0 - - - -
239B LEU* 3.4 26.7 - - + +
244B ILE* 3.5 31.9 - - + -
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Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 4.5 8.3 - - + +
112B TYR* 3.8 28.9 - - + -
124B LEU* 3.5 33.0 - - + -
165B VAL* 1.3 79.8 - - - +
167B TYR* 1.3 67.7 + - - +
175B TRP* 3.3 35.9 - - + -
176B TYR 3.3 13.0 - - - +
177B LEU* 4.0 6.1 - - + -
210B THR* 5.3 1.3 - - + -
239B LEU* 3.6 14.9 - - - +
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Residues in contact with TYR 167 (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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165B VAL 4.0 6.3 - - - -
166B VAL* 1.3 79.0 - - - +
168B ARG* 1.3 75.0 + - - +
169B ALA* 3.8 12.8 - - + -
175B TRP* 3.4 6.5 - - - -
176B TYR* 2.8 69.8 + - + +
177B LEU 3.9 1.1 - - - -
178B ALA* 3.9 13.9 - - + -
207B LEU* 3.3 21.4 - - + +
239B LEU* 3.9 25.8 - - + -
244B ILE* 3.9 22.2 - - + -
269B GLN* 4.0 20.6 - - + +
270B SER 2.9 34.8 + - - -
271B THR* 4.6 0.2 - - - -
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Residues in contact with ARG 168 (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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167B TYR* 1.3 82.9 - - - +
169B ALA* 1.3 64.0 + - - +
172B ASN 4.9 0.6 + - - -
173B ASN* 2.8 63.5 + - - +
174B ARG 3.2 5.2 - - - +
175B TRP* 3.3 65.3 - - + +
269B GLN* 4.4 12.6 + - - +
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Residues in contact with ALA 169 (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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167B TYR* 3.8 11.2 - - + -
168B ARG* 1.3 75.3 - - - +
170B GLY* 1.3 63.9 + - - +
173B ASN* 3.9 7.8 + - - -
174B ARG* 2.9 29.9 + - - +
176B TYR* 3.6 14.7 - - + -
269B GLN 3.9 3.6 - - - +
270B SER* 3.7 37.5 - - - -
271B THR* 3.9 3.6 - - + +
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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