Contacts of the strand formed by residues 164 - 169 (chain B) in PDB entry 1KMC
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 LYS 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLY* 1.3 75.6 - - - -
165B CYS* 1.3 64.5 + - - +
166B ILE* 3.4 28.3 - - + +
198B PHE* 3.6 3.6 - - - -
199B ASP* 3.8 16.6 - - + +
201B ILE* 3.2 30.6 - - + +
203B TYR* 4.2 6.5 + - - -
218B ALA* 4.5 7.4 - - + +
221B GLU* 3.1 38.3 + - - +
224B HIS* 4.8 10.5 + - + +
227B ALA* 5.3 0.6 - - - +
229B CYS 4.1 2.8 + - - -
230B PHE* 3.9 16.5 - - + -
231B ALA 3.0 24.7 + - - -
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Residues in contact with CYS 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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164B LYS* 1.3 80.9 - - - +
166B ILE* 1.3 61.7 + - - +
167B ILE* 3.4 8.0 + - - -
193B PHE* 3.7 32.5 - - - -
198B PHE* 3.7 23.8 - - + -
199B ASP 3.3 6.2 + - - -
200B VAL* 3.6 9.6 - - + +
201B ILE 3.2 23.5 + - - -
231B ALA* 2.9 13.7 - - - +
233B ILE* 3.9 20.9 - - - -
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Residues in contact with ILE 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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164B LYS* 3.4 42.0 - - + +
165B CYS* 1.3 71.4 - - - +
167B ILE* 1.3 58.2 + - - +
168B ILE* 4.2 14.4 - - + -
201B ILE* 3.9 3.6 - - + -
203B TYR* 3.4 35.0 - - + +
214B LEU* 4.4 7.9 - - + +
215B LEU* 4.4 15.3 - - + -
218B ALA* 4.5 7.9 - - + -
230B PHE* 3.7 24.5 - - + -
231B ALA 2.8 8.1 + - - +
232B CYS* 3.2 9.9 - - - -
233B ILE* 2.8 28.2 + - - +
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Residues in contact with ILE 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 CYS* 4.1 4.3 - - - +
166B ILE* 1.3 75.9 - - - +
168B ILE* 1.3 67.0 + - - +
169B ASN 4.5 0.4 - - - +
186B ALA* 4.4 6.3 - - + +
189B LEU* 4.1 4.3 - - + -
190B PHE* 3.8 25.4 - - + +
193B PHE* 5.7 0.2 - - + -
200B VAL* 3.7 28.5 - - + -
201B ILE 2.8 14.4 + - - +
202B VAL* 3.3 21.3 - - + -
203B TYR* 2.8 30.0 + - - +
233B ILE* 3.6 35.0 - - + +
235B LEU* 4.4 18.6 - - + -
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Residues in contact with ILE 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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166B ILE* 4.2 17.7 - - + +
167B ILE* 1.3 75.4 - - - +
169B ASN* 1.3 58.3 + - - +
170B ASN* 3.6 26.0 - - - +
203B TYR* 3.8 4.0 - - + -
206B CYS* 4.3 7.9 - - - -
211B MET* 3.9 38.1 - - + -
214B LEU* 4.2 18.4 - - + -
215B LEU* 4.9 11.0 - - + -
232B CYS* 5.2 0.2 - - - -
233B ILE 2.9 13.8 + - - +
234B LEU* 3.6 25.4 - - + -
235B LEU* 3.0 29.4 + - - +
236B SER* 6.0 0.4 - - - -
261B LEU* 5.7 0.2 - - + -
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Residues in contact with ASN 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 ILE* 3.8 0.8 + - + -
168B ILE* 1.3 72.1 - - - +
170B ASN* 1.3 60.3 + - - +
171B LYS* 3.6 3.4 + - - +
182B THR* 2.6 42.2 + - - +
183B ASP* 3.1 21.5 - - - +
186B ALA* 3.6 23.3 - - + +
202B VAL* 4.1 10.1 - - + -
203B TYR 2.8 9.9 + - - +
204B ASN* 3.2 26.3 - - - +
205B ASP* 3.0 19.6 + - - +
235B LEU* 4.0 5.2 - - + +
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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