Contacts of the helix formed by residues 192 - 204 (chain B) in PDB entry 3C6Q
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 TYR 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162B ASP* 5.7 3.6 - - - +
164B GLU* 4.7 34.7 + - + -
165B ASP* 5.5 0.7 - - - -
166B GLY* 4.2 31.3 - - - -
169B ALA* 5.6 1.8 - - + -
190B TYR* 4.8 13.2 - + + -
191B ALA* 1.3 77.8 - - + +
193B ASN* 1.3 68.2 + - - +
195B PRO* 3.3 13.2 - - - +
196B ALA* 3.3 19.2 + - - +
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Residues in contact with ASN 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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129B GLY* 3.0 36.0 + - - +
130B THR* 3.6 9.5 - - - -
131B GLY* 4.0 1.0 + - - -
162B ASP* 3.4 24.9 + - - +
169B ALA* 4.2 10.3 - - - +
188B GLY* 3.5 10.8 - - - -
190B TYR* 3.4 30.4 + - - +
191B ALA 3.2 2.0 - - - -
192B TYR* 1.3 79.2 - - - +
194B GLY* 1.3 62.1 + - - +
195B PRO 3.2 1.8 - - - -
196B ALA* 3.3 3.3 + - - +
197B GLN* 2.8 39.3 + - - +
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Residues in contact with GLY 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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190B TYR 4.3 2.2 + - - -
191B ALA 4.3 0.2 + - - -
193B ASN* 1.3 76.7 - - - +
195B PRO* 1.3 64.3 - - - +
197B GLN* 3.3 12.1 + - - +
198B ALA* 2.8 29.8 + - - +
212B ILE* 4.3 2.8 - - - +
214B CYS* 3.7 31.6 - - - +
215B PHE 5.8 0.2 + - - -
221B ILE* 5.6 0.4 - - - +
230B ILE* 3.7 9.5 - - - +
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Residues in contact with PRO 195 (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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191B ALA 3.2 20.9 - - - +
192B TYR* 3.3 10.8 - - - +
194B GLY* 1.3 86.9 - - - +
196B ALA* 1.3 54.5 + - - +
198B ALA* 3.4 0.5 - - - +
199B LEU* 2.7 37.0 + - - +
218B THR* 4.8 0.9 - - - +
220B ASP* 4.4 17.0 - - + +
221B ILE* 3.6 26.5 - - + -
224B TYR* 3.5 27.1 - - + -
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Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLY* 4.7 2.2 - - - +
169B ALA* 3.9 27.6 - - + +
170B VAL* 4.2 19.0 - - + +
173B ALA* 5.1 2.0 - - - -
192B TYR 3.3 17.6 + - - +
193B ASN* 3.3 5.3 + - - +
195B PRO* 1.3 78.3 - - - +
197B GLN* 1.3 62.7 + - + +
199B LEU* 3.4 8.6 + - - +
200B VAL* 3.2 26.9 + - - +
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Residues in contact with GLN 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B GLY* 3.6 14.2 - - - +
173B ALA* 4.5 12.8 - - + -
186B PHE* 3.0 51.3 - - + +
187B PHE 3.2 20.6 + - - -
188B GLY* 3.3 20.0 + - - -
193B ASN* 2.8 28.0 + - - +
194B GLY* 3.5 7.7 - - - +
196B ALA* 1.3 74.6 - - + +
198B ALA* 1.3 58.3 + - - +
200B VAL* 3.3 3.5 + - - +
201B VAL* 2.9 33.1 + - - +
212B ILE* 3.7 15.2 - - + +
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Residues in contact with ALA 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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194B GLY 2.8 18.4 + - - +
195B PRO 3.4 4.5 - - - +
197B GLN* 1.3 74.4 - - - +
199B LEU* 1.3 66.2 + - - +
201B VAL* 3.8 0.9 - - - +
202B LYS* 2.9 27.4 + - - +
212B ILE* 3.5 13.5 - - + -
224B TYR* 3.5 35.0 - - + -
229B VAL* 3.6 12.6 - - + +
230B ILE* 4.1 4.3 - - + -
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Residues in contact with LEU 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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170B VAL* 4.1 31.6 - - + -
195B PRO 2.7 19.3 + - - +
196B ALA* 3.5 6.5 - - - +
198B ALA* 1.3 74.6 - - - +
200B VAL* 1.3 57.5 + - - +
202B LYS* 3.7 5.0 - - + +
203B ASN* 2.9 66.5 + - - +
224B TYR* 3.5 17.8 + - - +
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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
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170B VAL* 3.4 38.1 - - + +
173B ALA* 3.7 12.6 - - + +
174B GLU* 3.6 30.7 - - + +
177B LEU* 3.4 24.5 - - + -
186B PHE* 5.1 1.1 - - + -
196B ALA 3.2 13.6 + - - +
197B GLN 3.6 7.2 - - - +
198B ALA 3.2 0.2 - - - -
199B LEU* 1.3 77.8 - - + +
201B VAL* 1.3 58.7 + - - +
203B ASN* 3.5 6.7 + - - +
204B ALA* 3.0 27.3 + - + +
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 4.6 3.6 - - + -
186B PHE* 3.9 22.2 - - + -
197B GLN 2.9 21.4 + - - +
198B ALA* 3.3 3.8 + - - +
200B VAL* 1.3 75.6 - - - +
202B LYS* 1.3 62.5 + - - +
204B ALA* 3.2 11.7 + - - +
205B GLY 3.2 0.2 + - - -
206B LYS* 3.0 56.5 + - + +
207B VAL* 3.8 8.5 - - + +
210B VAL* 4.0 20.9 - - + +
212B ILE* 3.7 18.6 - - + -
229B VAL* 4.8 7.2 - - + +
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Residues in contact with LYS 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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198B ALA 2.9 18.0 + - - +
199B LEU* 3.7 5.6 - - + +
201B VAL* 1.3 77.7 - - - +
203B ASN* 1.3 61.3 + - - +
205B GLY* 2.9 20.4 + - - -
207B VAL* 4.1 22.9 - - + +
224B TYR* 4.4 16.3 - - + +
227B GLU* 3.0 33.3 + - - +
229B VAL* 4.8 7.2 - - + +
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Residues in contact with ASN 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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174B GLU* 5.4 6.4 + - - +
199B LEU* 2.9 46.4 + - - +
200B VAL* 3.7 8.1 - - - +
201B VAL 3.3 0.2 - - - -
202B LYS* 1.3 80.4 - - - +
204B ALA* 1.3 58.6 + - - +
205B GLY 3.1 1.3 + - - -
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Residues in contact with ALA 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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177B LEU* 3.6 22.9 - - + -
200B VAL 3.0 18.1 + - - +
201B VAL 3.5 5.8 - - - +
202B LYS 3.1 0.2 - - - -
203B ASN* 1.3 76.0 - - - +
205B GLY* 1.3 63.4 + - - +
206B LYS* 4.0 19.7 + - + +
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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