Contacts of the helix formed by residues 192 - 207 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A ALA 4.2 4.2 + - - +
190A HIS* 5.4 6.7 - - - +
191A CYS* 1.3 77.3 - - - +
193A ARG* 1.3 65.4 + - - +
194A HIS* 3.3 17.3 - - + +
195A VAL* 3.2 25.3 + - + +
196A CYS* 3.2 19.9 + - - +
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Residues in contact with ARG 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A CYS* 3.4 6.3 + - - +
192A GLN* 1.3 73.0 - - - +
194A HIS* 1.3 59.6 + - - +
196A CYS* 3.3 2.6 + - - +
197A LEU* 2.9 48.1 + - + +
239A CYS* 3.1 32.5 - - - +
240A ALA 2.9 22.7 + - - +
241A LEU 4.4 6.3 - - - -
242A PRO* 3.5 36.5 - - - +
243A PRO* 6.1 0.9 - - - -
254A LEU* 5.8 4.8 - - - +
298A THR 5.3 1.0 + - - -
299A ALA* 5.1 12.9 + - - +
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Residues in contact with HIS 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A GLN* 4.0 24.2 - - + +
193A ARG* 1.3 78.1 + - - +
195A VAL* 1.3 83.1 + - + +
197A LEU* 3.8 12.3 - - + +
198A ARG* 3.1 27.4 + - - +
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ALA* 4.0 18.2 - - + +
192A GLN* 3.2 23.6 + - + +
194A HIS* 1.3 96.9 - - + +
196A CYS* 1.3 67.6 + - - +
198A ARG* 3.2 5.5 + - + +
199A GLN* 3.0 31.4 + - + +
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Residues in contact with CYS 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ALA* 3.5 14.3 - - - +
186A CYS* 2.1 50.7 - - - -
192A GLN 3.2 5.8 + - - +
193A ARG 3.6 4.7 - - - +
195A VAL* 1.3 77.1 - - - +
197A LEU* 1.3 63.4 + - - +
199A GLN* 3.2 1.6 + - - -
200A LEU* 2.9 34.5 + - - +
236A ALA 4.7 0.9 - - - -
239A CYS* 3.4 31.9 - - - -
240A ALA* 4.2 11.0 - - - -
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Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ARG* 2.9 52.0 + - + +
194A HIS* 3.8 10.3 - - + +
195A VAL 3.3 0.2 - - - -
196A CYS* 1.3 75.2 - - - +
198A ARG* 1.3 62.3 + - - +
200A LEU* 3.3 5.6 + - + +
201A LEU* 3.0 26.3 + - + +
240A ALA* 3.3 40.6 - - + +
297A GLY* 3.4 33.8 - - - +
298A THR 4.7 7.2 - - - +
299A ALA* 6.0 0.2 - - - -
301A THR* 4.6 5.6 - - - +
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Residues in contact with ARG 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A HIS 3.1 18.4 + - - +
195A VAL* 3.6 7.6 - - + +
197A LEU* 1.3 78.0 - - - +
199A GLN* 1.3 70.3 + - - +
201A LEU* 3.3 37.1 + - - +
202A THR* 3.1 40.5 + - - +
205A GLU* 3.5 20.0 + - - -
260A LEU* 4.3 13.3 - - - +
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Residues in contact with GLN 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LEU 4.8 1.9 - - - +
181A ALA* 3.3 27.5 - - - +
182A TYR* 3.5 26.0 - - + +
185A ALA* 3.6 17.0 - - + -
195A VAL* 3.0 27.6 + - + +
196A CYS 3.2 2.7 + - - +
198A ARG* 1.3 88.5 + - - +
200A LEU* 1.3 57.6 + - - +
202A THR* 3.5 14.4 + - - +
203A PHE* 3.0 27.7 + - - +
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A TYR* 3.6 36.1 - - + -
186A CYS* 4.3 4.5 - - - -
196A CYS* 2.9 23.0 + - - +
197A LEU* 3.5 12.3 - - + +
199A GLN* 1.3 74.3 - - - +
201A LEU* 1.3 65.1 + - - +
203A PHE* 3.1 11.0 + - - +
204A PHE* 3.1 28.4 + - + -
235A ILE* 3.6 42.8 - - + +
240A ALA* 3.9 19.7 - - + -
296A ILE* 4.1 10.8 - - + +
297A GLY* 4.1 10.5 - - - +
301A THR* 5.7 0.2 - - + -
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Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LEU 3.0 15.6 + - - +
198A ARG* 3.3 39.7 + - - +
200A LEU* 1.3 76.2 - - - +
202A THR* 1.3 62.7 + - - +
204A PHE* 3.4 3.0 + - - +
205A GLU* 3.0 25.2 + - - +
260A LEU* 4.1 16.4 - - + -
264A ARG* 3.8 29.0 + - - +
294A GLY 4.4 0.7 - - - +
296A ILE 3.4 17.5 - - - +
297A GLY 3.5 20.4 - - - +
298A THR* 3.9 20.9 - - + -
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Residues in contact with THR 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LEU* 4.0 16.4 - - + -
198A ARG* 3.1 35.9 + - - +
199A GLN* 3.7 18.3 + - - +
201A LEU* 1.3 73.8 - - - +
203A PHE* 1.3 68.4 + - - +
205A GLU* 4.1 5.8 + - - +
206A LYS* 2.8 41.7 + - + +
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Residues in contact with PHE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A CYS* 4.3 0.2 - - - -
175A CYS* 3.8 30.3 - - - -
178A LEU* 3.5 34.5 - - + +
179A ARG* 3.7 20.4 - - + -
182A TYR* 3.9 17.5 - + + -
199A GLN 3.0 16.1 + - - +
200A LEU* 3.1 8.9 + - - +
202A THR* 1.3 78.2 - - - +
204A PHE* 1.3 80.8 + + - +
207A ALA* 3.0 43.6 + - + +
212A ALA* 3.8 24.7 - - + -
215A LEU* 3.6 28.9 - - + -
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Residues in contact with PHE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A TYR* 5.8 1.1 - + - -
200A LEU* 3.1 31.2 + - + +
201A LEU* 4.3 3.1 - - - +
203A PHE* 1.3 101.4 - + - +
205A GLU* 1.3 62.4 + - - +
207A ALA 4.2 8.4 - - - +
209A GLU* 5.8 3.5 - - - +
212A ALA* 3.9 28.9 - - + +
215A LEU* 5.5 3.4 - - + -
216A LEU* 4.0 22.9 - - + -
234A THR* 6.6 0.2 - - + -
235A ILE* 4.4 9.2 - - + -
264A ARG* 6.4 0.2 - - - +
293A LEU* 3.9 43.1 - - + +
294A GLY* 5.1 3.1 - - - +
296A ILE* 3.7 33.0 - - + +
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Residues in contact with GLU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ARG* 3.5 23.7 + - - -
201A LEU* 3.0 15.7 + - - +
202A THR* 3.2 6.3 + - - +
204A PHE* 1.3 80.8 - - - +
206A LYS* 1.3 84.7 + - + +
207A ALA 4.7 2.0 - - - +
264A ARG* 4.5 20.2 + - - +
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Residues in contact with LYS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A LYS* 3.7 19.5 + - + +
178A LEU* 3.6 20.9 - - + -
202A THR* 2.8 35.0 + - + +
205A GLU* 1.3 102.3 + - + +
207A ALA* 1.3 65.1 + - - +
208A ALA 3.7 0.2 + - - -
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Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A LYS* 4.7 3.6 - - - +
175A CYS* 4.5 10.3 - - - +
178A LEU* 3.5 11.4 - - + +
203A PHE* 3.0 46.3 + - + +
204A PHE 4.2 8.7 - - - +
205A GLU 4.7 1.4 - - - +
206A LYS* 1.3 80.8 - - - +
208A ALA* 1.3 71.3 + - - +
209A GLU* 3.3 4.9 + - - +
212A ALA* 4.1 6.9 - - + +
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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