Contacts of the strand formed by residues 176 - 180 (chain A) in PDB entry 4U6Q
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 THR 176 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLY 4.4 4.0 + - - -
175A GLU* 1.3 73.4 - - - +
177A LEU* 1.3 65.7 + - - +
198A PHE* 4.5 2.5 - - - -
199A ASN* 3.2 28.3 + - - +
201A LEU* 3.6 24.2 - - + -
229A HIS* 3.2 29.0 + - + +
230A SER* 3.7 8.5 - - - +
231A ASP* 2.9 40.4 + - - +
232A CYS* 3.3 7.3 + - - +
256A ARG* 5.3 1.2 + - - -
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 4.1 14.4 - - + -
175A GLU 4.0 1.4 + - - -
176A THR* 1.3 74.1 - - - +
178A GLY* 1.3 58.7 + - - +
179A ILE* 3.9 9.1 + - + -
189A VAL* 4.1 20.2 - - + -
193A ALA* 3.6 28.7 - - + -
198A PHE* 3.8 23.7 - - + -
199A ASN 2.8 10.6 + - - +
200A VAL* 3.5 5.4 - - + +
201A LEU* 2.8 29.3 + - - +
232A CYS* 3.4 38.4 - - + +
234A THR* 3.9 20.2 - - + -
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Residues in contact with GLY 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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176A THR 3.8 0.2 + - - -
177A LEU* 1.3 71.9 - - - +
179A ILE* 1.3 61.9 + - - -
180A ILE 3.9 0.2 + - - -
201A LEU* 3.6 3.8 - - - -
226A LEU* 3.8 14.1 - - - -
230A SER* 3.3 23.8 + - - -
232A CYS 2.8 13.8 + - - -
233A VAL* 3.5 4.5 - - - +
234A THR* 3.0 29.3 + - - +
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Residues in contact with ILE 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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177A LEU* 4.4 7.9 - - + -
178A GLY* 1.3 74.7 - - - -
180A ILE* 1.3 63.9 + - - +
181A GLY 3.4 26.1 + - - +
182A LEU* 4.0 13.7 - - + -
186A GLY* 3.4 22.7 - - - +
189A VAL* 4.2 7.0 - - + -
190A ALA* 3.7 27.6 - - + +
200A VAL* 3.9 11.0 - - + -
201A LEU 2.8 16.3 + - - +
202A PHE* 3.0 4.6 - - + +
203A TYR 2.8 26.7 + - - -
226A LEU* 4.0 1.2 - - - +
234A THR* 3.7 17.3 - - + -
236A HIS* 4.1 11.4 - - + -
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Residues in contact with ILE 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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179A ILE* 1.3 73.8 - - - +
181A GLY* 1.3 61.0 + - - +
203A TYR* 3.7 9.2 - - + +
223A LEU* 3.7 24.9 - - + -
226A LEU* 3.8 18.8 - - + -
227A LEU* 4.4 2.5 - - + -
233A VAL* 3.6 20.9 - - + -
234A THR 3.1 7.3 + - - -
235A LEU* 3.4 33.0 - - + -
236A HIS* 2.8 28.8 + - - -
237A CYS* 3.3 13.5 + - - -
246A LEU* 4.4 12.3 - - + -
247A ILE* 4.7 1.1 - - + -
401A NAI 3.7 23.3 - - + +
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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