Contacts of the strand formed by residues 171 - 177 (chain B) in PDB entry 2QVS
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 ASN 171 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B PHE* 3.6 19.9 - - - -
170B ASP* 1.3 88.4 + - - +
172B PHE* 1.3 60.7 + - - +
173B TYR* 3.5 33.9 + - + +
206B ALA* 3.5 6.8 - - - +
207B LEU* 5.4 0.4 - - - -
213B ARG* 2.5 36.4 + - - +
228B LEU 3.1 7.7 - - - +
229B ASP* 3.0 41.6 - - - +
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Residues in contact with PHE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA 5.7 0.4 - - - -
130B CYS* 4.7 5.2 - - - -
133B ILE* 4.1 18.2 - - + -
136B PHE* 4.2 22.7 - + - -
151B MET* 4.1 13.9 - - + -
171B ASN* 1.3 75.2 - - - +
173B TYR* 1.3 61.3 + - - +
174B VAL* 3.8 20.6 - - + -
201B SER* 3.7 20.6 - - - -
202B PHE 3.5 21.3 - - - -
203B GLY 4.0 3.8 - - - +
204B GLU* 3.4 44.2 - - + -
207B LEU* 3.8 25.8 - - + -
226B TRP 3.7 0.5 - - - +
227B GLY* 3.3 4.9 - - - -
228B LEU* 2.9 30.6 + - + +
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Residues in contact with TYR 173 (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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152B PHE* 5.0 3.4 - + - -
154B LYS* 3.7 33.8 - - + +
162B VAL* 4.4 10.1 + - + -
163B ILE* 3.9 20.5 - - + +
171B ASN* 3.5 45.3 + - + +
172B PHE* 1.3 80.3 - - - +
174B VAL* 1.3 63.2 + - - +
201B SER* 3.0 27.4 - - - -
202B PHE* 3.1 48.8 + + + -
213B ARG* 4.4 4.4 + - - -
225B LEU* 4.4 17.3 - - + -
226B TRP 3.2 4.5 - - - +
227B GLY* 4.0 13.9 - - - -
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Residues in contact with VAL 174 (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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125B ARG 5.5 0.4 - - - +
126B LEU* 3.4 35.4 - - + -
129B ALA* 4.0 17.9 - - + -
130B CYS* 4.4 10.5 - - - -
151B MET* 4.2 7.6 - - + -
172B PHE* 3.8 24.2 - - + -
173B TYR* 1.3 77.2 - - - +
175B ILE* 1.3 73.7 + - - +
200B GLY 3.6 8.1 - - - +
201B SER* 4.3 4.7 - - - -
225B LEU* 3.2 6.2 - - - -
226B TRP* 2.6 42.3 + - + +
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Residues in contact with ILE 175 (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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125B ARG* 4.7 5.7 + - - +
174B VAL* 1.3 84.0 - - - +
176B GLU* 1.3 63.2 + - - +
177B ARG 3.7 12.8 - - - +
180B TYR* 3.7 28.9 - - + +
196B TYR* 3.5 30.5 - - + -
198B ASN* 3.9 22.7 - - - +
199B ARG* 3.2 28.6 - - - +
200B GLY* 3.0 19.9 + - - +
202B PHE* 4.4 9.9 - - + -
225B LEU* 3.2 20.4 - - + -
226B TRP* 5.2 0.3 - - - -
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Residues in contact with GLU 176 (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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122B GLN* 3.3 28.3 - - - +
125B ARG* 2.6 44.5 + - - +
153B GLU* 4.9 2.7 - - - +
174B VAL 3.6 0.4 + - - -
175B ILE* 1.3 76.6 - - - +
177B ARG* 1.3 74.6 + - + +
198B ASN* 4.5 7.9 - - - +
224B SER* 2.6 37.5 + - - +
225B LEU 4.2 0.7 - - - +
226B TRP* 2.8 38.0 + - + +
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Residues in contact with ARG 177 (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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155B ILE* 4.3 12.5 - - - +
175B ILE* 3.7 2.6 - - - +
176B GLU* 1.3 94.5 - - + +
178B GLY* 1.3 56.4 + - - +
180B TYR* 2.7 29.1 + - - -
198B ASN* 3.2 11.2 - - - +
222B GLU* 3.8 30.3 + - - +
223B GLY* 3.6 11.1 + - - -
224B SER* 2.9 34.4 + - - +
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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