Contacts of the helix formed by residues 216 - 231 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A PHE* 4.0 1.8 - - - -
212A LEU* 2.8 31.2 + - + +
214A GLU 3.9 0.4 - - - -
215A GLN* 1.3 78.2 - - + +
217A PRO* 1.3 68.0 - - - +
218A ALA* 3.2 20.4 + - - +
219A VAL* 3.1 26.5 + - + +
220A ALA* 3.0 18.5 + - - +
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Residues in contact with PRO 217 (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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108A PHE* 3.6 49.8 - - + +
110A THR* 6.1 0.4 - - - +
113A GLY* 5.5 5.4 - - - -
215A GLN 3.6 9.9 - - - +
216A ASP* 1.3 85.3 - - - +
218A ALA* 1.3 57.1 + - - +
220A ALA* 3.6 1.3 - - + +
221A TRP* 2.9 47.0 + - + +
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Residues in contact with ALA 218 (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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113A GLY* 5.5 4.0 - - - -
116A ASP* 6.2 4.9 - - + -
117A ALA* 4.8 2.1 - - - +
216A ASP* 3.1 11.3 + - - +
217A PRO* 1.3 80.1 - - - +
219A VAL* 1.3 62.0 + - - +
221A TRP* 4.2 5.2 - - - +
222A LYS* 3.4 31.1 + - - +
504A CL 4.0 14.8 - - + -
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Residues in contact with VAL 219 (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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202A LEU* 4.8 1.1 - - + +
204A ILE* 3.8 24.9 - - + -
206A LEU* 3.8 29.4 - - + -
212A LEU* 4.3 13.2 - - + +
213A VAL* 4.1 12.8 - - + -
216A ASP* 3.1 33.7 + - + +
218A ALA* 1.3 76.3 - - - +
220A ALA* 1.3 65.4 - - - +
222A LYS* 3.1 9.5 + - - +
223A THR* 2.9 29.9 + - + +
504A CL 3.9 9.2 - - + -
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Residues in contact with ALA 220 (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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108A PHE* 3.7 20.9 - - + -
109A TYR* 5.3 0.4 - - + -
185A GLY* 4.3 0.2 - - - -
186A PRO* 3.3 22.2 - - + +
213A VAL* 3.3 31.1 - - + +
216A ASP 3.0 8.6 + - - +
217A PRO 3.2 7.4 + - - +
219A VAL* 1.3 75.7 - - - +
221A TRP* 1.3 63.7 + - + +
223A THR* 2.6 26.1 + - - -
224A GLY 3.2 4.3 + - - -
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Residues in contact with TRP 221 (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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98A PHE* 4.3 10.5 - + - -
108A PHE* 6.2 0.2 - + - -
109A TYR* 3.9 33.0 - + + +
110A THR 3.9 19.8 + - - +
113A GLY* 3.3 26.8 - - - +
114A LEU* 3.5 41.5 - - + +
117A ALA* 3.6 20.4 - - + -
140A PHE* 4.4 14.1 - + - -
141A LEU* 4.6 6.1 - - + -
144A VAL* 4.8 1.6 - - + -
151A LEU* 4.2 19.5 - - + -
186A PRO* 3.9 23.8 - - + -
217A PRO* 2.9 33.0 + - + +
218A ALA* 4.2 2.0 - - - +
220A ALA* 1.3 77.3 - - + +
222A LYS* 1.3 63.3 + - - +
224A GLY* 3.1 12.1 + - - -
225A LEU* 3.1 16.3 + - - +
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Residues in contact with LYS 222 (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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117A ALA* 4.0 18.2 - - + +
120A ALA* 3.8 27.1 - - + -
121A TYR* 4.1 3.2 - - - -
202A LEU* 4.0 28.6 + - + +
204A ILE* 4.5 12.9 - - - +
218A ALA* 3.4 15.2 + - - +
219A VAL* 3.1 9.2 + - - +
221A TRP* 1.3 77.8 - - - +
223A THR* 1.3 56.2 + - - +
225A LEU* 3.3 7.2 + - - +
226A TRP* 2.8 30.7 + - - +
504A CL 3.1 32.4 - - - +
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Residues in contact with THR 223 (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 ARG 4.8 1.4 + - - -
186A PRO* 4.6 3.1 - - - +
187A ILE* 4.1 4.7 - - - +
189A LEU* 4.0 34.7 - - + +
198A ALA* 4.7 1.8 - - + -
202A LEU* 4.1 7.9 - - + -
206A LEU* 4.0 20.9 - - + -
213A VAL* 3.7 21.1 - - + +
219A VAL* 2.9 19.1 + - + +
220A ALA 2.6 19.2 + - - -
222A LYS* 1.3 75.8 - - - +
224A GLY* 1.3 61.3 + - - +
226A TRP* 3.4 14.0 + - - +
227A TYR* 3.1 21.0 + - - +
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Residues in contact with GLY 224 (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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140A PHE* 3.6 14.6 - - - -
186A PRO* 4.3 9.0 - - - -
187A ILE* 3.9 23.3 - - - +
220A ALA 3.2 3.4 + - - -
221A TRP 3.1 8.8 + - - -
223A THR* 1.3 82.8 + - - +
225A LEU* 1.3 61.2 + - - +
227A TYR* 3.4 4.3 + - - +
228A TRP* 3.1 23.4 + - - +
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Residues in contact with LEU 225 (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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114A LEU* 5.1 4.5 - - + +
117A ALA* 3.5 43.5 - - + +
118A LEU* 4.0 14.6 - - + -
121A TYR* 3.5 23.3 - - + -
124A PHE* 3.8 38.1 - - + -
140A PHE* 3.8 22.4 - - + -
221A TRP 3.1 11.3 + - - +
222A LYS* 3.3 5.4 + - - +
224A GLY* 1.3 73.2 - - - +
226A TRP* 1.3 59.5 + - - +
228A TRP* 4.3 1.1 - - - -
229A ASN* 2.7 42.4 + - - +
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Residues in contact with TRP 226 (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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121A TYR* 3.4 22.1 - - + +
189A LEU* 3.6 24.7 - - + -
194A ASN* 3.9 24.9 - - + -
197A ALA* 3.7 13.4 + - + -
198A ALA* 3.5 30.2 - - + +
201A ALA* 3.5 33.7 - - + +
202A LEU* 4.5 6.1 - - + -
222A LYS 2.8 18.1 + - - +
223A THR* 3.5 12.6 - - - +
225A LEU* 1.3 73.2 - - - +
227A TYR* 1.3 92.6 + + + +
230A SER* 2.7 55.0 + - - -
231A GLN* 3.3 31.4 - - + +
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Residues in contact with TYR 227 (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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187A ILE* 4.0 25.1 - - + -
194A ASN* 5.0 8.1 - - - -
223A THR 3.1 10.8 + - - +
224A GLY 3.7 7.2 - - - +
226A TRP* 1.3 102.3 - + + +
228A TRP* 1.3 68.2 + + - +
231A GLN* 3.0 53.3 + - + +
233A GLY* 3.4 13.9 - - - -
234A PRO* 4.4 1.2 - - - +
239A PRO* 4.0 3.2 - - + +
255A SER* 2.5 31.9 + - - -
256A ILE* 4.1 23.0 + - + -
401A GOL 3.9 31.9 - - - -
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Residues in contact with TRP 228 (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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124A PHE* 3.6 17.4 - + - -
136A GLU* 2.9 33.8 + - - +
139A ALA* 3.6 20.6 - - + -
140A PHE* 3.5 55.2 - + + -
143A ASN* 3.7 16.4 - - + -
187A ILE* 5.3 4.2 - - + +
224A GLY 3.1 13.9 + - - +
225A LEU 3.7 4.0 - - - +
227A TYR* 1.3 82.2 - + - +
229A ASN* 1.3 65.3 + - - +
238A THR* 3.8 0.2 - - - -
239A PRO* 3.2 50.7 - - + +
240A HIS 3.0 30.6 + - - +
243A ILE* 4.3 3.8 - - + -
252A THR* 3.7 11.9 - - + -
256A ILE* 4.0 13.5 - - + -
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Residues in contact with ASN 229 (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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121A TYR* 3.6 34.5 - - + +
123A ALA* 5.8 0.3 - - - +
124A PHE* 3.7 21.3 + - - +
225A LEU* 2.7 35.5 + - - +
228A TRP* 1.3 90.3 - - - +
230A SER* 1.3 60.4 + - - +
238A THR* 3.9 13.0 + - - +
240A HIS* 3.4 36.1 + - + +
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Residues in contact with SER 230 (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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121A TYR* 5.3 4.5 - - - -
226A TRP* 2.7 37.2 + - - -
228A TRP 3.5 0.2 - - - -
229A ASN* 1.3 80.7 - - - +
231A GLN* 1.3 84.5 + - - +
232A ASN* 4.1 1.4 + - - +
238A THR* 3.6 12.8 - - - +
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Residues in contact with GLN 231 (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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194A ASN* 4.7 5.4 - - - +
197A ALA* 5.3 3.5 - - - +
226A TRP* 3.3 39.6 - - + +
227A TYR* 3.0 40.7 + - + +
230A SER* 1.3 110.7 + - - +
232A ASN* 1.3 64.4 + - - +
233A GLY 4.3 3.1 + - - +
238A THR* 3.4 3.0 - - - +
239A PRO* 3.1 27.2 - - - +
255A SER* 4.4 0.7 - - - -
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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