Contacts of the helix formed by residues 193 - 207 (chain B) in PDB entry 2W99
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 THR 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B HIS* 2.9 40.1 + - + +
137B VAL* 3.2 23.4 - - - +
192B ALA* 1.3 71.0 - - - +
194B PRO* 1.3 86.5 - - + +
195B VAL 3.3 0.4 - - - -
196B ASP* 2.9 20.8 + - - +
197B MET 3.6 1.0 + - - -
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Residues in contact with PRO 194 (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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192B ALA* 3.4 13.9 - - + -
193B THR* 1.3 100.1 - - + +
195B VAL* 1.3 52.9 + - - +
196B ASP 2.8 5.4 - - - -
197B MET* 2.4 39.9 + - + +
198B TRP 3.1 4.0 + - - -
280B PRO* 3.8 41.5 - - + +
283B ARG* 3.5 11.8 + - + +
284B ILE 5.8 1.6 - - - +
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B VAL* 4.9 2.5 - - + -
138B HIS 5.5 2.7 - - - +
182B ALA* 3.4 16.9 + - + +
184B GLU* 3.1 25.8 - - + +
185B VAL* 3.5 18.5 - - + +
190B THR* 3.6 21.1 - - - +
191B TYR* 4.2 6.3 - - + -
192B ALA* 2.8 42.2 - - + +
194B PRO* 1.3 77.2 - - + +
196B ASP* 1.3 58.0 + - - +
197B MET 3.2 0.6 + - - -
198B TRP* 3.6 9.8 + - - +
199B SER* 3.2 17.7 + - - -
280B PRO* 5.6 1.1 - - + -
283B ARG* 3.6 8.7 - - - +
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Residues in contact with ASP 196 (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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128B LEU* 3.5 9.3 - - - +
132B HIS* 3.2 23.0 + - - +
137B VAL* 3.5 11.0 - - + -
138B HIS* 2.6 51.6 + - - +
141B LEU* 3.2 37.6 - - - +
193B THR 2.9 14.1 + - - +
194B PRO 2.8 0.8 + - - -
195B VAL* 1.3 79.8 - - - +
197B MET* 1.3 61.7 + - - +
199B SER* 3.9 4.6 + - - -
200B VAL* 3.4 3.3 - - - +
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Residues in contact with MET 197 (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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125B LEU* 3.5 23.6 - - + -
128B LEU* 4.1 8.1 - - + -
132B HIS* 5.0 2.6 - - + -
193B THR 3.6 1.5 + - - +
194B PRO* 2.4 32.6 + - + +
196B ASP* 1.3 72.4 - - - +
198B TRP* 1.3 63.0 + - - +
200B VAL* 2.9 44.1 - - + +
201B GLY 3.7 2.3 + - - -
275B MET* 4.9 7.5 - - + +
276B LEU* 4.7 1.6 - - - +
283B ARG* 4.8 7.4 - - + +
284B ILE* 3.5 39.3 - - + +
285B SER 3.7 0.7 - - - +
286B ALA* 3.5 37.5 - - + -
289B ALA* 4.9 1.3 - - - -
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Residues in contact with TRP 198 (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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180B TYR 3.3 24.8 + - - -
181B ARG 3.8 6.1 + - - -
182B ALA* 3.6 11.2 - - + -
183B PRO* 3.4 22.7 - - + +
194B PRO 3.1 4.9 + - - -
195B VAL 3.7 7.0 - - - +
197B MET* 1.3 70.5 - - - +
199B SER* 1.3 53.4 + - - +
200B VAL 2.6 16.7 + - - -
201B GLY 2.9 13.2 + - - -
202B CYS* 3.4 25.2 + - - -
214B PHE* 4.8 6.0 - + - -
226B ILE* 3.6 39.2 - - + +
230B ILE* 5.5 6.3 - - + -
275B MET 4.9 0.7 - - - -
276B LEU* 3.2 57.8 - - + +
277B THR 3.1 29.6 - - - -
278B PHE* 4.6 1.8 - + - -
283B ARG* 3.2 29.9 - - - +
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Residues in contact with SER 199 (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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138B HIS 5.7 0.2 + - - -
139B ARG 4.6 6.8 + - - -
141B LEU* 3.6 41.7 - - - +
180B TYR* 3.7 24.5 + - - +
181B ARG* 5.1 1.0 - - - -
182B ALA 4.9 1.2 + - - -
195B VAL 3.2 14.9 + - - -
196B ASP* 4.0 2.8 + - - -
197B MET 3.3 0.2 - - - -
198B TRP* 1.3 76.7 - - - +
200B VAL* 1.3 60.4 - - - +
202B CYS* 3.9 8.0 - - - +
203B ILE* 3.4 26.3 + - - +
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Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B MET* 3.9 5.8 - - + +
124B PHE* 3.2 44.0 - - + -
125B LEU* 4.0 7.4 - - + -
128B LEU* 4.7 3.4 - - + -
141B LEU* 3.8 2.0 - - + -
196B ASP 3.4 13.2 - - - +
197B MET* 2.9 36.9 + - + +
198B TRP 2.6 6.1 + - - -
199B SER* 1.3 71.0 - - - +
201B GLY* 1.3 52.1 + - - +
202B CYS 3.1 1.6 - - - -
203B ILE* 2.9 7.3 + - - +
204B PHE* 2.6 31.0 + - - +
275B MET* 3.8 25.4 - - + -
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Residues in contact with GLY 201 (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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197B MET 3.7 2.2 + - - -
198B TRP 2.9 7.2 + - - -
200B VAL* 1.3 79.6 - - - +
202B CYS* 1.3 56.3 + - - +
204B PHE* 3.3 8.0 - - - +
205B ALA* 2.9 30.7 + - - +
272B LEU* 3.3 30.4 - - - +
275B MET* 3.8 6.6 - - - -
276B LEU* 3.9 8.9 - - - +
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Residues in contact with CYS 202 (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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179B TRP 5.1 3.4 - - - +
180B TYR* 3.6 33.6 - - + -
198B TRP* 3.4 47.6 - - - -
199B SER 3.9 4.7 - - - +
200B VAL 3.1 0.4 - - - -
201B GLY* 1.3 77.3 - - - +
203B ILE* 1.3 59.0 + - - +
205B ALA 4.1 0.2 - - - -
206B GLU* 3.3 27.7 + - - +
213B LEU* 4.2 17.3 + - + +
214B PHE* 5.2 11.7 - - + +
276B LEU* 4.5 7.6 - - - -
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Residues in contact with ILE 203 (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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100B LEU* 3.7 24.0 - - + -
121B MET* 5.2 4.7 - - - -
124B PHE* 5.2 7.4 - - + -
141B LEU 4.6 6.5 - - - +
142B LYS* 4.1 3.8 - - - -
143B PRO* 3.3 43.7 - - + -
146B ILE* 4.7 11.4 - - + -
180B TYR* 3.4 17.9 - - + -
199B SER 3.4 14.3 + - - +
200B VAL* 2.9 9.4 + - - +
202B CYS* 1.3 75.5 - - - +
204B PHE* 1.3 62.7 + - - +
205B ALA 3.2 0.4 - - - -
206B GLU* 3.9 6.6 - - + +
207B MET* 2.9 41.9 + - + +
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Residues in contact with PHE 204 (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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117B ILE* 4.8 1.3 - - + -
121B MET* 3.6 26.7 - - + -
200B VAL 2.6 17.2 + - - +
201B GLY* 3.3 11.7 - - - +
203B ILE* 1.3 74.6 - - - +
205B ALA* 1.3 59.8 + - - +
207B MET* 3.1 29.5 - - + +
208B PHE* 3.3 20.4 - + - -
264B MET* 3.3 26.2 - - + +
268B GLY* 3.7 8.1 - - - -
271B LEU* 4.9 5.2 - - + -
272B LEU* 3.6 44.4 - - + -
275B MET* 4.1 13.2 - - + -
294B TYR* 3.6 26.9 - + - -
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Residues in contact with ALA 205 (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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201B GLY 2.9 16.3 + - - +
204B PHE* 1.3 73.6 - - - +
206B GLU* 1.3 53.2 + - - +
207B MET 2.6 4.8 + - - -
208B PHE* 2.6 42.8 + - - +
210B ARG* 5.1 1.3 - - - -
213B LEU* 3.8 28.0 - - + -
261B VAL* 4.2 15.8 - - + +
264B MET* 5.5 2.2 - - - -
272B LEU* 3.9 18.4 - - + -
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Residues in contact with GLU 206 (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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101B ARG* 4.2 7.4 + - - -
104B LEU* 4.4 10.9 - - + +
143B PRO* 3.7 16.6 - - - +
180B TYR* 2.8 38.6 + - - -
202B CYS 3.3 15.5 + - - +
203B ILE* 3.5 7.8 + - + +
205B ALA* 1.3 77.7 - - - +
207B MET* 1.3 59.7 + - - +
208B PHE 3.3 0.2 - - - -
209B ARG 3.8 0.5 - - - -
210B ARG* 3.2 27.8 + - - +
211B LYS* 3.4 35.4 - - - +
212B PRO* 3.6 12.6 - - - +
213B LEU* 4.5 3.9 - - - +
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Residues in contact with MET 207 (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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100B LEU* 5.2 4.3 - - + -
104B LEU* 4.0 24.1 - - + +
111B GLY 4.9 0.2 - - - +
117B ILE* 3.7 28.6 - - + +
120B LEU* 3.8 28.5 - - - -
121B MET* 3.2 37.0 - - + +
203B ILE* 2.9 26.9 - - + +
204B PHE* 3.1 25.8 - - + +
205B ALA 2.6 5.7 + - - -
206B GLU* 1.3 76.0 - - + +
208B PHE* 1.3 59.9 + - + +
209B ARG* 2.8 31.6 + - - +
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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