Contacts of the helix formed by residues 179 - 186 (chain A) in PDB entry 2WWA
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 SER 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A ALA* 4.7 3.8 + - - +
171A ILE* 3.8 4.9 - - - -
172A ASP* 4.2 17.7 + - - +
178A SER* 1.4 79.9 + - - +
180A GLY* 1.4 61.9 + - - +
181A ALA* 3.2 15.8 + - - +
182A MET* 3.3 12.6 + - - +
183A ILE* 3.1 27.5 + - - +
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Residues in contact with GLY 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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84A LEU* 4.7 0.5 - - - +
167A LEU* 4.3 2.5 - - - +
168A ALA* 3.9 23.8 + - - -
171A ILE* 3.6 35.3 - - - +
179A SER* 1.4 71.6 + - - +
181A ALA* 1.4 61.5 + - - +
182A MET 3.4 0.2 - - - -
183A ILE* 3.9 4.6 - - - +
184A ILE* 3.3 26.0 + - - +
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Residues in contact with ALA 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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84A LEU* 3.3 41.9 - - + +
87A ASN* 5.4 5.8 - - - +
168A ALA* 4.5 8.2 - - + +
179A SER* 3.2 11.9 + - - +
180A GLY* 1.4 75.4 - - - +
182A MET* 1.4 63.1 + - - +
184A ILE* 3.6 0.2 - - - +
185A ASN* 3.5 12.6 + - - +
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Residues in contact with MET 182 (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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178A SER* 3.8 17.9 - - - +
179A SER* 3.3 16.7 + - - +
181A ALA* 1.4 79.2 - - - +
183A ILE* 1.4 61.5 - - + +
185A ASN* 3.4 15.1 + - + +
186A THR* 3.2 49.2 + - + +
290A TYR* 4.7 17.7 - - + +
293A CYS* 4.5 17.0 - - - -
297A LEU* 5.7 7.9 - - + -
455A VAL* 3.7 25.1 - - + +
459A GLY* 5.0 11.7 - - - +
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Residues in contact with ILE 183 (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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36A THR* 3.3 33.9 - - + +
39A ALA* 5.9 0.4 - - + -
40A GLY* 5.5 7.9 - - - +
171A ILE* 4.2 11.0 - - + -
177A PHE* 3.2 28.0 - - + +
178A SER* 4.2 10.3 - - - -
179A SER 3.1 15.7 + - - +
180A GLY* 3.9 6.3 + - - +
181A ALA 3.4 0.4 - - - -
182A MET* 1.4 75.8 - - + +
184A ILE* 1.4 59.3 + - + +
186A THR* 3.1 11.2 + - - +
187A VAL* 3.1 37.1 + - + +
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Residues in contact with ILE 184 (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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43A TYR* 3.7 41.0 - - + -
73A GLY* 4.0 15.1 - - - +
80A LEU* 6.0 1.6 - - + -
83A GLY* 5.1 6.5 - - - -
84A LEU* 3.5 34.8 - - + -
164A THR* 3.3 26.7 - - - +
167A LEU* 5.1 7.9 - - + -
180A GLY 3.3 19.0 + - - +
181A ALA 3.6 0.4 - - - +
183A ILE* 1.4 76.6 - - + +
185A ASN* 1.4 61.4 + - - +
187A VAL* 3.7 7.2 - - + +
188A VAL* 3.2 25.1 + - - +
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Residues in contact with ASN 185 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A GLY 4.2 8.5 + - - +
71A VAL* 4.0 18.2 - - - +
73A GLY* 5.0 4.4 + - - -
84A LEU* 4.7 8.3 - - + +
181A ALA 3.5 10.9 + - - +
182A MET* 3.4 19.0 + - + +
183A ILE 3.2 0.4 - - - -
184A ILE* 1.4 83.3 - - - +
186A THR* 1.4 57.2 + - - +
187A VAL 3.4 0.7 - - - -
188A VAL* 3.3 22.9 + - - +
189A ILE* 3.7 5.5 - - - +
297A LEU* 4.4 16.4 - - + +
452A GLY* 3.8 14.8 + - - -
455A VAL* 3.8 26.9 - - - +
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Residues in contact with THR 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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182A MET* 3.2 37.3 + - + +
183A ILE* 3.1 14.0 + - - +
185A ASN* 1.4 76.4 - - + +
187A VAL* 1.4 63.9 + - - +
188A VAL 3.6 0.4 - - - -
189A ILE* 3.5 21.4 - - - +
190A ALA* 4.2 3.5 + - - +
455A VAL 4.5 0.2 - - - +
456A GLY* 3.6 34.3 - - - +
459A GLY 5.4 4.7 - - - +
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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