Contacts of the helix formed by residues 183 - 193 (chain B) in PDB entry 1WVA
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 ASP 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B ASN* 2.6 21.4 + - - +
136B THR* 5.6 3.6 + - - -
181B ASP* 4.1 1.2 + - - +
182B VAL* 1.3 78.2 - - - +
184B PRO* 1.3 71.2 - - + +
185B GLY 3.4 3.8 - - - +
186B GLU* 2.9 23.1 + - + +
187B HIS* 3.0 24.4 + - - +
1316B S2C 2.6 33.3 + - - +
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Residues in contact with PRO 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B VAL 4.5 0.9 - - - +
183B ASP* 1.3 90.7 - - + +
185B GLY* 1.3 57.0 + - - +
187B HIS* 3.3 7.7 + - + +
188B TYR* 3.0 27.0 + - - +
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Residues in contact with GLY 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ASN* 5.0 3.6 - - - -
134B THR* 5.1 17.9 - - - +
183B ASP* 3.4 2.8 - - - +
184B PRO* 1.3 78.6 - - - +
186B GLU* 1.3 61.4 + - - +
188B TYR* 3.5 9.6 - - - +
189B ILE* 3.0 30.1 + - - +
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Residues in contact with GLU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B THR* 3.1 13.1 + - - -
128B ASP* 3.2 9.9 + - - -
129B ILE* 3.0 44.0 + - + +
130B ASN* 3.4 31.5 + - - +
142B GLY 4.1 0.2 - - - +
181B ASP 4.7 0.2 - - - +
182B VAL* 3.6 15.2 - - + -
183B ASP* 2.9 38.0 + - + +
184B PRO 3.2 0.4 - - - -
185B GLY* 1.3 73.2 - - - +
187B HIS* 1.3 62.1 + - - +
189B ILE* 3.1 7.7 + - - +
190B LEU* 2.9 30.0 + - - +
1316B S2C 3.2 9.4 + - - -
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Residues in contact with HIS 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B VAL* 3.7 14.5 - - + +
183B ASP 3.0 16.8 + - - +
184B PRO* 3.7 8.0 + - + +
186B GLU* 1.3 76.8 - - - +
188B TYR* 1.3 63.8 + - - +
190B LEU* 3.2 17.5 + - + +
191B LYS* 3.2 56.2 + - + +
197B TYR* 4.6 6.6 + + - -
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Residues in contact with TYR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B PRO 3.0 14.7 + - - +
185B GLY* 3.5 13.2 - - - +
186B GLU 3.1 0.2 - - - -
187B HIS* 1.3 79.9 - - - +
189B ILE* 1.3 73.1 + - + +
191B LYS* 3.4 3.4 + - + +
192B THR* 2.9 62.4 + - + +
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Residues in contact with ILE 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ILE* 3.4 40.2 - - + +
131B THR* 5.2 9.0 - - + -
134B THR* 5.6 8.1 - - + +
152B LEU* 3.9 28.5 - - + -
185B GLY 3.0 19.1 - - - +
186B GLU* 3.1 10.9 + - - +
188B TYR* 1.3 92.1 - - + +
190B LEU* 1.3 62.9 + - - +
192B THR* 4.5 0.4 - - - -
193B LEU* 3.0 41.1 + - + +
195B ILE* 4.1 0.6 - - + +
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B THR* 3.9 23.1 - - + -
129B ILE* 5.2 5.8 - - + -
176B TYR* 4.0 17.3 - - + -
179B LEU* 4.5 3.1 - - + -
182B VAL* 4.6 7.0 - - + -
186B GLU 2.9 16.1 + - - +
187B HIS* 3.2 22.4 + - + +
189B ILE* 1.3 76.6 - - - +
191B LYS* 1.3 59.1 + - + +
194B GLY* 3.3 5.7 + - - -
195B ILE* 2.9 64.8 + - + +
197B TYR* 4.0 35.9 - - + -
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Residues in contact with LYS 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B HIS* 3.2 41.7 + - + +
188B TYR* 4.0 3.8 - - - +
190B LEU* 1.3 75.3 - - + +
192B THR* 1.3 67.5 + - - +
194B GLY* 3.5 10.1 + - - +
197B TYR* 3.4 28.6 + - + +
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Residues in contact with THR 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B TYR* 2.9 59.2 + - + +
189B ILE* 4.5 0.4 - - + -
191B LYS* 1.3 77.6 - - - +
193B LEU* 1.3 77.5 + - + +
194B GLY 3.3 0.6 + - - -
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B LEU* 4.1 20.4 - - + -
151B GLU* 3.5 36.7 - - + +
152B LEU* 3.6 25.1 - - + -
171B ALA* 3.3 17.1 - - + +
189B ILE* 3.0 34.5 + - + +
192B THR* 1.3 95.2 - - + +
194B GLY* 1.3 67.2 + - - +
195B ILE* 3.3 10.3 - - + -
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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