Contacts of the helix formed by residues 190 - 202 (chain B) in PDB entry 3CWR
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 ILE 190 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B TYR* 3.8 13.8 - - + -
98B ALA* 4.0 9.2 - - + -
99B GLN* 3.7 24.8 - - - +
102B LEU* 3.9 22.7 - - + -
169B VAL* 3.8 31.4 - - + +
173B PRO* 4.4 0.4 - - + -
185B LEU* 3.9 9.9 - - + -
188B TRP* 3.6 34.9 + - + -
189B ASP* 1.3 70.4 + - - +
191B ALA* 1.3 66.9 + - - +
192B PRO* 3.3 2.7 - - - -
193B ARG* 3.1 16.6 + - + -
194B VAL* 2.9 24.8 + - + +
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Residues in contact with ALA 191 (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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91B GLU* 5.0 1.2 - - - +
95B TYR* 4.1 21.6 - - + -
189B ASP* 3.0 15.8 + - - +
190B ILE* 1.3 81.1 - - - +
192B PRO* 1.3 66.7 - - + +
194B VAL* 3.2 5.2 + - - +
195B ALA* 2.9 24.0 + - - +
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Residues in contact with PRO 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ASP* 3.4 34.3 - - + +
190B ILE 3.5 2.9 - - - -
191B ALA* 1.3 92.7 - - + +
193B ARG* 1.3 55.9 + - - +
195B ALA* 3.3 6.9 + - + +
196B ASP* 2.9 39.3 + - - +
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Residues in contact with ARG 193 (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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168B ALA 2.9 21.1 + - - +
169B VAL* 2.9 34.6 + - - +
172B GLU* 3.8 26.1 - - - +
173B PRO* 3.7 17.6 - - - +
176B GLN* 5.9 0.2 + - - -
182B ARG* 6.0 3.3 - - - +
188B TRP* 5.2 5.2 - - + -
189B ASP 5.2 0.4 + - - -
190B ILE* 3.1 20.9 + - + +
192B PRO* 1.3 79.2 - - - +
194B VAL* 1.3 64.6 + - - +
196B ASP* 3.3 8.0 + - + +
197B ALA* 2.9 24.9 + - + +
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLU* 3.4 41.1 - - + +
94B VAL* 4.1 13.7 - - + -
95B TYR* 4.1 25.4 - - + +
169B VAL* 3.8 27.4 - - + -
190B ILE* 2.9 25.2 + - + +
191B ALA* 3.2 8.5 + - - +
193B ARG* 1.3 76.4 - - - +
195B ALA* 1.3 63.0 + - - +
197B ALA* 3.3 1.7 + - - +
198B VAL* 3.0 25.8 + - + +
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Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLU* 3.6 31.2 + - - +
191B ALA 2.9 14.7 + - - +
192B PRO* 3.7 7.2 - - + +
194B VAL* 1.3 79.8 - - - +
196B ASP* 1.3 64.4 + - - +
198B VAL* 3.4 1.9 + - - +
199B ARG* 3.0 24.1 + - - +
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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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192B PRO* 2.9 25.8 + - - +
193B ARG* 3.7 7.2 - - + +
195B ALA* 1.3 79.9 - - - +
197B ALA* 1.3 63.7 + - - +
199B ARG* 3.3 7.3 + - - +
200B LEU* 3.1 24.3 + - - +
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Residues in contact with ALA 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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165B LEU* 3.7 13.2 - - + -
168B ALA* 4.5 13.2 - - + -
169B VAL* 3.4 34.1 - - + +
193B ARG* 2.9 11.5 + - + +
194B VAL 3.7 1.1 - - - +
196B ASP* 1.3 74.2 - - - +
198B VAL* 1.3 61.6 + - - +
200B LEU* 3.2 6.0 + - - -
201B ILE* 2.8 38.4 + - + +
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Residues in contact with VAL 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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87B ALA* 4.1 29.8 - - + +
90B LEU* 4.1 26.5 - - + +
91B GLU* 3.9 25.8 - - + +
94B VAL* 5.2 1.8 - - + -
165B LEU* 4.4 12.6 - - + -
194B VAL* 3.0 23.8 + - + +
195B ALA 3.9 3.8 - - - +
197B ALA* 1.3 77.9 - - - +
199B ARG* 1.3 62.3 + - - +
202B ALA* 3.0 47.1 + - - +
203B PRO* 3.6 1.3 - - + +
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Residues in contact with ARG 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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195B ALA 3.0 17.3 + - - +
196B ASP* 3.7 7.9 - - - +
197B ALA 3.3 0.2 - - - -
198B VAL* 1.3 78.1 - - - +
200B LEU* 1.3 59.4 + - - +
203B PRO* 3.5 25.5 - - + +
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Residues in contact with LEU 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 ASP 3.1 16.1 + - - +
197B ALA* 3.7 4.9 - - - +
198B VAL 3.1 0.2 - - - -
199B ARG* 1.3 79.7 - - - +
201B ILE* 1.3 74.9 - - + +
202B ALA 3.7 0.2 - - - -
203B PRO* 4.4 4.5 - - - +
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Residues in contact with ILE 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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154B LEU* 5.1 0.5 - - - +
155B PRO* 5.1 11.4 - - - +
161B VAL* 4.2 19.7 - - + +
164B LEU* 4.0 16.8 - - + +
165B LEU* 4.0 31.2 - - + +
168B ALA* 3.4 32.5 - - + -
197B ALA* 2.8 20.6 + - + +
200B LEU* 1.3 97.8 - - + +
202B ALA* 1.3 56.5 + - + +
203B PRO* 3.7 4.3 - - - +
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Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ALA* 5.0 0.2 - - - +
90B LEU* 3.9 22.8 - - + +
143B LEU* 5.3 1.6 - - + -
152B LEU* 3.6 12.8 - - + +
153B PRO 5.5 0.7 - - - -
154B LEU* 4.4 14.1 - - + -
161B VAL* 4.2 17.9 - - + -
165B LEU* 4.6 4.9 - - + -
198B VAL* 3.0 22.2 + - - +
201B ILE* 1.3 83.2 - - + +
203B PRO* 1.3 69.1 - - - +
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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