Contacts of the strand formed by residues 174 - 180 (chain B) in PDB entry 2KH2
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 LEU 174 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B GLN* 5.1 2.9 - - - +
44B PRO* 4.8 11.2 - - + -
87B TYR* 4.4 14.1 - - + -
97B THR* 3.7 4.9 - - - +
98B PHE* 3.2 64.7 + - + +
166B VAL* 3.9 7.9 - - + -
167B ARG 3.3 4.3 - - - +
168B GLN* 3.7 38.1 - - + +
173B ARG* 1.3 77.8 - - - +
175B GLU* 1.3 60.3 + - - +
176B TRP 4.4 0.2 + - - -
224B TYR* 4.8 4.0 - - + -
238B TRP* 3.6 36.1 - - + -
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Residues in contact with GLU 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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97B THR* 4.1 18.0 - - + +
166B VAL* 3.3 4.3 - - - +
167B ARG* 2.7 87.0 + - + +
168B GLN* 5.5 0.4 - - - -
172B LYS* 2.7 37.5 + - + +
173B ARG* 4.6 7.8 - - + +
174B LEU* 1.3 74.8 - - - +
176B TRP* 1.3 67.7 + - - +
218B GLU 4.9 0.2 - - - +
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Residues in contact with TRP 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A PHE* 6.2 1.1 - - + -
94B LEU* 4.8 2.7 - - + -
95B PRO 3.8 18.6 + - - +
96B PHE* 3.7 50.1 + + + +
164B SER* 3.7 11.9 + - - -
165B TRP 3.4 15.3 - - - -
166B VAL* 3.9 15.9 - - + +
167B ARG* 5.6 1.0 + - - +
175B GLU* 1.3 77.0 - - - +
177B VAL* 1.3 59.8 + - - +
178B ALA 3.3 15.6 + - - -
179B TYR* 3.4 27.8 - + + -
188B TYR* 3.6 34.8 - + + -
189B PHE 5.5 0.2 - - - -
190B PRO* 3.6 39.8 - - + +
193B VAL* 4.6 10.9 - - - +
233B THR* 5.3 7.6 + - - -
235B PHE* 4.0 12.4 - + - -
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Residues in contact with VAL 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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165B TRP* 2.8 26.2 + - + +
166B VAL 3.8 4.5 - - - -
167B ARG* 3.5 50.0 - - + +
176B TRP* 1.3 77.9 - - - +
178B ALA* 1.3 65.1 + - + +
189B PHE* 4.2 1.4 - - - -
190B PRO* 5.1 1.1 - - - -
193B VAL* 3.2 28.5 - - + +
197B PHE* 3.9 33.2 - - + -
210B LEU* 4.6 5.8 - - + -
223B TYR* 4.0 15.5 - - + -
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Residues in contact with ALA 178 (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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164B SER* 3.4 0.3 - - - -
165B TRP* 2.8 29.1 + - + +
176B TRP* 3.3 20.6 + - - +
177B VAL* 1.3 87.7 - - + +
179B TYR* 1.3 61.1 + - - +
188B TYR 4.1 7.2 - - - -
189B PHE* 3.6 28.9 - - + -
190B PRO* 5.2 0.2 - - - -
199B ILE* 3.9 16.8 - - + -
210B LEU* 5.0 1.8 - - + -
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Residues in contact with TYR 179 (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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108A ASN* 4.3 8.1 + - - -
162B ASP* 3.1 34.2 + - - +
163B MET 4.0 0.9 - - - -
164B SER* 3.4 20.0 - - - -
176B TRP* 3.4 19.7 - + + -
178B ALA* 1.3 74.4 - - - +
180B ILE* 1.3 59.4 + - - +
181B SER* 3.5 28.1 + - - -
186B SER 3.9 5.8 - - - +
187B THR* 4.9 0.3 - - - +
188B TYR* 3.4 54.9 + + + +
199B ILE* 3.5 18.9 - - - +
228B GLN* 3.4 13.5 - - - -
233B THR* 6.0 5.4 - - - -
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Residues in contact with ILE 180 (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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162B ASP* 3.0 11.1 - - - +
163B MET* 3.2 35.8 + - + +
164B SER 4.2 1.6 - - - +
165B TRP* 4.2 18.8 - - + +
179B TYR* 1.3 72.3 - - - +
181B SER* 1.3 59.2 + - - +
199B ILE* 3.6 20.4 - - + -
200B SER* 3.3 37.9 - - - +
201B ARG* 2.8 53.5 + - + +
208B LEU* 3.8 12.8 - - + -
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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