Contacts of the helix formed by residues 192 - 207 (chain B) in PDB entry 2GH0
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 GLN 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185B ALA 4.2 4.5 + - - +
190B HIS 3.6 7.1 + - - +
191B CYS* 1.4 77.9 - - - +
193B ARG* 1.3 66.1 + - - +
194B HIS* 3.2 30.3 + - + -
195B VAL* 3.1 24.0 + - + +
196B CYS* 3.0 19.9 + - - +
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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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191B CYS 3.7 4.6 + - - +
192B GLN* 1.3 72.4 - - - +
194B HIS* 1.3 60.1 + - - +
196B CYS* 3.2 3.8 + - - +
197B LEU* 2.9 45.5 + - + +
239B CYS* 3.0 31.0 - - - +
240B ALA* 3.7 20.0 + - - +
241B LEU 4.1 12.3 - - - -
242B PRO* 4.2 26.6 - - - +
243B PRO* 5.3 5.8 - - - +
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Residues in contact with HIS 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 GLN* 3.2 31.7 + - + -
193B ARG* 1.3 83.3 + - - +
195B VAL* 1.3 73.6 + - + +
197B LEU* 3.6 12.3 + - + +
198B ARG* 3.1 26.5 + - - +
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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
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185B ALA* 4.1 17.7 - - + +
192B GLN* 3.1 30.9 + - + +
194B HIS* 1.3 98.3 - - + +
196B CYS* 1.3 66.0 + - - +
198B ARG* 3.4 6.8 + - - +
199B GLN* 3.2 28.1 + - + +
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Residues in contact with CYS 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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185B ALA* 3.6 12.9 + - - +
186B CYS* 2.1 50.3 - - - -
192B GLN 3.0 5.5 + - - -
193B ARG 3.4 5.2 - - - +
195B VAL* 1.3 76.1 - - - +
197B LEU* 1.3 57.3 + - - +
199B GLN* 3.2 4.2 + - - +
200B LEU* 2.9 39.6 + - - +
236B ALA 4.7 0.7 - - - -
239B CYS* 3.4 28.9 - - - -
240B ALA* 4.1 13.5 - - - -
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Residues in contact with LEU 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 ARG* 2.9 39.4 + - + +
194B HIS* 3.9 9.4 - - + +
195B VAL 3.3 0.2 - - - -
196B CYS* 1.3 76.4 - - - +
198B ARG* 1.3 63.8 + - - +
200B LEU* 3.2 2.8 + - + -
201B LEU* 3.0 21.9 + - - +
240B ALA* 3.4 40.8 - - + +
297B GLY* 3.4 44.3 - - - +
298B THR 4.4 8.5 - - - +
299B ALA* 5.9 1.6 - - - -
301B THR* 4.1 7.6 - - - +
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Residues in contact with ARG 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 HIS 3.1 15.9 + - - +
195B VAL* 3.6 7.4 - - + +
197B LEU* 1.3 78.2 - - - +
199B GLN* 1.3 66.2 + - - +
201B LEU* 3.4 29.4 + - - +
202B THR* 3.0 41.4 + - - +
205B GLU* 4.8 9.1 + - - -
260B LEU* 5.1 8.8 - - - +
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Residues in contact with GLN 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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178B LEU 5.0 1.4 - - - +
181B ALA* 3.7 24.7 - - - +
182B TYR* 3.6 26.3 + - + +
185B ALA* 3.5 19.1 - - + -
195B VAL* 3.2 18.0 + - + +
196B CYS 3.2 6.3 + - - +
198B ARG* 1.3 84.2 + - - +
200B LEU* 1.3 61.1 + - - +
202B THR* 3.5 16.2 + - - +
203B PHE* 2.9 27.0 + - - +
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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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182B TYR* 3.6 38.6 - - + -
186B CYS* 4.4 0.9 - - - -
196B CYS* 2.9 24.5 + - - +
197B LEU* 3.2 12.5 + - + +
199B GLN* 1.3 75.4 - - - +
201B LEU* 1.3 64.5 + - - +
203B PHE* 3.1 11.2 + - - +
204B PHE* 3.1 35.0 + - + -
235B ILE* 3.6 34.5 - - + +
240B ALA* 3.9 19.5 - - + -
296B ILE* 4.2 16.2 - - + -
297B GLY* 4.1 8.1 - - - -
301B THR* 5.7 0.4 - - + -
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Residues in contact with LEU 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 LEU 3.0 13.1 + - - +
198B ARG* 3.5 35.4 - - - +
200B LEU* 1.3 75.9 - - - +
202B THR* 1.3 58.4 + - - +
204B PHE* 3.4 2.7 + - - +
205B GLU* 2.9 36.9 + - - +
260B LEU* 4.1 22.9 - - + -
264B ARG* 3.8 27.6 + - - +
296B ILE 3.5 18.6 + - - +
297B GLY 3.6 23.6 - - - +
298B THR* 3.9 12.1 - - + -
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Residues in contact with THR 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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178B LEU* 4.2 18.2 - - + -
198B ARG* 3.0 29.2 + - - +
199B GLN* 3.7 20.8 + - - +
201B LEU* 1.3 77.9 - - - +
203B PHE* 1.3 63.1 + - - +
205B GLU* 3.3 8.7 + - - +
206B LYS* 2.8 42.2 + - + +
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Residues in contact with PHE 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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169B CYS* 4.5 0.2 - - - -
175B CYS* 4.0 17.3 - - - -
178B LEU* 3.6 34.1 - - + +
179B ARG* 3.7 25.4 - - + -
182B TYR* 3.9 16.8 - + + -
199B GLN 2.9 15.7 + - - +
200B LEU* 3.1 9.3 + - - +
202B THR* 1.3 75.9 - - - +
204B PHE* 1.3 89.4 + + + +
207B ALA* 2.8 51.3 + - + +
212B ALA* 3.9 17.3 - - + -
215B LEU* 3.6 29.6 - - + -
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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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182B TYR* 5.8 1.6 - + - -
200B LEU* 3.1 35.2 + - + +
201B LEU* 4.2 2.9 - - - +
203B PHE* 1.3 102.8 - + - +
205B GLU* 1.3 61.9 + - - +
207B ALA 4.3 7.8 - - - +
209B GLU* 6.0 2.1 - - - +
212B ALA* 3.9 30.6 - - + +
215B LEU* 5.4 4.0 - - + -
216B LEU* 4.1 11.7 - - + -
234B THR* 6.3 0.9 - - + -
235B ILE* 4.6 4.5 - - + -
264B ARG* 6.4 0.2 - - - +
293B LEU* 4.0 41.7 - - + +
294B GLY* 5.3 1.8 - - - +
296B ILE* 3.7 44.4 - - + +
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Residues in contact with GLU 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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198B ARG* 4.8 11.4 + - - -
201B LEU* 2.9 24.2 + - - +
202B THR* 3.5 9.2 + - - +
204B PHE* 1.3 78.7 - - - +
206B LYS* 1.3 76.2 + - + +
207B ALA 4.6 1.7 - - - +
260B LEU* 5.8 1.7 - - - +
264B ARG* 4.1 22.8 + - - +
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Residues in contact with LYS 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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174B LYS* 3.0 25.1 + - - -
178B LEU* 3.7 21.1 - - + -
202B THR* 2.8 38.3 + - + +
205B GLU* 1.3 91.6 + - + +
207B ALA* 1.3 64.1 + - - +
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Residues in contact with ALA 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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174B LYS* 4.1 2.0 - - - +
175B CYS* 4.6 10.3 - - - +
178B LEU* 3.5 15.6 - - + +
203B PHE* 2.8 49.0 + - + +
204B PHE 4.3 8.1 - - - +
205B GLU 4.6 1.6 - - - +
206B LYS* 1.3 76.2 - - - +
208B ALA* 1.3 70.8 + - - +
209B GLU* 3.3 6.2 + - - +
212B ALA* 4.2 6.1 - - + +
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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