Contacts of the helix formed by residues 190 - 199 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A SER* 1.3 80.5 + - - +
191A ILE* 1.3 62.4 + - - -
192A PRO* 3.6 6.5 - - - -
193A GLU* 2.6 28.4 + - - +
194A MET* 4.1 6.2 - - - +
233A GLY* 3.8 25.4 - - - -
237A HIS* 4.3 6.5 + - - +
481A CYS 5.3 1.6 - - - -
578A TYR* 6.0 1.1 - - - -
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Residues in contact with ILE 191 (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 GLY* 1.3 72.9 - - - -
192A PRO* 1.4 64.0 - - + +
193A GLU 3.3 1.3 - - - -
194A MET* 3.2 14.7 + - - +
195A LYS* 2.9 38.1 + - + +
232A GLU* 4.3 11.7 - - - +
233A GLY* 4.3 4.9 - - - +
236A VAL* 3.7 36.3 - - + -
271A CYS* 5.5 3.1 - - - -
288A PHE* 5.2 12.1 - - + -
292A VAL* 5.8 4.9 - - + -
293A THR* 5.5 5.8 - - + -
578A TYR* 3.5 54.4 - - + +
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Residues in contact with PRO 192 (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 GLY* 3.6 3.8 - - - -
191A ILE* 1.4 87.5 - - + +
193A GLU* 1.3 64.6 + - - +
195A LYS* 3.2 15.9 - - + +
196A THR* 2.7 37.1 + - - -
578A TYR* 3.6 42.6 - - + +
581A ILE* 4.1 20.2 - - + -
582A ILE* 3.7 20.5 - - + +
587A LEU* 6.2 0.2 - - + -
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Residues in contact with GLU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLY 4.4 6.0 - - - +
189A SER* 3.2 5.6 + - - -
190A GLY 2.6 40.0 + - - +
192A PRO* 1.3 88.7 - - - +
194A MET* 1.3 61.7 + - + +
196A THR* 3.2 8.5 + - - -
197A ILE* 2.9 32.1 + - + +
203A LEU* 6.1 4.0 - - + -
206A TYR* 3.1 43.5 + - + +
237A HIS* 4.9 1.5 + - - +
582A ILE* 4.8 0.4 - - - +
587A LEU* 5.0 15.6 - - + +
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Residues in contact with MET 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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190A GLY 4.1 5.2 - - - +
191A ILE* 3.2 27.8 - - - +
193A GLU* 1.3 80.1 - - + +
195A LYS* 1.3 68.4 + - - +
197A ILE* 3.5 14.8 - - + +
198A LEU* 2.9 46.1 + - + +
236A VAL* 4.4 16.6 - - + -
237A HIS* 5.1 13.2 - - + +
240A SER* 4.4 16.6 - - - +
267A LEU* 3.7 35.0 - - + +
271A CYS* 4.2 15.5 - - + -
293A THR* 5.2 5.4 - - - -
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Residues in contact with LYS 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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191A ILE* 2.9 23.9 + - + +
192A PRO* 3.2 32.3 - - + +
194A MET* 1.3 77.5 - - - +
196A THR* 1.3 62.7 + - - +
198A LEU* 3.6 13.1 - - + +
199A ARG* 3.4 38.2 + - - +
292A VAL* 4.4 26.9 + - + +
293A THR* 4.0 23.3 - - + -
576A SER* 6.0 0.2 + - - -
578A TYR* 5.0 5.6 - - + +
579A ASP* 3.6 22.3 + - - +
582A ILE* 6.0 1.6 - - + -
589A TYR* 4.2 21.1 + - + -
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Residues in contact with THR 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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192A PRO 2.7 20.8 + - - -
193A GLU* 3.3 10.6 - - - -
194A MET 3.1 0.2 - - - -
195A LYS* 1.3 78.0 - - - +
197A ILE* 1.3 63.5 + - + +
199A ARG* 3.3 4.3 + - - +
200A GLY 3.2 14.9 + - - -
201A VAL* 3.3 17.7 + - + +
582A ILE* 4.1 12.8 - - - +
587A LEU* 5.3 7.1 - - + +
588A PRO* 3.2 27.8 - - + +
589A TYR* 3.6 28.8 - - + -
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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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193A GLU* 2.9 21.3 + - + +
194A MET* 3.1 17.4 + - + +
196A THR* 1.3 76.1 - - - +
198A LEU* 1.3 58.2 + - - +
200A GLY* 2.8 23.9 + - - -
201A VAL 3.3 21.8 - - - +
202A VAL* 4.5 5.1 - - - +
203A LEU* 4.5 17.7 - - + +
206A TYR* 4.5 16.6 - - + -
207A LEU* 4.2 23.6 - - + -
237A HIS* 6.1 0.4 - - + -
263A TYR* 3.5 32.8 - - + +
267A LEU* 3.8 13.5 - - + -
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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 MET* 2.9 33.3 + - + +
195A LYS* 3.6 21.3 - - - +
197A ILE* 1.3 75.4 - - - +
199A ARG* 1.3 69.0 + - + +
200A GLY* 3.2 0.7 + - - -
263A TYR* 5.2 1.8 - - - -
264A SER* 3.2 33.5 + - - +
267A LEU* 3.7 26.2 - - + +
268A THR* 5.0 9.0 - - - +
271A CYS* 6.3 0.2 - - + -
293A THR* 3.3 42.2 - - - +
294A SER* 4.6 2.0 - - - +
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Residues in contact with ARG 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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195A LYS* 3.4 27.2 + - - +
196A THR 3.3 7.5 + - - +
197A ILE 3.2 1.2 - - - -
198A LEU* 1.3 84.5 - - + +
200A GLY* 1.3 55.7 + - - +
201A VAL* 4.0 1.7 - - - +
292A VAL 2.8 20.2 + - - -
293A THR 4.7 0.4 - - - -
294A SER* 2.4 43.7 + - - +
295A THR* 4.4 7.5 + - - -
589A TYR* 2.3 54.1 + - + -
590A LEU 5.2 4.4 + - - +
591A PRO 6.1 1.0 - - - -
863A LEU* 5.2 8.7 - - - +
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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