Contacts of the strand formed by residues 230 - 235 (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 PHE 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B LYS* 3.9 19.5 - - + -
166B ILE* 3.7 32.1 - - + -
215B LEU* 4.6 1.8 - - + -
218B ALA* 4.6 7.0 - - + -
224B HIS* 4.2 17.3 - + - +
229B CYS* 1.3 79.3 - - - +
231B ALA* 1.3 72.1 + - - +
232B CYS* 3.8 21.3 - - + -
265B PHE* 3.5 43.1 - + - -
273B LEU* 3.8 20.4 - - + -
277B PRO 3.0 6.0 + - - +
278B LYS* 4.6 8.1 - - + -
279B LEU* 2.8 33.3 + - - +
280B PHE* 4.0 13.9 - + - -
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Residues in contact with ALA 231 (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 3.0 9.2 + - - +
165B CYS* 2.9 20.4 - - - -
166B ILE 2.8 23.6 + - - -
193B PHE* 4.5 9.4 - - + -
198B PHE* 3.5 30.1 - - + -
230B PHE* 1.3 83.1 - - - +
232B CYS* 1.3 60.8 + - - +
279B LEU* 3.3 14.8 - - + +
281B PHE* 4.7 1.8 - - + -
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Residues in contact with CYS 232 (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* 3.2 13.5 - - - -
168B ILE* 5.0 0.2 - - - -
215B LEU* 3.7 26.2 - - - -
230B PHE* 3.8 10.3 - - + -
231B ALA* 1.3 75.8 - - - +
233B ILE* 1.3 68.1 + - - +
234B LEU* 3.8 25.0 - - - +
279B LEU 2.9 6.3 + - - +
280B PHE* 3.2 33.8 - - + -
281B PHE* 2.9 26.0 + - - +
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Residues in contact with ILE 233 (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* 3.9 21.1 - - - -
166B ILE 2.8 12.4 + - - +
167B ILE* 3.9 20.4 - - + +
168B ILE 2.9 27.7 + - - +
189B LEU* 3.5 28.0 - - + -
193B PHE* 3.8 35.2 - - + -
232B CYS* 1.3 80.9 - - - +
234B LEU* 1.3 67.3 + - - +
235B LEU* 3.6 17.9 - - + -
281B PHE* 3.3 27.8 - - + +
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Residues in contact with LEU 234 (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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168B ILE* 3.6 33.4 - - + -
211B MET* 5.4 1.3 - - - -
215B LEU* 5.2 0.7 - - + -
232B CYS* 3.8 18.8 - - - +
233B ILE* 1.3 80.8 - - - +
235B LEU* 1.3 62.0 + - - +
236B SER* 4.0 0.9 - - - -
243B ILE* 3.4 32.5 - - + -
258B ILE* 5.0 8.3 - - + -
261B LEU* 3.8 24.9 - - + -
262B THR* 6.1 0.4 - - + -
280B PHE* 5.4 6.5 - - + -
281B PHE 2.8 12.6 + - - +
282B ILE* 4.0 22.2 - - + +
283B GLN 2.8 33.7 + - - +
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Residues in contact with LEU 235 (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* 4.4 8.1 - - + -
168B ILE* 3.0 15.2 + - - +
169B ASN* 4.3 3.8 - - - +
170B ASN 2.8 28.9 + - - -
179B ARG* 3.2 9.1 + - - +
182B THR* 3.7 16.2 - - - +
185B ASP* 4.1 8.3 - - + -
186B ALA* 3.9 33.7 - - + +
189B LEU* 4.0 18.6 - - + -
233B ILE* 3.6 20.0 - - + -
234B LEU* 1.3 84.2 - - - +
236B SER* 1.3 61.8 + - - +
283B GLN* 3.4 25.8 - - + -
350B VAL* 4.5 3.6 - - + -
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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