Contacts of the strand formed by residues 223 - 229 (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 GLY 223 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B ILE* 3.7 6.9 - - - +
156B VAL* 2.9 35.6 + - - +
177B ARG* 3.1 26.7 + - - -
178B GLY* 3.9 2.2 - - - -
180B TYR* 3.9 8.5 - - - -
221B SER 3.3 3.0 + - - -
222B GLU* 1.3 75.4 - - - +
224B SER* 1.3 61.1 + - - -
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Residues in contact with SER 224 (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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153B GLU* 3.2 36.1 + - - +
154B LYS 3.5 4.0 - - - -
155B ILE* 3.3 7.4 - - - +
176B GLU* 2.6 46.7 + - - +
177B ARG* 2.9 37.9 + - - +
180B TYR* 3.7 1.2 + - - -
223B GLY* 1.3 74.8 - - - -
225B LEU* 1.3 55.6 + - - +
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Residues in contact with LEU 225 (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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153B GLU* 3.6 1.9 - - - +
154B LYS* 2.8 44.4 + - + +
156B VAL* 4.4 10.3 - - + -
162B VAL* 3.5 43.3 - - + -
173B TYR* 4.4 22.7 - - + -
174B VAL 3.2 8.3 - - - +
175B ILE* 3.2 47.1 - - + +
176B GLU 4.1 0.2 - - - +
180B TYR* 3.5 21.1 - - + +
202B PHE* 4.4 3.8 - - + -
224B SER* 1.3 74.6 + - - +
226B TRP* 1.3 64.6 + - - +
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Residues in contact with TRP 226 (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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116B HIS* 5.0 2.7 - - + -
117B PRO 3.7 10.1 - - - -
118B LYS* 3.4 37.9 - - + +
122B GLN* 3.7 23.1 + - - +
126B LEU* 3.7 39.7 - - + +
151B MET* 3.6 26.5 - - + +
152B PHE* 3.5 20.0 - - - -
153B GLU* 3.3 46.4 - - + -
172B PHE 3.7 0.5 - - - +
173B TYR* 3.2 5.1 - - - -
174B VAL* 2.6 45.6 + - + +
175B ILE 5.2 0.2 - - - -
176B GLU* 2.8 33.2 + - + -
225B LEU* 1.3 72.8 - - - +
227B GLY* 1.3 56.4 + - - +
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Residues in contact with GLY 227 (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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151B MET* 3.3 8.3 - - - -
152B PHE* 2.8 59.9 + - - -
154B LYS* 5.4 0.2 - - - +
172B PHE 3.3 7.4 - - - -
173B TYR* 4.0 10.7 - - - -
225B LEU 3.8 2.0 + - - -
226B TRP* 1.3 74.8 - - - +
228B LEU* 1.3 61.0 + - - -
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Residues in contact with LEU 228 (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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136B PHE* 3.9 20.4 - - + -
147B VAL* 4.0 12.8 - - + +
150B ALA* 4.5 15.7 - - + +
151B MET* 3.7 21.5 - - + -
152B PHE* 3.8 2.9 - - - -
171B ASN* 3.1 7.3 - - - +
172B PHE* 2.9 35.0 + - + +
207B LEU* 3.7 13.1 - - + +
227B GLY* 1.3 73.6 - - - +
229B ASP* 1.3 72.1 + - - +
232B THR* 4.5 11.4 - - + -
233B PHE* 3.6 47.1 - - + +
236B ILE* 5.7 0.2 - - + -
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Residues in contact with ASP 229 (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* 4.0 8.6 - - + -
170B ASP* 3.5 12.0 - - - +
171B ASN* 3.0 20.2 + - - +
207B LEU* 4.1 1.1 - - - -
228B LEU* 1.3 76.0 - - - +
230B ARG* 1.3 72.8 + - - +
231B VAL* 3.4 18.4 + - - +
232B THR* 2.8 41.5 + - - +
233B PHE* 2.9 21.3 + - - +
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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