Contacts of the helix formed by residues 172 - 190 (chain B) in PDB entry 2WVL
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 PHE 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A PHE* 3.4 64.2 - + + -
307A ASN* 3.6 17.9 - - + +
308A PRO* 3.9 41.1 - - + -
310A LEU* 4.5 14.6 - - + -
170B ASN* 3.3 5.6 + - - +
171B TYR* 1.3 94.4 - - + +
173B PRO* 1.3 70.5 - - - +
174B GLY 3.1 0.7 - - - -
175B ALA* 2.9 28.3 + - + +
176B VAL* 3.1 14.4 + - - +
308B PRO 5.5 0.4 - - - -
310B LEU* 3.9 19.7 - - + -
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Residues in contact with PRO 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.8 10.3 - - + -
306A ARG* 3.7 28.7 - - + +
307A ASN* 3.5 9.2 - - - +
71B GLY* 3.4 37.7 - - - +
74B SER* 3.8 14.1 - - - +
75B GLY* 3.7 12.4 - - - -
170B ASN 5.1 0.4 - - - +
171B TYR 3.6 9.9 - - - +
172B PHE* 1.3 84.6 - - - +
174B GLY* 1.3 49.7 + - - +
176B VAL* 2.9 15.4 + - + +
177B TRP* 2.8 31.4 + - - +
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Residues in contact with GLY 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.7 10.5 - - - +
174A GLY* 4.1 17.4 - - - -
177A TRP* 6.6 0.2 - - - -
307A ASN* 2.8 30.0 + - - +
173B PRO* 1.3 78.3 - - - +
175B ALA* 1.3 60.2 + - - +
177B TRP* 3.3 6.3 + - - +
178B GLU* 3.1 21.7 + - - +
307B ASN* 4.0 7.2 + - - -
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PHE* 5.2 0.2 - - + -
170B ASN* 4.2 7.6 - - - +
172B PHE* 2.9 25.9 + - + +
174B GLY* 1.3 71.5 - - - +
176B VAL* 1.3 66.6 + - - +
178B GLU* 3.1 3.8 + - - +
179B TYR* 2.9 45.6 + - + +
307B ASN* 3.7 33.5 + - + +
308B PRO 4.4 5.4 - - - +
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 3.7 31.0 - - + +
75B GLY* 4.1 8.5 - - - -
76B ILE* 4.1 9.0 - - + -
166B ILE* 4.0 21.3 - - + -
170B ASN* 4.0 28.7 - - + +
172B PHE 3.4 13.7 - - - +
173B PRO* 3.1 15.0 - - + +
175B ALA* 1.3 76.5 - - - +
177B TRP* 1.3 63.3 + - - +
179B TYR* 3.2 10.8 + - - +
180B VAL* 3.0 26.3 + - + +
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Residues in contact with TRP 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.3 14.4 - - + -
27A ASP* 3.4 35.2 + - + +
174A GLY* 6.3 1.1 - - - -
177A TRP* 3.5 53.4 - + + -
26B LEU* 4.1 32.3 - - + -
27B ASP* 4.7 2.7 - - + -
49B ARG* 6.0 0.4 - - - -
75B GLY 3.3 23.6 + - - +
77B PRO* 3.6 18.2 - - + +
173B PRO 2.8 13.0 + - - +
174B GLY* 3.5 10.5 - - - +
176B VAL* 1.3 72.9 - - - +
178B GLU* 1.3 77.1 + - - +
180B VAL* 3.1 3.8 + - - +
181B ARG* 2.9 72.7 + - + +
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Residues in contact with GLU 178 (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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1B MET* 4.1 1.4 - - + +
23B ILE* 3.2 25.1 - - + +
26B LEU* 3.5 26.0 - - + +
174B GLY 3.1 3.8 + - - +
175B ALA 3.1 7.4 + - - +
177B TRP* 1.3 87.0 - - - +
179B TYR* 1.3 56.2 + - - +
181B ARG* 3.3 4.3 + - - +
182B ALA* 2.9 27.8 + - + +
305B THR* 2.9 23.0 + - - +
306B ARG* 3.0 26.5 + - - +
307B ASN* 2.4 45.4 + - - +
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Residues in contact with TYR 179 (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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166B ILE* 3.6 18.6 - - + -
170B ASN* 3.7 25.1 + - - -
175B ALA* 2.9 34.9 + - + +
176B VAL* 3.2 10.5 + - - +
178B GLU* 1.3 71.8 - - - +
180B VAL* 1.3 58.2 + - - +
182B ALA* 3.2 9.0 + - - +
183B TYR* 2.9 40.0 + - + +
199B ILE* 4.3 13.0 - - + -
251B GLU* 3.5 28.3 - - + -
305B THR* 3.5 31.4 - - + -
307B ASN 3.6 6.4 + - - -
308B PRO 3.4 21.7 + - - -
309B HIS* 3.6 20.3 - + - -
311B HIS* 5.4 1.1 - - - -
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Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.7 26.0 - - + +
57B ILE* 3.5 37.7 - - + -
76B ILE* 4.8 5.4 - - + -
77B PRO* 3.6 29.8 - - + -
80B ALA* 4.8 0.7 - - + -
166B ILE* 4.1 17.0 - - + -
176B VAL* 3.0 20.1 + - + +
177B TRP 3.1 1.1 + - - +
179B TYR* 1.3 77.7 - - - +
181B ARG* 1.3 63.7 + - - +
183B TYR* 3.2 8.5 + - + +
184B ALA 3.2 16.1 + - - -
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Residues in contact with ARG 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASP* 4.5 2.6 + - - -
49A ARG* 4.8 0.8 - - - +
1B MET* 3.6 22.5 - - + +
26B LEU 5.3 2.4 + - - -
27B ASP* 4.0 17.6 + - - -
45B ASP* 3.1 31.7 + - - +
48B LEU* 3.6 36.3 - - + +
49B ARG* 3.8 27.0 - - - +
52B LEU* 4.2 18.2 - - - +
77B PRO* 4.4 2.2 - - + -
79B GLU* 5.6 0.4 + - - -
177B TRP* 2.9 67.1 + - + +
178B GLU* 3.7 1.8 - - - +
180B VAL* 1.3 76.0 - - - +
182B ALA* 1.3 50.7 + - - +
184B ALA* 3.3 6.5 + - - +
185B ALA* 2.8 32.9 + - - +
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Residues in contact with ALA 182 (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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1B MET* 3.9 3.1 - - - +
23B ILE* 4.7 7.2 - - + -
178B GLU* 2.9 15.6 + - + +
179B TYR* 3.2 10.3 + - - +
181B ARG* 1.3 72.9 - - - +
183B TYR* 1.3 62.3 + - - +
185B ALA* 3.3 9.9 - - - +
186B GLY* 2.8 25.5 + - - -
197B VAL* 3.9 0.2 - - - +
199B ILE* 3.6 22.4 - - + -
303B ILE* 3.6 25.6 - - + +
305B THR* 6.0 0.7 - - - +
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Residues in contact with TYR 183 (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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52B LEU* 5.7 0.2 - - + -
55B THR* 5.7 4.3 - - + -
57B ILE* 3.8 16.8 - - + -
164B GLY* 4.0 9.2 - - - -
165B PHE 2.5 29.2 + - - -
166B ILE* 3.6 17.3 - - + +
179B TYR* 2.9 16.8 + - + -
180B VAL* 3.2 14.1 + - + +
182B ALA* 1.3 76.9 - - - +
184B ALA* 1.3 62.8 + - - +
186B GLY* 3.3 1.9 + - - -
187B PHE* 3.0 33.3 + - + -
197B VAL* 3.8 12.7 - - + +
199B ILE* 3.5 28.0 - - + -
251B GLU* 3.0 25.0 - - + +
252B HIS* 3.7 17.5 - - - -
253B ALA* 3.4 24.2 - - + -
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Residues in contact with ALA 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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48B LEU* 3.6 35.7 - - + +
51B VAL* 3.8 21.2 - - + +
52B LEU* 4.0 12.3 - - + +
180B VAL 3.2 9.0 + - - +
181B ARG* 3.6 4.5 - - - +
182B ALA 3.1 0.8 - - - -
183B TYR* 1.3 75.7 - - - +
185B ALA* 1.3 67.7 + - - +
187B PHE* 3.1 4.4 + - - +
188B LEU* 2.8 26.2 + - - +
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Residues in contact with ALA 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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1B MET* 3.7 20.0 - - - -
3B LEU* 4.0 7.6 - - + -
43B LEU* 3.7 21.5 - - + -
48B LEU* 3.5 10.7 - - + +
181B ARG 2.8 18.9 + - - +
182B ALA* 3.3 7.0 - - - +
184B ALA* 1.3 76.5 - - - +
186B GLY* 1.3 66.1 + - - +
188B LEU* 3.2 2.5 + - - +
189B MET* 3.1 28.0 + - + +
303B ILE* 5.0 1.6 - - + -
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Residues in contact with GLY 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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182B ALA 2.8 14.5 + - - -
184B ALA 3.2 0.2 - - - -
185B ALA* 1.3 71.9 - - - +
187B PHE* 1.3 56.2 + - - +
189B MET* 2.9 34.0 + - - +
190B ALA 3.1 8.7 + - - -
197B VAL* 3.5 24.5 - - - -
301B PHE* 3.8 13.0 - - - -
303B ILE* 4.2 4.9 - - - +
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Residues in contact with PHE 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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51B VAL* 4.2 13.0 - - + -
55B THR* 5.1 6.3 - - + -
162B TYR* 3.4 52.8 + + + +
163B VAL 4.8 0.7 - - - -
183B TYR* 3.0 29.7 + - + -
184B ALA* 3.1 10.1 + - - +
186B GLY* 1.3 73.2 - - - +
188B LEU* 1.3 62.0 + - - +
190B ALA* 3.5 20.6 + - - +
195B ALA* 4.1 18.8 - - + -
197B VAL* 4.2 10.8 - - + -
253B ALA* 3.6 29.2 - - + -
254B MET* 3.8 15.9 - - - -
255B SER 3.4 19.5 - - - -
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Residues in contact with LEU 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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43B LEU* 4.0 27.0 - - + +
47B ASP* 3.7 37.0 - - + +
48B LEU* 3.9 25.6 - - + +
51B VAL* 4.0 22.0 - - + -
184B ALA 2.8 15.4 + - - +
185B ALA 3.5 5.2 - - - +
187B PHE* 1.3 78.5 - - - +
189B MET* 1.3 59.9 + - - +
190B ALA 3.5 5.4 + - - +
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Residues in contact with MET 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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3B LEU* 3.7 28.9 - - + -
21B GLN* 3.8 20.0 - - - +
41B ARG* 3.9 32.8 + - - +
43B LEU* 4.0 16.6 - - + -
185B ALA* 3.1 27.8 + - + +
186B GLY* 2.9 7.6 + - - +
188B LEU* 1.3 73.9 - - - +
190B ALA* 1.3 66.6 + - - +
191B LYS* 3.5 13.7 + - - +
299B GLU* 4.1 2.9 - - - +
301B PHE* 3.6 36.0 - - + -
303B ILE* 4.6 5.8 - - + -
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Residues in contact with ALA 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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186B GLY 3.1 9.7 + - - +
187B PHE* 3.6 15.0 - - - +
188B LEU 3.3 8.1 - - - +
189B MET* 1.3 82.1 - - - +
191B LYS* 1.3 61.2 + - - +
192B THR* 3.3 14.5 + - + +
195B ALA* 3.8 29.2 - - + -
299B GLU* 3.5 9.4 - - - +
301B PHE* 3.7 9.4 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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