Contacts of the helix formed by residues 216 - 231 (chain B) in PDB entry 1WVV
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 216 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B PHE* 3.7 2.0 - - - -
212B LEU* 2.8 25.6 + - + +
215B GLN* 1.3 80.6 - - + +
217B PRO* 1.3 64.6 - - - +
218B ALA* 2.9 23.7 + - - +
219B VAL* 3.1 25.9 + - + +
220B ALA* 2.9 26.2 + - - +
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Residues in contact with PRO 217 (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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108B PHE* 3.3 46.4 - - + +
109B TYR* 4.9 0.7 - - + -
110B THR* 3.8 24.7 - - + +
113B GLY* 4.1 4.9 - - - -
215B GLN 3.9 3.8 - - - +
216B ASP* 1.3 86.7 - - - +
218B ALA* 1.3 57.3 + - + +
220B ALA* 3.5 2.1 - - + +
221B TRP* 2.9 38.8 + - + -
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Residues in contact with ALA 218 (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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113B GLY* 3.6 20.8 - - - +
116B ASP* 4.1 20.2 - - + +
117B ALA* 3.8 3.4 - - - +
216B ASP* 2.9 9.4 + - - +
217B PRO* 1.3 77.3 - - - +
219B VAL* 1.3 61.9 + - + +
221B TRP 3.5 0.7 + - - -
222B LYS* 2.9 44.2 + - - +
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Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LEU* 5.7 0.2 - - + -
204B ILE* 4.1 23.6 - - + -
206B LEU* 3.9 28.0 - - + -
212B LEU* 4.0 24.0 - - + +
213B VAL* 4.4 4.9 - - + +
216B ASP* 3.1 34.8 + - + +
218B ALA* 1.3 76.5 - - + +
220B ALA* 1.3 65.2 + - - +
222B LYS* 3.2 11.7 + - + +
223B THR* 3.0 24.6 + - + +
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Residues in contact with ALA 220 (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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108B PHE* 3.8 16.6 - - + -
109B TYR* 4.8 2.7 - - + -
185B GLY* 4.5 0.4 - - - -
186B PRO* 3.2 23.7 - - + +
213B VAL* 3.2 29.6 + - - +
216B ASP 2.9 12.4 + - - +
217B PRO* 3.5 8.7 - - + +
219B VAL* 1.3 75.8 - - - +
221B TRP* 1.3 61.7 + - + +
223B THR* 2.6 26.2 + - - -
224B GLY 3.3 1.7 + - - -
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Residues in contact with TRP 221 (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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98B PHE* 3.9 15.9 - + - -
109B TYR* 4.3 16.4 - + + -
110B THR 3.2 23.5 + - - +
113B GLY* 3.4 2.5 - - - +
114B LEU* 3.2 39.7 - - + -
117B ALA* 3.6 21.1 - - + -
140B PHE* 3.8 15.9 - + - -
141B LEU* 3.7 30.5 - - + -
144B VAL* 4.1 9.0 - - + -
151B LEU* 3.7 33.0 - - + -
186B PRO* 4.0 20.9 - - + -
217B PRO* 2.9 28.7 + - + +
218B ALA 4.0 0.2 - - - +
220B ALA* 1.3 76.1 - - + +
222B LYS* 1.3 61.2 + - - +
224B GLY* 3.0 4.2 + - - -
225B LEU* 2.9 24.4 + - - +
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Residues in contact with LYS 222 (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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116B ASP* 4.4 7.0 - - - -
117B ALA* 3.6 29.8 - - + +
119B SER* 5.5 1.6 - - - -
120B ALA* 4.2 19.3 - - + +
202B LEU* 3.8 25.3 + - + +
204B ILE* 4.4 23.7 - - + +
218B ALA* 2.9 33.4 + - - +
219B VAL* 3.4 7.9 - - - +
221B TRP* 1.3 74.6 - - - +
223B THR* 1.3 57.7 + - - +
225B LEU* 3.2 6.3 + - - +
226B TRP* 2.8 29.1 + - - +
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Residues in contact with THR 223 (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 ARG 4.8 0.3 + - - -
186B PRO* 4.3 3.8 - - - +
187B ILE* 3.4 15.3 - - - +
189B LEU* 3.9 27.1 - - + +
198B ALA* 4.7 2.5 - - + -
202B LEU* 4.1 6.5 - - + -
206B LEU* 3.9 28.0 - - + -
213B VAL* 3.7 21.2 - - + +
219B VAL* 3.0 18.6 + - + +
220B ALA 2.6 19.1 + - - -
222B LYS* 1.3 72.4 - - - +
224B GLY* 1.3 64.3 + - - +
226B TRP* 3.4 10.8 + - - +
227B TYR 3.3 16.6 + - - -
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Residues in contact with GLY 224 (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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140B PHE* 3.5 21.5 - - - -
186B PRO* 4.3 4.7 - - - -
187B ILE* 3.6 26.8 - - - +
220B ALA 3.3 4.2 + - - -
221B TRP 3.0 7.7 + - - -
223B THR* 1.3 80.8 + - - +
225B LEU* 1.3 63.3 + - - +
227B TYR* 3.3 4.9 + - - +
228B TRP* 3.1 17.5 + - - +
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Residues in contact with LEU 225 (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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114B LEU* 5.0 4.0 - - + -
117B ALA* 3.6 40.8 - - + +
118B LEU* 4.1 15.9 - - + +
121B TYR* 3.7 21.6 - - + -
124B PHE* 3.7 39.3 - - + -
140B PHE* 3.6 24.5 - - + -
221B TRP 2.9 12.1 + - - +
222B LYS* 3.7 5.8 - - - +
224B GLY* 1.3 74.9 - - - +
226B TRP* 1.3 65.5 + - - +
228B TRP* 4.3 0.7 - - - -
229B ASN* 2.8 33.9 + - - +
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Residues in contact with TRP 226 (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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121B TYR* 3.4 19.4 - - + +
189B LEU* 3.6 23.6 - - + -
194B ASN* 4.1 26.5 - - + -
197B ALA* 3.9 13.6 + - + +
198B ALA* 3.6 32.7 - - + +
201B ALA* 3.5 30.0 - - + +
202B LEU* 4.5 7.4 - - + -
222B LYS 2.8 16.5 + - - +
223B THR* 3.5 13.9 - - - +
224B GLY 3.3 0.2 - - - -
225B LEU* 1.3 76.4 - - - +
227B TYR* 1.3 88.7 + + + +
230B SER* 2.7 51.9 + - - -
231B GLN* 3.4 32.7 - - + +
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Residues in contact with TYR 227 (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 ILE* 3.4 28.5 - - + -
223B THR 3.3 3.4 + - - -
224B GLY 3.8 3.1 - - - +
225B LEU 3.3 0.2 - - - -
226B TRP* 1.3 95.8 - + + +
228B TRP* 1.3 70.1 + + - +
231B GLN* 3.0 53.9 + - + +
233B GLY* 3.3 14.6 - - - -
234B PRO* 4.2 0.9 - - - +
239B PRO* 4.1 3.8 - - + +
255B SER 2.5 30.4 + - - -
256B ILE* 3.8 21.3 + - + -
402B GOL 3.6 39.0 - - - -
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Residues in contact with TRP 228 (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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124B PHE* 3.7 17.4 - + - -
136B GLU* 2.9 38.2 + - + +
139B ALA* 3.5 20.2 - - + -
140B PHE* 3.4 53.4 - + + -
143B ASN* 3.7 19.3 - - + -
224B GLY 3.1 14.7 + - - +
225B LEU 3.8 3.8 - - - +
226B TRP 3.4 0.4 - - - -
227B TYR* 1.3 82.4 - + - +
229B ASN* 1.3 64.2 + - - +
238B THR* 3.7 0.2 - - - -
239B PRO* 3.2 51.6 - - + +
240B HIS* 3.0 31.6 + - + +
243B ILE* 4.3 0.9 - - + -
252B THR* 3.8 10.5 - - + -
256B ILE* 4.0 11.9 - - + -
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Residues in contact with ASN 229 (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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121B TYR* 3.5 38.3 - - + +
123B ALA* 5.6 0.9 - - - +
124B PHE* 3.7 19.8 + - - +
225B LEU* 2.8 33.2 + - - +
228B TRP* 1.3 91.5 - - - +
230B SER* 1.3 59.9 + - - +
238B THR* 3.8 12.7 + - - +
240B HIS* 3.3 36.9 + - + +
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Residues in contact with SER 230 (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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121B TYR* 4.8 7.9 - - - -
201B ALA* 6.1 0.4 - - - -
226B TRP* 2.7 35.9 + - - -
229B ASN* 1.3 81.4 - - - +
231B GLN* 1.3 84.2 + - - +
232B ASN* 4.2 2.1 + - - +
238B THR* 3.6 10.5 - - - +
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Residues in contact with GLN 231 (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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194B ASN* 5.6 1.2 + - - -
197B ALA* 5.8 0.6 - - - +
226B TRP* 3.4 33.6 - - + +
227B TYR* 3.0 46.7 + - + +
230B SER* 1.3 108.8 + - - +
232B ASN* 1.3 63.5 + - - +
233B GLY* 3.5 2.7 + - - +
238B THR* 3.5 3.8 - - - +
239B PRO* 3.3 26.3 - - - +
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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