Contacts of the helix formed by residues 174 - 181 (chain A) in PDB entry 2W77
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 ARG 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A THR* 2.9 17.2 + - - +
142A GLU* 3.7 18.4 - - + +
143A ASP 5.2 0.4 - - - +
173A THR* 1.3 72.2 - - - +
175A GLN* 1.3 61.7 + - - +
177A MET* 2.9 45.4 + - - +
178A ASP* 2.8 31.4 + - - +
182A LEU 4.7 2.2 + - - -
183A ASN* 5.7 3.2 - - - +
240A MET* 3.1 19.2 + - - +
243A TYR 2.9 23.7 + - - -
244A ASP* 3.0 19.5 + - - +
271A LYS* 4.0 3.4 - - - +
1820A PO4 3.4 35.2 - - - +
1823A PO4 2.8 29.0 + - - -
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Residues in contact with GLN 175 (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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141A THR 5.1 4.0 + - - +
143A ASP* 4.9 10.3 + - - +
144A SER* 5.6 0.7 - - - +
145A GLY* 4.3 28.0 + - - +
146A SER 3.7 18.2 - - - +
147A TYR* 4.1 6.5 - - + -
173A THR* 3.1 1.6 + - - -
174A ARG* 1.3 76.5 - - - +
176A ASN* 1.3 55.7 + - - +
177A MET 3.0 2.0 - - - -
178A ASP* 3.0 20.1 + - - +
179A ASP* 2.9 64.3 + - - +
768A ARG* 3.8 12.5 - - - +
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Residues in contact with ASN 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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147A TYR* 3.8 38.8 + - + +
172A VAL* 4.0 17.6 - - + +
173A THR* 3.0 22.5 + - - +
175A GLN* 1.3 77.1 - - - +
177A MET* 1.3 63.9 - - - +
179A ASP 4.6 0.2 - - - +
180A PHE* 3.0 40.0 + - - +
182A LEU* 4.0 9.6 - - - +
191A HIS* 4.6 7.1 + - - +
688A GLN* 3.3 26.7 + - - +
716A TYR* 5.0 4.8 - - - +
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Residues in contact with MET 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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172A VAL* 3.7 21.1 - - + +
173A THR 3.2 10.0 + - - +
174A ARG* 2.9 56.9 + - - +
175A GLN 3.0 0.8 - - - -
176A ASN* 1.3 80.4 - - - +
178A ASP* 1.3 56.9 + - - +
181A GLY* 2.9 26.0 + - - -
182A LEU* 3.0 23.6 + - + +
183A ASN* 5.5 0.7 + - - -
188A VAL* 3.7 27.8 - - + -
240A MET* 3.7 21.8 - - + +
243A TYR 4.2 5.2 - - - +
244A ASP 4.9 3.1 - - - +
245A ARG* 4.8 3.8 - - - +
246A VAL* 4.0 11.9 - - - -
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Residues in contact with ASP 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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174A ARG* 2.8 27.6 + - - +
175A GLN* 3.0 25.0 + - - +
177A MET* 1.3 74.5 - - - +
179A ASP* 1.3 65.3 + - - +
180A PHE 3.5 0.2 + - - -
181A GLY* 3.5 7.8 + - - -
282A GLU* 5.8 3.8 - - - +
768A ARG* 4.4 7.4 + - - +
780A ASN* 5.3 0.7 - - - +
812A ARG* 3.7 9.4 + - - +
1820A PO4 2.6 24.9 + - - -
1823A PO4 2.7 23.1 + - - -
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Residues in contact with ASP 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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147A TYR* 2.7 39.7 + - - +
175A GLN* 2.9 31.8 + - - +
178A ASP* 1.3 73.8 - - - +
180A PHE* 1.3 68.0 + - + +
718A SER* 3.9 6.7 + - - +
729A THR* 5.4 1.0 - - - +
766A MET* 3.3 28.2 - - + +
768A ARG* 2.6 44.9 + - - +
780A ASN* 2.8 19.6 + - - +
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Residues in contact with PHE 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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147A TYR* 3.5 30.5 - + - -
176A ASN* 3.0 30.6 + - - +
179A ASP* 1.3 84.2 - - + +
181A GLY* 1.3 62.0 + - - +
182A LEU* 3.2 10.9 + - + +
191A HIS* 3.8 26.0 + + + +
716A TYR* 3.8 25.6 - + + -
717A THR 3.5 26.2 - - - -
718A SER* 5.1 0.7 - - - -
731A GLY* 4.8 2.5 - - - -
732A GLY* 3.7 21.3 - - - -
764A ASP* 4.8 9.2 - - + -
765A LEU 5.8 0.4 - - - -
766A MET* 4.4 14.4 - - + -
780A ASN* 3.2 16.4 + - - +
782A ASN* 5.0 8.6 + - - +
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Residues in contact with GLY 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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177A MET 2.9 9.0 + - - -
178A ASP* 3.5 5.8 + - - -
179A ASP 3.3 4.6 + - - -
180A PHE* 1.3 77.3 - - - +
182A LEU* 1.3 58.6 + - - +
183A ASN* 2.8 30.2 + - - +
187A ASP* 4.0 4.3 - - - +
780A ASN* 3.7 8.9 - - - +
808A MET* 6.3 3.1 - - - -
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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