Contacts of the helix formed by residues 192 - 204 (chain B) in PDB entry 2WK6
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 VAL 192 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU 3.5 17.9 - - - +
96B ALA* 4.1 1.2 + - - +
98B SER* 3.7 5.2 - - - -
99B GLY* 4.3 4.2 - - - +
100B GLN 5.0 2.0 + - - +
143B ILE* 4.5 3.8 - - + -
187B GLN* 3.6 25.4 - - + +
190B GLN 4.0 1.0 + - - -
191B LEU* 1.3 82.5 - - + +
193B PRO* 1.3 74.1 - - - +
194B ALA 3.2 2.7 - - - -
195B ASP* 3.0 16.8 + - + -
196B GLY 3.0 9.5 + - - -
220B SER* 3.8 33.0 - - - +
221B LYS* 3.8 16.6 - - + +
224B VAL* 3.9 14.0 - - + +
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Residues in contact with PRO 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 4.0 19.7 - - + -
98B SER* 3.1 22.2 - - - +
99B GLY* 3.4 14.6 - - - +
188B SER 3.2 15.7 - - - +
189B GLU* 2.9 33.0 - - - +
191B LEU 3.2 1.3 - - - -
192B VAL* 1.3 88.2 - - - +
194B ALA* 1.3 60.3 + - - +
196B GLY* 3.1 4.3 + - - +
197B ILE* 3.1 31.1 + - + +
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Residues in contact with ALA 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B VAL* 3.6 10.8 - - + +
61B VAL* 4.2 4.0 - - + +
62B VAL* 3.4 16.2 - - + +
95B LEU* 3.5 23.1 - - + -
98B SER* 3.1 25.8 + - - +
193B PRO* 1.3 79.9 - - - +
195B ASP* 1.3 62.3 + - - +
197B ILE* 3.3 8.2 + - - +
198B LEU* 3.1 27.8 + - + +
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Residues in contact with ASP 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 4.1 15.9 - - + +
187B GLN* 2.9 23.6 + - - +
192B VAL* 3.0 21.8 + - + +
194B ALA* 1.3 75.1 - - - +
196B GLY* 1.3 58.3 + - - +
198B LEU* 4.5 3.1 - - - +
199B TYR* 2.6 41.6 + - - +
202B ARG* 4.9 0.3 + - - -
217B SER* 2.5 40.1 + - - -
220B SER* 4.1 9.2 - - - +
221B LYS* 2.8 24.2 + - - +
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Residues in contact with GLY 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLN* 3.7 30.5 - - - +
192B VAL 3.0 11.1 + - - -
193B PRO* 3.1 4.7 + - - -
195B ASP* 1.3 77.4 + - - +
197B ILE* 1.3 62.1 + - - +
199B TYR* 3.7 1.2 - - - +
200B ALA* 3.1 24.8 + - - +
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Residues in contact with ILE 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 2.9 56.5 - - + +
62B VAL* 3.8 11.4 - - - +
71B ILE* 5.0 13.2 - - + -
193B PRO* 3.1 19.5 + - + +
194B ALA 3.7 0.9 - - - +
195B ASP 3.1 0.4 - - - -
196B GLY* 1.3 74.6 - - - +
198B LEU* 1.3 68.4 + - + +
200B ALA* 3.5 3.7 + - - +
201B ALA* 3.1 22.8 + - + +
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 4.4 17.9 - - + -
58B VAL* 5.8 0.7 - - + -
61B VAL* 4.0 28.9 - - + -
71B ILE* 4.0 17.7 - - + -
75B LEU* 4.6 14.4 - - + -
91B LEU* 4.7 8.7 - - + -
95B LEU* 3.8 31.0 - - + -
194B ALA 3.1 13.3 + - - +
195B ASP* 3.9 5.4 - - - +
197B ILE* 1.3 76.1 - - - +
199B TYR* 1.3 53.3 + - - +
201B ALA* 3.2 3.2 + - - +
202B ARG* 2.8 52.7 + - - +
213B LEU* 5.0 8.1 - - + -
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Residues in contact with TYR 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLY* 3.7 11.8 + - - -
146B ARG* 2.6 45.9 + - + -
147B GLY 3.8 5.2 - - - -
148B LEU* 3.3 34.9 - - + +
153B GLY* 5.2 0.2 - - - -
187B GLN* 3.4 22.7 - - - +
195B ASP* 2.6 24.4 + - - +
196B GLY 3.7 4.3 - - - +
198B LEU* 1.3 72.8 - - - +
200B ALA* 1.3 66.8 + - + +
202B ARG* 3.9 11.7 - - - +
203B ASP* 3.2 24.1 + - - +
217B SER* 3.8 16.2 - - - -
221B LYS* 4.2 0.4 - - - -
1482B IUR 3.6 33.8 + + - -
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Residues in contact with ALA 200 (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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196B GLY 3.1 14.5 + - - +
197B ILE* 4.1 3.8 - - - +
199B TYR* 1.3 85.4 - - + +
201B ALA* 1.3 60.5 + - - +
203B ASP* 3.7 16.6 - - - +
204B VAL* 3.8 12.5 - - - +
410B ARG 4.8 2.1 - - - +
411B ALA* 5.1 18.8 - - + +
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Residues in contact with ALA 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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69A ALA* 4.0 22.0 - - + -
71B ILE* 4.1 9.2 - - + -
75B LEU* 3.9 15.7 - - + -
197B ILE* 3.1 17.9 + - + +
198B LEU 3.8 2.5 - - - +
200B ALA* 1.3 75.0 - - - +
202B ARG* 1.3 59.6 + - - +
203B ASP 3.1 1.8 - - - -
204B VAL* 3.2 8.8 + - - +
205B THR* 2.7 35.9 + - - +
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Residues in contact with ARG 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.5 18.8 - - + -
148B LEU* 4.6 4.2 - - + +
195B ASP* 4.9 0.4 + - - -
198B LEU* 2.8 38.0 + - - +
199B TYR* 3.9 15.3 - - - +
201B ALA* 1.3 72.4 - - - +
203B ASP* 1.3 64.4 + - - +
205B THR* 3.0 13.3 + - - -
206B ALA 3.4 8.1 + - - -
207B THR* 3.1 41.0 + - - +
208B VAL* 3.0 39.4 + - + +
213B LEU* 3.6 23.8 + - - +
214B ILE* 3.6 10.3 - - - +
217B SER* 3.7 20.4 + - - -
1482B IUR 3.0 29.5 + - - -
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Residues in contact with ASP 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PRO* 4.7 4.9 - - - +
147B GLY 3.6 14.1 - - - +
148B LEU* 3.4 12.4 + - + +
149B GLY* 2.5 43.2 + - - +
199B TYR 3.2 15.0 + - - +
200B ALA* 3.7 9.2 - - - +
202B ARG* 1.3 80.2 - - - +
204B VAL* 1.3 72.7 + - - +
205B THR 3.7 0.5 + - - -
206B ALA 4.6 2.6 + - - -
208B VAL* 3.7 12.1 - - - +
402B HIS* 5.7 0.2 - - - -
408B ARG* 3.8 27.2 + - - +
410B ARG 4.6 0.2 - - - +
411B ALA 5.1 0.3 - - - +
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PRO* 3.5 18.2 - - + +
40A ILE* 4.2 0.2 - - - +
67A GLN* 3.8 20.9 - - - +
69A ALA* 5.7 1.8 - - + -
70A GLN* 2.9 41.7 + - + +
200B ALA 3.8 9.6 - - - +
201B ALA* 3.6 12.8 - - - +
203B ASP* 1.3 92.5 - - - +
205B THR* 1.3 56.2 + - + +
206B ALA 3.8 0.4 - - - -
408B ARG 4.2 3.8 - - - +
409B SER* 3.6 8.5 - - - +
410B ARG 2.8 35.0 - - - +
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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