Contacts of the strand formed by residues 181 - 185 (chain B) in PDB entry 3KXK
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 SER 181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B ILE 5.3 0.9 - - - -
180B PRO* 1.3 73.8 - - - +
182B ILE* 1.3 63.5 + - - +
229B MET* 3.5 12.1 + - - +
231B VAL* 3.9 16.8 - - - +
257B TYR 5.4 0.9 - - - -
258B SER* 3.5 21.6 + - - -
259B ASP* 2.9 40.5 + - - -
260B ALA 3.4 5.4 + - - -
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Residues in contact with ILE 182 (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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180B PRO* 4.8 8.3 - - + -
181B SER* 1.3 80.4 + - - +
183B GLY* 1.3 62.5 + - - +
184B ILE* 3.9 1.7 + - + +
228B ILE* 3.8 23.8 - - + -
229B MET 2.8 12.3 + - - +
230B LEU* 3.5 11.2 - - + +
231B VAL* 2.8 28.2 + - - +
258B SER* 4.1 1.6 - - - -
259B ASP* 5.1 1.8 - - + -
260B ALA* 3.4 33.9 - - + +
261B LEU 4.5 0.4 - - - -
262B ILE* 3.5 38.1 - - + +
348B ILE* 4.8 11.0 - - + +
351B LEU* 4.6 13.0 - - + -
352B ALA* 6.0 3.8 - - + +
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Residues in contact with GLY 183 (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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182B ILE* 1.3 72.0 - - - +
184B ILE* 1.3 62.9 + - - -
185B VAL* 3.5 2.3 + - - -
231B VAL* 3.5 9.0 - - - -
233B THR* 4.2 7.6 - - - -
258B SER* 3.6 12.1 + - - -
260B ALA 2.9 12.7 + - - -
261B LEU* 3.2 22.4 - - - +
262B ILE 2.8 23.8 + - - -
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Residues in contact with ILE 184 (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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182B ILE* 4.7 5.2 - - + +
183B GLY* 1.3 70.6 - - - -
185B VAL* 1.3 61.1 + - - +
192B LYS* 3.2 30.8 + - + +
195B LEU* 3.6 25.8 - - + -
196B PHE* 3.9 32.5 - - + -
199B LEU* 4.8 3.6 - - + -
230B LEU* 4.7 9.0 - - + -
231B VAL 2.8 15.4 + - - +
232B ASP* 4.6 4.7 - - - +
233B THR* 3.0 19.8 + - - +
262B ILE* 3.6 24.7 - - + +
264B VAL* 3.7 26.9 - - + -
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Residues in contact with VAL 185 (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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183B GLY 3.5 6.7 + - - +
184B ILE* 1.3 73.8 - - - +
186B GLY* 1.3 60.7 + - - +
192B LYS* 3.4 10.9 - - - +
233B THR* 3.2 27.8 - - + +
234B VAL 5.8 0.2 - - - +
236B PHE* 3.9 17.9 - - + -
252B LEU* 4.9 5.4 - - + -
255B ALA* 4.4 9.2 - - + -
261B LEU* 4.3 22.0 - - + -
262B ILE 2.9 17.2 + - - +
263B LEU* 4.0 19.5 - - + -
264B VAL* 2.9 26.3 + - - +
285B LEU* 4.5 12.6 - - + -
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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