Contacts of the strand formed by residues 181 - 188 (chain A) in PDB entry 1R5M
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 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A GLU* 2.8 36.7 + - + +
179A ASN* 3.6 17.0 - - + +
180A SER* 1.3 80.4 - - - +
182A ALA* 1.3 74.7 + - - +
183A ARG* 3.9 22.4 - - - +
205A GLU* 4.5 3.4 - - + -
206A LEU 3.6 18.8 - - - +
207A ARG* 3.7 27.6 - - + +
223A VAL* 3.3 9.7 - - - +
1001A SO4 3.9 13.9 - - - +
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Residues in contact with ALA 182 (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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175A TYR 3.1 14.8 - - - +
176A GLY* 4.0 8.7 - - - -
177A GLU* 4.3 1.1 - - - +
181A VAL* 1.3 75.6 - - - +
183A ARG* 1.3 69.3 + - - +
206A LEU* 2.8 40.7 + - + +
223A VAL* 3.9 8.9 - - + +
226A LEU* 4.0 15.5 - - + -
237A THR* 4.1 14.8 - - + -
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Residues in contact with ARG 183 (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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158A ASP* 5.9 2.9 - - - -
173A LEU 3.8 0.7 - - - +
174A ALA* 3.4 4.2 - - - -
175A TYR* 2.8 63.6 + - + +
177A GLU* 2.7 35.7 + - - +
181A VAL* 3.9 8.7 - - - +
182A ALA* 1.3 78.0 - - - +
184A LEU* 1.3 67.8 + - - +
185A ALA 4.1 0.4 + - - -
202A ILE* 4.1 18.5 - - + +
204A ALA 3.4 12.8 - - - +
205A GLU* 3.2 35.4 + - - +
206A LEU* 4.6 1.3 - - - +
207A ARG* 4.0 0.9 - - - +
1001A SO4 3.0 41.0 + - - -
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Residues in contact with LEU 184 (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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172A ILE* 5.3 1.6 - - + -
173A LEU 3.5 1.8 - - - +
174A ALA* 3.5 28.7 - - + -
183A ARG* 1.3 73.6 - - - +
185A ALA* 1.3 55.1 + - - +
202A ILE* 3.6 4.7 - - - +
203A ILE* 2.7 44.6 + - + -
204A ALA* 3.0 13.1 + - + +
206A LEU* 3.8 29.6 - - + -
228A TRP* 3.9 16.8 - - + -
235A ILE* 4.4 5.4 - - + -
248A ASN 4.0 8.7 - - - +
249A LYS* 3.4 33.2 - - - +
250A THR 4.5 0.9 - - - -
251A GLY* 4.0 14.1 - - - +
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Residues in contact with ALA 185 (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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171A SER 3.6 0.3 - - - +
172A ILE* 3.4 5.6 - - - +
173A LEU* 2.8 41.2 + - + +
175A TYR* 4.2 13.0 - - + -
184A LEU* 1.3 76.4 - - - +
186A ARG* 1.3 62.5 + - - +
187A ILE* 5.3 0.4 - - + -
200A LEU* 3.7 23.6 - - + -
201A THR 3.3 10.8 - - - +
202A ILE* 4.0 12.8 - - + -
203A ILE* 3.9 5.6 - - - +
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Residues in contact with ARG 186 (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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169A ASP* 5.8 1.0 + - - -
171A SER* 3.2 24.7 - - - +
172A ILE* 4.8 9.3 - - + +
185A ALA* 1.3 75.4 - - - +
187A ILE* 1.3 63.9 + - - +
188A VAL* 3.8 21.2 - - + +
199A LYS 3.4 3.3 - - - +
200A LEU* 3.5 2.8 - - - +
201A THR* 2.8 48.4 + - - +
203A ILE* 3.9 32.4 - - + +
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Residues in contact with ILE 187 (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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154A ILE* 4.8 1.1 - - + -
155A VAL* 3.9 25.6 - - + -
157A LEU* 5.1 0.2 - - + -
165A TRP* 3.8 22.7 - - + -
171A SER* 2.8 26.5 + - - +
173A LEU* 4.5 8.1 - - + -
185A ALA 5.3 2.0 - - - +
186A ARG* 1.3 78.2 - - - +
188A VAL* 1.3 67.5 + - - +
198A TRP* 4.2 10.0 - - + -
199A LYS 3.4 4.9 - - - +
200A LEU* 3.9 19.5 - - + -
520A LYS* 4.1 26.4 + - + -
532A VAL* 3.6 33.4 - - + -
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Residues in contact with VAL 188 (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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171A SER* 4.1 9.0 - - - -
186A ARG* 3.8 25.8 - - + +
187A ILE* 1.3 81.8 - - - +
189A GLU* 1.3 62.8 + - - +
190A THR* 5.6 1.1 - - - +
198A TRP* 4.1 5.2 - - - -
199A LYS* 2.8 57.3 + - + +
201A THR* 5.8 1.6 - - - +
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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