Contacts of the helix formed by residues 190 - 198 (chain M) in PDB entry 6NR8
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 VAL 190 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162M THR* 4.2 28.8 - - + +
165M LEU* 3.8 32.8 - - + +
166M ILE* 4.3 7.2 - - + +
169M ALA* 5.9 1.8 - - + -
186M ALA 3.5 16.1 + - - +
187M GLU* 3.3 20.9 - - - +
189M ALA* 1.3 78.8 - - + +
191M ASN* 1.3 67.6 + - - +
192M ALA 3.5 0.4 - - - -
193M VAL 4.0 3.7 + - - -
194M LEU* 3.3 25.8 - - - +
409M ILE* 3.8 18.8 - - + +
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Residues in contact with ASN 191 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162M THR* 5.5 3.1 - - - +
187M GLU* 2.4 29.5 + - - +
188M ILE* 2.8 13.0 + - - +
190M VAL* 1.3 85.2 - - - +
192M ALA* 1.3 61.5 + - - +
193M VAL 3.2 2.5 + - - -
194M LEU* 3.7 9.7 + - - +
195M THR* 2.9 22.2 + - - -
224M LEU* 4.3 11.9 - - + +
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Residues in contact with ALA 192 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188M ILE 3.0 5.7 + - - +
189M ALA* 3.9 6.5 + - - +
190M VAL 3.5 0.2 - - - -
191M ASN* 1.3 78.2 - - - +
193M VAL* 1.3 62.4 - - + +
195M THR* 3.4 20.5 - - - -
196M VAL* 3.9 8.1 + - - +
209M ILE* 4.4 6.7 - - + +
224M LEU* 3.7 28.4 - - + +
383M VAL* 3.9 15.7 - - + +
385M ILE* 3.7 17.9 - - + -
406M LEU* 5.5 5.4 - - + -
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Residues in contact with VAL 193 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189M ALA 3.4 21.3 - - - +
190M VAL 4.3 1.1 - - - +
191M ASN 3.2 1.0 - - - -
192M ALA* 1.3 77.8 - - + +
194M LEU* 1.3 60.8 + - + +
195M THR 3.1 1.6 - - - -
196M VAL* 3.2 3.6 + - - +
197M ALA* 2.9 26.5 + - - +
204M VAL* 4.0 21.2 - - + +
209M ILE* 5.4 3.6 - - + -
406M LEU* 4.5 13.7 - - + +
409M ILE* 3.7 37.7 - - + -
413M ILE* 3.7 35.0 - - + -
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Residues in contact with LEU 194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158M ASP* 3.3 39.9 - - - +
159M ILE* 5.9 1.6 - - + -
162M THR* 4.9 13.9 - - + -
190M VAL 3.3 22.2 - - - +
191M ASN* 3.7 11.1 + - - +
192M ALA 3.5 0.4 - - - -
193M VAL* 1.3 78.8 - - + +
195M THR* 1.3 60.2 + - - +
196M VAL 3.2 0.2 - - - -
197M ALA* 4.0 6.5 - - - -
198M ASP* 3.0 29.6 + - - +
202M ARG* 4.8 8.1 - - - +
409M ILE* 5.3 3.8 - - + -
413M ILE* 5.2 11.0 - - + -
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Residues in contact with THR 195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191M ASN 2.9 17.7 + - - -
192M ALA* 3.4 13.2 + - - -
193M VAL 3.1 0.6 - - - -
194M LEU* 1.3 79.9 - - - +
196M VAL* 1.3 56.7 + - - +
198M ASP* 2.9 14.2 - - - +
199M MET* 4.1 4.7 - - - +
224M LEU* 4.6 5.5 - - - +
226M LYS* 4.2 20.0 - - + +
380M SER* 3.1 34.6 + - - +
383M VAL* 3.7 20.3 - - + +
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Residues in contact with VAL 196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192M ALA 3.9 4.0 - - - +
193M VAL 3.2 2.4 + - - +
195M THR* 1.3 81.4 - - - +
197M ALA* 1.3 62.3 - - - +
198M ASP* 3.3 3.1 - - - -
199M MET* 3.3 6.6 + - + +
200M GLU* 3.1 40.5 + - + +
203M ASP 4.1 0.2 - - - -
204M VAL* 3.7 19.7 - - + -
208M LEU* 3.8 23.8 - - + +
209M ILE* 3.7 20.6 - - + -
380M SER* 3.8 12.6 - - - +
383M VAL* 3.7 25.6 - - + -
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Residues in contact with ALA 197 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193M VAL 2.9 19.6 + - - +
194M LEU* 3.9 3.1 + - - -
196M VAL* 1.3 77.4 - - - +
198M ASP* 1.3 56.7 + - - +
200M GLU 3.0 10.6 + - - -
202M ARG* 2.9 47.4 + - - +
203M ASP 3.3 16.4 + - - +
204M VAL* 4.9 0.2 - - - +
413M ILE* 3.9 26.7 - - + -
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Residues in contact with ASP 198 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194M LEU 3.0 18.9 + - - +
195M THR* 2.9 23.6 - - - +
197M ALA* 1.3 74.1 - - - +
199M MET* 1.3 90.2 + - + +
200M GLU 3.5 0.5 + - - -
201M ARG* 4.3 4.2 + - - -
202M ARG* 4.7 13.0 + - - +
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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