Contacts of the helix formed by residues 190 - 199 (chain B) in PDB entry 6QVC
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 GLY 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189B SER* 1.3 81.2 + - - +
191B ILE* 1.3 63.2 + - - -
192B PRO* 3.6 6.5 - - - -
193B GLU* 2.6 28.8 + - - +
194B MET* 4.1 6.3 - - - +
233B GLY* 3.8 24.7 - - - -
237B HIS* 4.3 6.7 + - - +
481B CYS 5.3 1.6 - - - -
578B TYR* 6.0 1.6 - - - -
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Residues in contact with ILE 191 (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 GLY* 1.3 71.7 - - - -
192B PRO* 1.4 64.4 - - + +
193B GLU 3.3 1.3 - - - -
194B MET* 3.2 15.6 + - - +
195B LYS* 2.9 38.6 + - + +
232B GLU* 4.3 11.0 - - - +
233B GLY* 4.3 5.1 - - - +
236B VAL* 3.7 36.8 - - + -
271B CYS* 5.5 3.1 - - - -
288B PHE* 5.2 12.8 - - + -
292B VAL* 5.8 5.4 - - + -
293B THR* 5.5 5.6 - - + -
578B TYR* 3.5 54.4 - - + +
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Residues in contact with PRO 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 GLY* 3.6 3.4 - - - -
191B ILE* 1.4 88.6 - - + +
193B GLU* 1.3 64.6 + - - +
195B LYS* 3.2 15.2 - - + +
196B THR* 2.7 37.7 + - - -
578B TYR* 3.6 41.5 - - + +
581B ILE* 4.1 20.2 - - + -
582B ILE* 3.7 21.0 - - + +
587B LEU* 6.2 0.4 - - + -
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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
----------------------------------------------------------
188B GLY 4.4 5.9 - - - +
189B SER* 3.2 6.1 + - - -
190B GLY 2.6 40.1 + - - +
192B PRO* 1.3 89.6 - - - +
194B MET* 1.3 62.6 + - + +
196B THR* 3.2 9.5 + - - -
197B ILE* 2.9 32.1 + - + +
203B LEU* 6.1 4.0 - - + -
206B TYR* 3.1 43.6 + - + +
237B HIS* 4.8 1.3 + - - +
582B ILE* 4.8 0.2 - - - +
587B LEU* 5.0 16.2 - - + +
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Residues in contact with MET 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 GLY 4.1 5.2 - - - +
191B ILE* 3.2 28.0 - - - +
193B GLU* 1.3 81.4 - - + +
195B LYS* 1.3 68.5 + - - +
197B ILE* 3.5 15.8 - - + +
198B LEU* 2.9 45.4 + - + +
236B VAL* 4.4 16.2 - - + -
237B HIS* 5.1 13.5 - - - +
240B SER* 4.4 17.7 - - - +
267B LEU* 3.7 33.1 - - + +
271B CYS* 4.2 15.5 - - + -
293B THR* 5.2 5.6 - - - -
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Residues in contact with LYS 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 ILE* 2.9 23.2 + - + +
192B PRO* 3.2 33.0 - - + +
194B MET* 1.3 77.8 - - - +
196B THR* 1.3 60.3 + - - +
198B LEU* 3.6 12.4 - - + +
199B ARG* 3.4 39.6 + - - +
292B VAL* 4.4 26.4 + - - +
293B THR* 4.0 24.0 - - + -
576B SER* 6.0 0.2 + - - -
578B TYR* 5.0 5.4 - - + +
579B ASP* 3.6 23.3 + - - +
582B ILE* 6.0 1.3 - - + -
589B TYR* 4.2 20.8 + - + -
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Residues in contact with THR 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 PRO 2.7 20.4 + - - -
193B GLU* 3.3 10.4 - - - -
194B MET 3.1 0.2 - - - -
195B LYS* 1.3 78.9 - - - +
197B ILE* 1.3 64.2 + - - +
199B ARG* 3.3 4.7 + - - +
200B GLY 3.2 15.2 + - - -
201B VAL* 3.3 16.7 + - + +
582B ILE* 4.1 13.0 - - - +
587B LEU* 5.3 7.2 - - + +
588B PRO* 3.2 27.6 - - + +
589B TYR* 3.6 29.1 - - + +
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Residues in contact with ILE 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* 2.9 21.7 + - + +
194B MET* 3.1 18.8 + - + +
196B THR* 1.3 76.0 - - - +
198B LEU* 1.3 57.8 + - - +
200B GLY* 2.8 24.3 + - - -
201B VAL 3.3 21.5 - - - +
202B VAL* 4.5 5.3 + - - -
203B LEU* 4.5 17.3 - - + +
206B TYR* 4.5 16.4 - - + -
207B LEU* 4.2 23.8 - - + -
237B HIS* 6.1 0.9 - - + -
263B TYR* 3.5 32.4 - - + +
267B LEU* 3.8 12.8 - - + -
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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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194B MET* 2.9 32.6 + - + +
195B LYS* 3.6 22.4 - - - +
197B ILE* 1.3 77.0 - - - +
199B ARG* 1.3 69.7 + - + +
200B GLY* 3.2 0.7 + - - -
263B TYR* 5.2 1.6 - - - -
264B SER* 3.2 34.3 + - - +
267B LEU* 3.7 26.2 - - + -
268B THR* 5.0 8.5 - - - +
271B CYS* 6.4 0.7 - - + -
293B THR* 3.3 41.7 - - - +
294B SER* 4.6 2.0 - - - +
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Residues in contact with ARG 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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195B LYS* 3.4 25.5 + - - +
196B THR 3.3 8.1 + - - +
197B ILE 3.2 0.8 - - - -
198B LEU* 1.3 84.3 - - + +
200B GLY* 1.3 55.4 + - - +
201B VAL* 4.0 1.3 - - - +
292B VAL 2.8 20.2 + - - -
293B THR* 4.7 0.6 - - - +
294B SER* 2.4 43.9 + - - +
295B THR* 4.4 7.4 + - - -
589B TYR* 2.3 54.4 + - + -
590B LEU 5.2 4.4 + - - +
591B PRO 6.1 1.6 - - - -
863B LEU* 5.2 8.1 - - - +
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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