Contacts of the helix formed by residues 184 - 191 (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 ASN 184 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LEU 3.5 0.8 - - - -
183A ASN* 1.3 80.0 - - - +
185A ILE* 1.3 64.8 + - - +
186A ASP* 3.1 6.6 + - - +
187A ASP* 2.7 39.4 + - - +
188A VAL* 3.0 13.7 + - - +
237A LEU* 4.1 15.2 + - - +
238A SER 3.4 14.1 - - - +
239A ASP* 4.3 3.1 - - - +
240A MET* 3.8 7.9 - - - -
318A LYS* 5.1 3.4 - - - +
327A ARG* 4.5 7.5 - - - +
1819A PO4 3.5 27.5 + - - -
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Residues in contact with ILE 185 (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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184A ASN* 1.3 73.4 - - - +
186A ASP* 1.3 65.4 + - - +
188A VAL* 4.4 2.5 - - + -
189A MET* 2.9 43.1 + - + +
207A TYR* 3.9 13.5 - - + +
217A PHE* 5.0 2.2 - - + -
235A ASN 3.6 9.4 - - - +
236A THR 3.4 20.0 - - - +
237A LEU 3.8 0.4 - - - -
238A SER* 3.0 38.3 + - - +
240A MET* 3.8 10.5 - - + +
246A VAL* 4.1 28.9 - - + -
266A ILE* 4.2 15.3 - - + -
268A LEU* 4.4 14.4 - - + -
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Residues in contact with ASP 186 (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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184A ASN* 3.1 6.1 + - - +
185A ILE* 1.3 81.4 - - - +
187A ASP* 1.3 62.4 + - - +
189A MET* 3.4 2.1 + - - +
190A ARG* 3.1 38.4 + - - +
197A VAL* 4.7 1.5 - - - +
205A ASN* 3.0 22.9 + - - +
207A TYR* 2.3 38.7 + - - -
236A THR* 3.1 24.9 + - - +
237A LEU* 4.2 2.8 - - - +
1819A PO4 2.8 29.0 + - - +
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Residues in contact with ASP 187 (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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181A GLY 4.0 4.1 - - - +
182A LEU* 3.6 34.3 - - + +
183A ASN* 3.0 23.3 + - - +
184A ASN* 2.7 33.2 + - - +
186A ASP* 1.3 70.3 - - - +
188A VAL* 1.3 62.1 + - - +
190A ARG* 3.2 33.6 + - - +
191A HIS* 3.3 9.2 + - - -
1819A PO4 3.6 5.9 + - - -
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Residues in contact with VAL 188 (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 23.4 - - + +
177A MET* 3.7 30.3 - - + -
182A LEU* 4.2 13.5 - - + -
184A ASN 3.0 20.1 + - - +
185A ILE* 3.8 7.9 - - + +
187A ASP* 1.3 70.4 - - - +
189A MET* 1.3 63.6 + - + +
191A HIS* 3.1 5.7 + - - +
192A THR* 2.6 32.6 + - - +
240A MET* 3.8 16.8 - - + -
246A VAL* 3.3 24.7 - - + -
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Residues in contact with MET 189 (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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185A ILE* 2.9 29.9 + - + +
186A ASP 3.9 2.2 - - - +
188A VAL* 1.3 83.4 - - + +
190A ARG* 1.3 64.6 + - - +
192A THR* 2.9 33.6 + - + +
195A ILE* 3.6 32.2 - - + +
197A VAL* 3.7 18.3 - - + +
207A TYR* 3.6 29.2 - - + -
246A VAL* 4.1 17.9 - - + -
248A VAL* 4.3 10.8 - - + -
266A ILE* 3.6 25.6 - - + -
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Residues in contact with ARG 190 (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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186A ASP* 3.1 24.2 + - - +
187A ASP* 3.2 23.1 + - - +
189A MET* 1.3 76.6 - - - +
191A HIS* 1.3 66.1 + - + +
192A THR 3.7 0.5 + - - -
195A ILE 5.1 1.0 - - - +
197A VAL* 3.7 30.0 - - + +
205A ASN* 4.0 13.5 + - - +
714A SER* 4.8 2.9 + - - -
716A TYR* 4.9 2.9 + - - -
735A ARG* 4.7 20.6 + - - +
789A TYR* 5.6 5.8 - - - -
791A THR* 6.0 4.0 - - - +
803A ASP* 4.8 14.4 + - - -
1819A PO4 3.0 41.2 + - - -
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Residues in contact with HIS 191 (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* 4.5 5.0 - - + +
176A ASN* 4.6 6.0 + - - +
180A PHE* 3.8 17.1 + + + +
182A LEU* 3.6 46.8 - - + +
187A ASP* 3.3 3.8 + - - +
188A VAL 3.1 10.8 + - - +
190A ARG* 1.3 81.3 - - + +
192A THR* 1.3 59.0 + - - +
193A PRO* 3.4 11.3 - - - +
688A GLN* 4.3 6.9 - - - +
714A SER* 4.9 3.1 + - - -
716A TYR* 3.4 57.8 + + + -
764A ASP* 3.4 20.8 + - - -
782A ASN* 5.4 2.0 + - - -
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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