Contacts of the helix formed by residues 192 - 202 (chain A) in PDB entry 2QMQ
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 SER 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A SER* 1.3 75.9 - - - +
193A ILE* 1.3 64.8 + - - +
194A PRO* 3.5 14.4 - - - +
195A ASP* 2.8 38.9 + - - -
196A MET* 2.9 23.4 + - - +
222A GLN* 4.4 1.7 + - - -
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Residues in contact with ILE 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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184A HIS* 6.3 0.9 - - + +
191A SER 5.9 0.2 - - - +
192A SER* 1.3 72.0 - - - +
194A PRO* 1.3 73.1 - - + +
196A MET* 3.0 12.8 + - - +
197A ILE* 2.9 41.8 + - + +
227A LEU* 5.1 4.9 - - + -
231A GLU* 3.6 49.4 - - + +
234A TRP* 4.3 17.0 + - + +
235A ASN* 5.7 1.1 - - - +
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Residues in contact with PRO 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 SER* 3.5 12.1 - - - +
193A ILE* 1.3 97.8 - - + +
195A ASP* 1.3 60.6 + - - +
197A ILE* 3.2 5.3 + - + +
198A LEU* 2.9 27.8 + - - +
221A ILE* 4.0 22.3 - - + +
222A GLN* 3.3 38.6 - - - +
227A LEU* 4.1 22.9 - - + -
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Residues in contact with ASP 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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190A THR 4.6 1.9 - - - +
191A SER* 3.7 15.9 + - - +
192A SER* 2.8 43.9 + - - +
194A PRO* 1.3 75.5 - - - +
196A MET* 1.3 58.1 + - - +
198A LEU* 3.4 7.8 + - - +
199A GLY* 3.0 23.6 + - - -
204A GLN* 5.4 1.2 + - - -
207A LEU* 5.0 2.4 - - - +
222A GLN* 2.9 24.7 + - - +
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Residues in contact with MET 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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184A HIS* 3.4 51.4 - - + +
187A THR* 3.9 16.8 - - + -
188A GLY* 3.7 28.5 - - - -
191A SER* 3.6 16.6 - - - +
192A SER 2.9 18.8 + - - +
193A ILE* 3.0 10.3 + - - +
195A ASP* 1.3 73.8 - - - +
197A ILE* 1.3 60.6 + - - +
199A GLY* 3.2 3.9 + - - -
200A HIS* 3.0 25.5 + - - +
234A TRP* 3.9 21.5 - - + +
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Residues in contact with ILE 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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71A VAL* 3.7 26.0 - - + +
72A GLY* 4.1 11.4 - - - -
193A ILE* 2.9 38.0 + - + +
194A PRO* 3.8 6.1 - - + +
196A MET* 1.3 73.9 - - - +
198A LEU* 1.3 65.3 + - - +
200A HIS* 3.0 18.5 + - + +
201A LEU* 3.1 17.3 + - + +
221A ILE* 4.2 11.7 - - + -
227A LEU* 4.8 3.8 - - + -
230A ILE* 3.5 26.2 - - + +
231A GLU* 4.6 0.9 - - - -
234A TRP* 3.7 35.2 - - + -
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Residues in contact with LEU 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 PRO 2.9 20.5 + - - +
195A ASP* 3.6 7.0 - - - +
197A ILE* 1.3 75.1 - - - +
199A GLY* 1.3 58.0 + - - +
201A LEU* 3.2 5.6 + - + +
202A PHE* 2.8 53.3 + - + +
207A LEU* 3.9 19.7 - - + -
214A ILE 5.5 0.4 - - - +
217A TYR 3.8 24.2 - - - +
218A ARG* 4.0 31.6 - - + +
221A ILE* 3.8 16.8 - - + -
222A GLN* 3.7 25.4 - - + +
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Residues in contact with GLY 199 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A ASP 3.0 13.9 + - - -
196A MET* 3.2 5.4 + - - -
197A ILE 3.1 0.2 - - - -
198A LEU* 1.3 74.4 - - - +
200A HIS* 1.3 62.7 + - - +
202A PHE 3.3 18.0 - - - +
204A GLN* 3.9 21.3 + - - -
207A LEU* 4.0 1.3 - - - +
266A PRO* 3.5 14.6 - - - +
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Residues in contact with HIS 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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70A ASP* 2.8 37.1 + - - +
71A VAL* 4.3 13.5 - - + +
146A GLY* 4.8 4.3 - - - -
147A ALA 4.5 0.4 + - - -
170A ASN* 5.0 0.3 + - - -
196A MET 3.0 6.8 + - - +
197A ILE 3.0 8.3 + - - +
199A GLY* 1.3 77.7 - - - +
201A LEU* 1.3 72.0 + - + +
234A TRP* 3.5 28.4 - + + -
237A TYR* 3.6 37.9 - + - -
266A PRO* 4.5 2.8 - - - +
267A HIS* 3.0 59.8 + + - -
294A GLN* 4.8 1.0 + - - -
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Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ASP* 3.5 30.7 - - + +
71A VAL 3.4 26.7 - - - +
73A LEU* 4.2 22.4 - - + -
197A ILE* 3.1 19.2 + - + +
198A LEU* 3.8 6.3 - - - +
200A HIS* 1.3 81.5 - - + +
202A PHE* 1.3 77.8 + - + +
217A TYR* 5.6 0.4 - - + -
221A ILE* 4.2 19.7 - - + -
266A PRO* 5.2 1.3 - - - -
293A GLY* 3.2 18.1 - - - +
294A GLN* 3.0 35.3 + - + +
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Residues in contact with PHE 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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198A LEU* 2.8 34.3 + - + +
199A GLY* 3.3 21.0 - - - +
201A LEU* 1.3 94.9 - - + +
203A SER* 1.3 65.3 + - - +
204A GLN* 3.8 0.7 + - - -
206A GLU* 3.4 24.5 - - + +
207A LEU* 4.0 20.0 - - + +
213A LEU* 4.3 11.0 - - + -
214A ILE* 4.0 19.7 - - + -
217A TYR* 3.7 40.4 - + + -
266A PRO* 3.6 6.1 - - - +
293A GLY* 4.1 1.3 - - - -
294A GLN* 3.5 30.5 - - + -
297A LEU* 4.2 4.9 - - + -
298A THR* 5.9 0.2 - - + -
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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