Contacts of the strand formed by residues 175 - 181 (chain B) in PDB entry 3K5N
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 GLN 175 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170B LEU 3.7 1.7 - - - +
171B GLU* 3.3 2.8 - - - +
172B GLY 2.9 30.2 + - - +
173B CYS 2.8 18.7 - - - +
174B GLY* 1.3 80.2 - - - +
176B ARG* 1.3 70.9 + - - +
177B ILE* 5.7 3.0 - - + +
194B GLU* 4.3 14.5 + - - -
211B TRP* 3.9 18.9 - - + +
215B TYR* 2.5 49.0 + - + -
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Residues in contact with ARG 176 (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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29A ASN* 3.4 39.3 - - - +
170B LEU 3.7 3.4 - - - -
171B GLU* 3.8 18.2 - - + +
174B GLY 6.2 0.4 - - - -
175B GLN* 1.3 83.3 - - - +
177B ILE* 1.3 61.6 + - - +
192B ASP* 2.5 46.5 + - - -
193B PHE* 3.7 7.2 - - + +
194B GLU* 3.4 26.6 + - - +
333B LEU* 3.8 22.1 - - + +
337B GLU* 2.8 28.9 + - - +
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Residues in contact with ILE 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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169B GLY* 3.5 0.7 - - - -
170B LEU* 3.1 40.2 + - + +
175B GLN* 5.7 3.4 - - - +
176B ARG* 1.3 77.0 - - - +
178B VAL* 1.3 87.0 + - - +
179B TYR* 3.1 50.3 - - + +
193B PHE* 5.2 0.2 - - - -
194B GLU* 3.5 39.3 - - + +
196B GLU* 4.6 7.9 - - + +
211B TRP* 4.1 13.7 - - + +
333B LEU* 3.9 4.4 - - - +
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Residues in contact with VAL 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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167B CYS* 4.4 1.8 - - + -
168B ILE 3.4 11.0 - - - +
169B GLY* 4.1 7.9 - - - -
177B ILE* 1.3 92.9 - - - +
179B TYR* 1.3 74.9 + - - +
180B MET* 4.3 6.7 - - + -
193B PHE* 4.2 17.9 - - + -
194B GLU 3.4 5.2 + - - +
195B LEU* 3.4 24.1 - - + -
196B GLU 2.9 24.3 + - - -
329B ALA* 4.0 13.9 - - + +
332B ASN* 4.3 13.2 - - - +
333B LEU* 4.2 18.6 - - + -
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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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167B CYS* 3.0 9.4 - - - +
168B ILE* 2.7 50.4 + - + +
170B LEU* 4.0 18.8 - - + -
177B ILE* 3.1 41.9 - - + +
178B VAL* 1.3 74.9 - - - +
180B MET* 1.3 61.4 + - - +
196B GLU* 3.6 19.0 + - + -
198B VAL* 4.7 1.3 - - + -
204B LEU* 4.0 18.7 - - + +
207B LYS* 3.3 62.0 + - + +
208B LEU* 5.4 1.1 - - - -
211B TRP* 3.7 15.4 - + - +
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Residues in contact with MET 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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166B TYR 3.9 7.9 - - - +
167B CYS* 3.4 26.9 - - + +
178B VAL* 4.3 1.1 - - + -
179B TYR* 1.3 75.9 - - - +
181B LEU* 1.3 62.5 + - - +
195B LEU* 3.7 13.5 - - + -
196B GLU 2.8 13.9 + - - +
197B TYR* 3.6 22.9 - - + -
198B VAL* 2.5 44.2 + - - +
204B LEU* 4.1 2.7 - - - -
321B PHE* 4.0 13.7 - - + -
325B LYS* 3.3 34.5 - - + +
328B LEU* 3.9 9.9 - - + -
329B ALA* 3.7 28.3 - - + +
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Residues in contact with LEU 181 (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 LEU 4.3 2.9 - - - +
166B TYR* 3.7 13.8 + - - +
180B MET* 1.3 80.4 - - - +
182B GLY* 1.3 61.2 - - - +
197B TYR* 4.0 3.2 - - - -
198B VAL 3.4 6.1 - - - +
199B ALA 4.3 3.6 - - - +
200B SER* 3.6 35.0 - - - +
201B ARG* 3.7 43.3 - - + +
204B LEU* 5.0 3.6 - - + -
321B PHE* 3.8 22.6 - - + -
325B LYS* 2.0 37.6 + - - +
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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