Contacts of the strand formed by residues 175 - 181 (chain A) in PDB entry 3K57
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A LEU 4.5 0.7 - - - -
171A GLU* 3.5 1.9 - - - +
172A GLY* 2.8 40.1 + - - +
173A CYS 3.1 19.7 + - - +
174A GLY* 1.3 91.5 + - - +
176A ARG* 1.3 68.8 + - - +
177A ILE* 4.0 4.9 - - + -
194A GLU* 3.8 15.7 - - - +
211A TRP* 3.8 20.2 - - + +
215A TYR* 3.3 47.2 + - + -
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Residues in contact with ARG 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LEU 3.8 3.8 - - - -
171A GLU* 4.2 13.7 - - + +
174A GLY 5.9 0.2 - - - -
175A GLN* 1.3 78.9 - - - +
177A ILE* 1.3 61.9 + - - +
192A ASP* 2.3 60.4 + - - +
193A PHE* 3.6 10.5 - - + +
194A GLU* 3.1 29.1 + - - +
333A LEU* 3.9 18.6 - - + +
337A GLU* 2.8 30.7 + - - +
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Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ILE 3.9 0.5 - - - +
169A GLY* 3.5 1.9 - - - -
170A LEU* 2.8 52.6 + - + +
175A GLN* 4.7 3.6 - - + -
176A ARG* 1.3 77.0 - - - +
178A VAL* 1.3 77.2 + - - +
179A TYR* 3.6 32.1 - - + +
193A PHE* 5.0 0.4 - - - -
194A GLU* 3.4 36.1 - - + +
196A GLU* 3.8 16.6 - - + +
211A TRP* 3.7 29.2 - - + +
333A LEU* 4.1 2.3 - - - +
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A CYS* 4.1 7.9 - - + -
168A ILE 3.4 3.6 - - - +
169A GLY* 4.4 1.6 - - - -
177A ILE* 1.3 80.5 - - - +
179A TYR* 1.3 72.7 + - - +
180A MET* 3.7 1.4 + - + -
193A PHE* 3.8 14.4 - - + -
194A GLU 2.9 10.4 + - - +
195A LEU* 3.6 8.2 - - + +
196A GLU* 2.9 28.1 + - - +
329A ALA* 3.5 42.6 - - + +
332A ASN* 3.8 24.2 - - - +
333A LEU* 4.1 11.7 - - + -
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Residues in contact with TYR 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A CYS* 3.2 5.2 - - - +
168A ILE* 2.9 46.6 + - + +
170A LEU* 3.6 30.1 - - + -
177A ILE* 3.6 27.3 - - + +
178A VAL* 1.3 71.9 - - - +
180A MET* 1.3 59.5 + - - +
196A GLU* 3.2 34.7 + - + +
198A VAL* 5.4 0.7 - - + -
204A LEU* 3.6 20.7 - - + +
207A LYS* 3.7 46.5 + - + +
208A LEU* 4.5 2.7 - - - -
211A TRP* 3.3 27.1 - + - +
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Residues in contact with MET 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A TYR 3.8 7.6 - - - +
167A CYS* 3.7 19.7 - - + -
178A VAL* 3.7 0.6 + - + -
179A TYR* 1.3 76.5 - - - +
181A LEU* 1.3 71.1 + - - +
195A LEU* 3.9 15.7 - - + -
196A GLU 2.9 8.7 + - - -
197A TYR* 3.2 23.8 - - + -
198A VAL* 3.0 24.8 + - - +
204A LEU* 4.1 4.5 - - - +
321A PHE* 3.9 11.0 - - - -
325A LYS* 3.3 32.1 - - + +
328A LEU* 3.8 24.9 - - + -
329A ALA* 3.7 22.9 - - + +
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU 3.8 2.7 - - - +
166A TYR 2.9 21.8 + - - +
180A MET* 1.3 78.3 - - - +
182A GLY* 1.3 66.4 + - - +
197A TYR* 4.0 0.4 - - - -
198A VAL* 3.8 9.2 - - + +
199A ALA 3.9 4.5 - - - +
200A SER* 3.6 35.9 - - - +
201A ARG* 3.4 50.0 - - + +
204A LEU* 4.2 5.7 - - + +
321A PHE* 3.5 17.4 - - + -
325A LYS* 2.8 30.0 + - - +
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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