Contacts of the strand formed by residues 163 - 168 (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 MET 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU* 5.6 2.5 - - + -
153B ALA* 4.8 1.6 - - + -
156B PHE* 4.1 32.8 - - + -
158B PHE* 4.2 19.5 - - + -
161B TYR 3.6 13.7 - - - +
162B ASP* 1.3 83.8 + - - +
164B SER* 1.3 69.2 + - - +
179B TYR* 4.0 0.2 - - - -
180B ILE* 3.2 32.5 + - + +
201B ARG* 3.0 31.0 - - - +
208B LEU* 3.5 31.0 - - + -
225B CYS* 5.8 0.7 - - - -
226B ALA 3.0 15.0 - - - +
227B ARG* 4.1 5.2 - - + -
228B GLN* 3.2 6.7 + - - -
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Residues in contact with SER 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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163B MET* 1.3 76.1 + - - +
165B TRP* 1.3 72.6 + - - +
176B TRP* 3.7 6.8 + - - -
178B ALA 3.4 13.7 - - - -
179B TYR* 3.4 15.5 - - - +
180B ILE* 4.3 3.1 - - - +
208B LEU* 5.4 0.5 - - - +
225B CYS* 4.6 1.2 - - - -
226B ALA* 2.9 30.7 + - - +
228B GLN* 2.9 24.1 + - - -
233B THR* 5.7 0.7 + - - -
235B PHE* 3.7 21.9 - - - -
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Residues in contact with TRP 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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135B GLU* 4.7 7.9 - - + -
149B LEU* 4.6 12.6 - - + -
150B SER 4.6 1.1 - - - -
151B CYS* 3.7 26.7 - - + -
164B SER* 1.3 79.7 - - - +
166B VAL* 1.3 57.7 + - - +
176B TRP* 3.4 7.3 - - - -
177B VAL* 2.8 46.4 + - + -
178B ALA* 2.8 19.9 + - + +
180B ILE* 4.2 18.0 - - + +
199B ILE* 4.2 23.6 - - + +
208B LEU* 3.9 36.0 - - + +
209B TYR 5.3 0.4 + - - -
210B LEU* 3.9 41.9 - - + +
223B TYR* 4.6 16.2 - + + -
224B TYR 3.9 21.8 - - - -
225B CYS* 4.5 7.6 - - - -
242B THR* 5.5 0.2 - - - -
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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
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98B PHE* 4.7 4.3 - - + -
165B TRP* 1.3 80.5 - - - +
167B ARG* 1.3 64.3 + - - +
174B LEU* 3.9 17.5 - - + -
175B GLU 3.3 20.2 - - - +
176B TRP* 3.9 7.0 - - + +
177B VAL* 3.8 3.8 - - - -
223B TYR* 3.8 1.7 - - - +
224B TYR* 2.9 35.6 + - - +
226B ALA* 4.0 7.4 - - + -
235B PHE* 3.7 35.0 - - + -
238B TRP* 3.5 32.1 - - + -
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Residues in contact with ARG 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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166B VAL* 1.3 75.7 - - - +
168B GLN* 1.3 61.7 + - - +
174B LEU* 3.3 2.4 - - - -
175B GLU* 2.7 74.8 + - + +
176B TRP 5.7 1.2 + - - -
177B VAL* 3.5 16.2 - - + +
193B VAL* 5.1 9.9 - - - +
196B ARG* 4.8 4.6 - - - +
197B PHE* 3.7 10.4 - - - -
218B GLU* 3.5 22.8 + - - +
219B ASP* 2.6 33.4 + - - +
221B ALA* 4.2 12.5 - - + +
222B VAL 3.1 13.5 - - - +
223B TYR* 2.8 49.4 + - + -
224B TYR* 4.7 0.9 - - - -
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Residues in contact with GLN 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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38B GLN* 2.9 32.7 + - - -
85B ASN* 4.3 6.5 - - - +
87B TYR* 4.9 2.0 - - - -
167B ARG* 1.3 75.1 - - - +
169B ALA* 1.3 64.8 + - - +
172B LYS 3.5 25.2 + - - +
173B ARG 3.6 7.6 - - - +
174B LEU* 3.7 27.3 - - + +
221B ALA* 3.9 0.7 - - - -
222B VAL* 2.8 36.8 + - - +
224B TYR* 2.8 38.0 + - + -
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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