Contacts of the helix formed by residues 191 - 201 (chain B) in PDB entry 3GSB
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 ASP 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B PHE* 5.4 0.2 - - - -
187B THR* 4.7 0.2 + - - -
188B PRO* 3.0 32.9 + - + +
189B TYR 3.4 0.2 - - - -
190B ASN* 1.3 76.8 - - - +
192B LEU* 1.3 64.4 + - - +
193B GLU* 3.1 13.3 + - - +
194B ALA* 3.2 38.4 + - + +
195B VAL* 3.4 16.3 + - - +
227B PHE* 4.2 2.7 - - - -
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Residues in contact with LEU 192 (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 ASN 3.5 5.5 + - - -
191B ASP* 1.3 72.2 - - - +
193B GLU* 1.3 64.3 + - - +
195B VAL* 3.3 6.5 + - + +
196B LYS* 3.1 46.6 + - + +
226B GLY 5.3 0.9 - - - +
227B PHE* 3.5 48.0 - - + +
230B GLY* 4.2 9.0 - - - -
231B LEU* 3.9 17.5 - - + +
234B ILE* 4.2 17.0 - - + -
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Residues in contact with GLU 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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191B ASP* 3.2 10.0 - - - +
192B LEU* 1.3 73.7 - - + +
194B ALA* 1.3 57.5 + - - +
195B VAL 3.0 1.8 - - - -
196B LYS* 3.0 36.5 + - - +
197B ALA* 2.8 34.6 + - - +
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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
----------------------------------------------------------
187B THR* 3.8 19.3 - - - +
188B PRO* 4.1 7.4 - - + -
191B ASP* 3.2 25.7 + - + +
193B GLU* 1.3 78.3 - - - +
195B VAL* 1.3 57.5 + - - +
197B ALA* 3.2 8.9 - - - +
198B LEU* 2.8 34.6 + - + +
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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
----------------------------------------------------------
144B ILE* 4.8 8.5 - - + -
146B PHE* 3.8 21.5 - - + -
187B THR* 3.7 19.7 - - + +
191B ASP 3.6 15.0 - - - +
192B LEU* 3.3 9.2 + - + +
193B GLU 3.0 0.4 - - - -
194B ALA* 1.3 74.2 - - - +
196B LYS* 1.3 65.8 + - - +
197B ALA 3.0 0.9 - - - -
198B LEU* 3.1 8.3 + - - +
199B PHE* 3.0 37.1 + - + -
209B VAL* 5.2 2.5 - - + -
227B PHE* 5.3 0.4 - - + -
231B LEU* 3.9 20.4 - - + -
234B ILE* 3.6 21.1 - - + -
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Residues in contact with LYS 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 LEU* 3.1 41.0 + - + +
193B GLU* 3.0 47.8 + - - +
195B VAL* 1.3 74.3 - - - +
197B ALA* 1.3 62.6 + - - +
199B PHE* 3.4 4.5 + - - +
200B ALA* 3.0 24.8 + - - +
234B ILE* 4.0 20.4 - - + -
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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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193B GLU 2.8 13.3 + - - +
194B ALA* 3.2 15.0 - - - +
196B LYS* 1.3 72.2 - - - +
198B LEU* 1.3 58.5 + - + +
200B ALA* 2.8 9.1 + - - +
201B GLU* 2.7 43.8 + - + +
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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
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144B ILE* 4.3 15.7 - - + -
185B LEU* 4.0 31.4 - - + +
186B THR 3.3 27.6 - - - +
187B THR* 3.5 23.1 - - + -
194B ALA* 2.8 21.9 + - + +
195B VAL* 3.1 5.4 + - - +
197B ALA* 1.3 73.1 - - + +
199B PHE* 1.3 56.2 + - - +
201B GLU* 3.6 26.8 + - - +
202B ASN* 3.0 34.5 + - - +
206B ILE* 4.6 1.4 - - - +
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Residues in contact with PHE 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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144B ILE* 3.5 20.0 - - + -
195B VAL* 3.0 29.9 + - + +
196B LYS* 3.7 9.4 - - - +
197B ALA 2.9 0.2 + - - -
198B LEU* 1.3 73.0 - - - +
200B ALA* 1.3 66.7 + - - +
202B ASN 3.2 22.5 - - - +
203B PRO* 3.5 5.9 - - - +
206B ILE* 3.6 40.6 - - + -
209B VAL* 4.2 15.5 - - + -
234B ILE* 3.8 17.3 - - + -
235B THR* 4.4 4.7 - - + -
238B HIS* 3.2 54.4 - + + +
240B ALA* 4.0 17.9 - - + -
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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 LYS 3.0 17.2 + - - +
197B ALA* 2.8 8.5 + - - +
199B PHE* 1.3 74.3 - - - +
201B GLU* 1.3 62.2 + - - +
202B ASN 3.1 1.6 + - - -
203B PRO* 3.5 13.6 - - - +
238B HIS* 5.1 1.7 + - - -
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Residues in contact with GLU 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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185B LEU* 6.1 0.2 - - - +
197B ALA* 2.7 25.5 + - + +
198B LEU* 3.7 27.3 + - - +
200B ALA* 1.3 72.9 - - - +
202B ASN* 1.3 72.4 + - - +
203B PRO* 3.8 4.1 - - - +
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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