Contacts of the strand formed by residues 191 - 199 (chain A) in PDB entry 1OMW
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 PHE 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A LEU* 4.3 14.1 - - + -
187A THR 3.6 12.1 - - - -
188A MET 3.2 15.7 + - - +
189A ASN* 3.2 4.8 - - - +
190A ASP* 1.3 87.1 - - + +
192A SER* 1.3 65.2 + - - +
193A VAL* 3.8 5.4 + - + +
208A CYS* 3.9 18.2 - - + -
209A ARG 3.5 3.8 - - - +
210A LYS* 3.7 45.8 - - + -
211A ALA* 4.7 1.3 - - - +
217A TYR* 4.3 4.7 - + - -
219A MET* 3.6 21.3 - - + -
259A TYR* 4.8 0.7 - + - -
261A PHE* 3.8 21.5 - + - -
270A ILE* 3.6 36.6 - - + -
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Residues in contact with SER 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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30A LYS* 6.2 1.8 - - - -
191A PHE* 1.3 69.7 - - - +
193A VAL* 1.3 65.6 + - - +
194A HIS* 4.0 13.4 - - - -
208A CYS* 3.4 4.0 - - - -
209A ARG* 2.9 52.1 + - - +
211A ALA* 4.9 7.0 - - - +
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Residues in contact with VAL 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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191A PHE* 3.8 6.6 + - + +
192A SER* 1.3 77.6 + - - +
194A HIS* 1.3 74.4 + - - +
206A TYR* 4.0 41.1 - - + -
207A GLY 4.0 3.6 - - - +
208A CYS* 4.2 9.4 - - + -
219A MET* 4.6 15.3 - - + -
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Residues in contact with HIS 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* 4.0 17.0 - - - -
193A VAL* 1.3 83.9 + - - +
195A ARG* 1.3 72.4 + - + +
207A GLY* 3.2 10.6 + - - +
208A CYS* 4.2 22.4 - - - -
209A ARG* 3.6 39.4 + - + +
216A MET* 5.4 5.2 - - + -
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Residues in contact with ARG 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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194A HIS* 1.3 87.2 - - + +
196A ILE* 1.3 66.4 + - - +
197A ILE* 5.1 3.8 - - + -
206A TYR* 3.4 7.8 - - - +
207A GLY* 2.7 33.9 + - - +
475A GLY 4.6 18.4 - - - -
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Residues in contact with ILE 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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195A ARG* 1.3 84.0 - - - +
197A ILE* 1.3 75.9 + - - +
198A GLY 3.8 22.7 - - - +
199A ARG* 5.1 17.0 - - + +
204A GLU* 5.0 7.6 - - + -
205A VAL 3.9 7.2 - - - +
206A TYR* 4.0 25.8 - - + +
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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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195A ARG* 4.1 4.3 - - + +
196A ILE* 1.3 84.0 - - - +
198A GLY* 1.3 60.0 + - - +
205A VAL* 2.8 19.3 + - + +
206A TYR 4.1 1.8 - - - +
207A GLY* 3.3 31.2 - - - +
218A ALA* 5.2 1.6 - - + -
273A LEU* 3.4 25.4 - - + -
274A MET 3.8 19.3 - - - +
275A ASN* 4.1 20.6 - - + +
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Residues in contact with GLY 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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196A ILE* 3.8 9.7 - - - +
197A ILE* 1.3 81.8 - - - +
199A ARG* 1.3 60.4 + - - -
200A GLY 4.0 0.7 - - - -
204A GLU* 3.6 1.6 - - - -
205A VAL* 2.8 41.0 + - - +
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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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196A ILE* 5.1 17.4 - - + +
198A GLY* 1.3 74.0 - - - +
200A GLY* 1.3 65.2 + - - +
203A GLY 4.2 2.2 - - - -
204A GLU* 4.3 14.4 - - + +
205A VAL* 5.2 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