Contacts of the strand formed by residues 190 - 196 (chain M) in PDB entry 6O81
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 ILE 190 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188M VAL* 4.2 1.0 - - - +
189M LYS* 1.3 68.9 - - - +
191M ARG* 1.3 61.4 + - - +
192M ALA* 5.6 0.2 - - - -
236M MET 4.0 2.3 - - - +
237M THR* 3.8 1.6 - - - -
238M THR* 2.8 39.8 + - - +
240M THR 5.6 0.4 + - - -
243M ARG* 5.4 8.3 - - + +
246M GLY* 4.5 25.1 - - - +
247M LEU* 4.5 8.7 - - + +
250M LEU* 5.0 7.3 - - + +
274M PRO* 5.4 1.3 - - + -
275M LYS 3.4 15.7 - - - +
276M VAL* 4.3 2.5 - - + +
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Residues in contact with ARG 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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189M LYS* 3.3 6.9 + - + +
190M ILE* 1.3 72.5 - - - +
192M ALA* 1.3 61.9 + - - +
236M MET 4.1 2.7 - - - -
237M THR* 4.2 13.9 - - - +
273M GLU 3.5 1.7 - - - +
275M LYS* 2.9 34.7 + - - +
277M VAL* 4.9 11.2 - - + -
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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
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191M ARG* 1.3 77.8 - - - +
193M ASP* 1.3 59.1 + - - +
194M ILE* 6.4 0.4 - - + -
235M VAL* 3.5 5.1 - - - +
236M MET* 2.7 48.8 + - + +
250M LEU* 5.2 9.4 - - + +
272M MET* 3.9 8.7 - - - +
273M GLU 3.7 20.0 - - - +
274M PRO* 4.2 6.7 - - + -
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Residues in contact with ASP 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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192M ALA* 1.3 75.4 - - - +
194M ILE* 1.3 61.2 + - - +
233M ARG* 6.1 2.5 - - + -
234M TYR 3.4 9.2 - - - +
235M VAL* 4.4 4.5 - - + +
270M VAL* 4.0 1.4 - - - -
271M GLN* 3.2 17.1 + - + -
272M MET* 2.9 48.6 + - + +
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Residues in contact with ILE 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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192M ALA* 4.3 0.6 + - + -
193M ASP* 1.3 74.8 - - - +
195M GLU* 1.3 58.2 + - - +
196M VAL* 3.7 7.0 + - + +
233M ARG* 4.7 0.7 - - - -
234M TYR* 2.8 49.5 + - + +
236M MET* 5.2 9.6 - - + +
254M MET* 5.5 12.6 - - + -
257M ILE* 6.4 2.0 - - + -
269M ASN 3.7 8.1 - - - +
270M VAL* 4.7 2.5 - - - +
271M GLN* 4.2 2.5 - - - +
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Residues in contact with GLU 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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194M ILE* 1.3 69.7 - - - +
196M VAL* 1.3 58.7 + - - +
197M ALA* 4.2 1.0 + - - -
232M PRO* 3.4 21.5 - - + +
233M ARG* 4.2 7.9 - - + +
267M VAL 4.1 1.4 - - - +
268M PHE* 3.4 2.0 + - - -
269M ASN* 2.8 53.1 + - + +
271M GLN* 4.4 9.9 - - + +
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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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194M ILE* 3.7 8.8 + - + +
195M GLU* 1.3 73.0 - - - +
197M ALA* 1.3 62.0 + - - +
207M VAL* 5.2 5.3 - - - +
210M ALA* 5.7 7.4 - - + -
232M PRO 3.9 2.9 + - - +
234M TYR* 3.3 30.5 - - + -
257M ILE* 5.4 9.4 - - + +
261M ILE* 4.8 8.7 - - + -
267M VAL 3.7 6.5 - - - +
268M PHE* 4.2 11.4 - - + +
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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