Contacts of the strand formed by residues 164 - 169 (chain A) in PDB entry 1RWM
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 LEU 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A THR* 3.6 3.4 + - - +
163A ARG* 1.3 82.3 - - - +
165A ALA* 1.3 59.3 + - - +
198A TYR* 3.5 13.1 - - - -
199A SER* 3.8 17.3 - - - +
201A ASP* 6.5 0.2 - - + -
218A PHE* 3.8 12.3 - - + -
221A ARG* 3.7 47.6 - - + +
223A GLU* 3.8 34.1 - - + +
224A HIS* 3.6 33.2 - - + +
227A SER* 4.1 4.0 + - - -
229A SER 4.6 0.6 + - - -
230A THR* 2.8 24.2 + - - -
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Residues in contact with ALA 165 (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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164A LEU* 1.3 75.3 - - - +
166A LEU* 1.3 62.9 + - - +
193A LEU* 3.7 26.5 - - + -
198A TYR* 3.7 21.7 - - + +
199A SER 3.1 9.4 + - - +
200A VAL* 4.3 10.8 - - + -
201A ASP* 3.0 25.2 + - - +
218A PHE* 3.6 7.3 - - - -
231A PHE* 3.5 12.8 - - + +
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Residues in contact with LEU 166 (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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165A ALA* 1.3 77.0 - - - +
167A ILE* 1.3 70.5 + - - +
168A ILE* 4.3 15.0 - - + -
201A ASP* 3.3 31.2 - - + +
203A LYS* 4.2 17.7 - - + -
214A GLU* 4.3 10.1 - - + +
215A LEU* 3.9 24.2 - - + -
218A PHE* 3.6 38.8 - - + -
231A PHE 3.0 8.5 + - - +
232A LEU* 3.6 12.2 - - + +
233A VAL 2.9 26.2 + - - +
234A PHE* 5.8 0.4 - - + -
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Residues in contact with ILE 167 (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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166A LEU* 1.3 77.5 - - - +
168A ILE* 1.3 63.7 + - - +
169A CYS* 4.6 3.6 - - + +
186A ILE* 4.8 2.5 - - + +
189A MET* 3.8 11.7 - - + -
190A THR* 3.4 39.7 - - - +
193A LEU* 3.9 10.3 - - + -
200A VAL* 3.6 14.1 - - + -
201A ASP 2.7 11.7 + - - +
202A VAL* 3.4 11.2 - - + -
203A LYS* 2.7 33.6 + - - +
233A VAL* 3.4 26.7 - - + +
235A MET* 3.7 28.9 - - + -
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Residues in contact with ILE 168 (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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166A LEU* 4.3 22.4 - - + -
167A ILE* 1.3 77.5 - - - +
169A CYS* 1.3 61.7 + - - +
170A ASN* 4.2 8.7 - - - +
203A LYS* 3.3 13.5 - - + +
206A LEU* 3.7 28.9 - - + -
211A MET* 3.8 40.6 - - + +
214A GLU* 4.5 6.7 - - + -
215A LEU* 4.6 1.8 - - + -
233A VAL 2.9 11.3 + - - +
234A PHE* 3.4 29.3 - - + -
235A MET* 3.0 24.9 + - - +
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Residues in contact with CYS 169 (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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167A ILE* 4.0 3.1 - - + -
168A ILE* 1.3 74.5 - - - +
170A ASN* 1.3 68.6 + - - +
171A GLU* 3.9 2.8 + - - -
179A ARG* 4.0 2.2 - - - -
182A ALA* 3.8 22.9 - - - -
186A ILE* 3.6 41.7 - - + -
202A VAL* 5.8 0.4 - - + -
203A LYS 2.8 12.0 + - - +
204A LYS* 3.1 11.2 - - + +
205A ASN 3.0 19.4 + - - -
235A MET* 3.2 29.2 - - + -
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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