Contacts of the helix formed by residues 176 - 187 (chain A) in PDB entry 1RI5
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 SER 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A VAL 3.6 0.2 + - - -
175A PRO* 1.3 71.6 - - - +
177A ARG* 1.3 59.4 + - - +
178A ASP* 3.5 9.2 + - - +
179A VAL* 3.2 35.7 + - - +
180A ILE* 2.9 32.4 + - - +
247A ARG* 4.9 0.9 + - - -
283A ILE 2.7 14.7 + - - -
284A TYR 5.0 0.4 - - - -
285A GLU* 3.9 34.3 + - - -
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Residues in contact with ARG 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PRO 3.8 4.4 + - - -
176A SER* 1.3 70.8 + - - +
178A ASP* 1.3 62.9 + - - +
180A ILE* 3.3 1.4 + - - +
181A LEU* 2.8 55.1 + - + +
206A MET 3.9 4.0 + - - -
207A GLU* 3.2 50.3 + - - +
209A VAL 3.5 21.3 + - - -
227A PHE* 3.5 50.3 - - + +
228A VAL* 4.2 24.0 - - - +
229A ASP* 5.5 2.9 - - - +
247A ARG* 6.0 0.6 - - - +
285A GLU* 5.1 0.6 + - - -
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Residues in contact with ASP 178 (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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176A SER* 3.2 6.0 + - - +
177A ARG* 1.3 83.2 + - - +
179A VAL* 1.3 57.4 + - + +
181A LEU* 3.9 7.2 - - - +
182A GLU* 2.9 38.4 + - + +
247A ARG* 3.7 23.5 + - - +
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER* 3.2 27.9 + - - +
178A ASP* 1.3 77.9 - - + +
180A ILE* 1.3 64.5 + - + +
182A GLU* 3.2 7.6 + - - +
183A ARG* 3.0 52.4 + - + +
282A GLY 3.5 25.6 - - - +
283A ILE* 4.4 6.3 - - + +
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Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PRO* 4.0 15.9 - - + -
176A SER 2.9 23.0 + - - +
177A ARG 3.6 3.8 - - - +
179A VAL* 1.3 76.9 - - + +
181A LEU* 1.3 63.4 + - + +
183A ARG* 3.2 10.7 + - - +
184A TYR* 3.1 19.4 + - - +
189A MET* 4.0 9.4 - - + +
196A ILE* 4.3 34.3 - - + -
198A LEU* 4.9 1.8 - - + -
212A TYR* 3.8 24.5 - - + +
227A PHE* 3.5 37.9 - - + -
283A ILE* 4.5 12.8 - - + -
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Residues in contact with LEU 181 (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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177A ARG* 2.8 63.4 + - + +
178A ASP* 4.0 7.2 - - - +
180A ILE* 1.3 73.1 - - - +
182A GLU* 1.3 63.0 + - + +
184A TYR* 3.1 14.5 + - - +
185A LYS* 3.2 22.6 + - - +
198A LEU* 4.3 10.1 - - + -
206A MET* 3.9 33.2 - - + +
207A GLU* 4.0 16.6 - - - +
209A VAL* 4.5 0.2 - - + -
227A PHE* 4.0 22.4 - - + -
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Residues in contact with GLU 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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178A ASP* 2.9 27.6 + - + +
179A VAL* 3.5 7.2 - - - +
181A LEU* 1.3 76.8 - - + +
183A ARG* 1.3 62.0 + - + +
185A LYS* 3.4 31.8 + - - +
186A GLN* 3.0 37.5 + - - +
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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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179A VAL* 3.0 26.0 + - + +
180A ILE* 3.6 9.9 - - - +
181A LEU 3.2 0.2 - - - -
182A GLU* 1.3 75.4 - - + +
184A TYR* 1.3 65.0 + - - +
186A GLN* 3.2 17.4 + - - +
187A GLY 3.0 17.8 + - - -
188A ARG* 3.1 42.6 + - - +
189A MET* 4.1 4.7 - - - -
194A TYR* 3.0 28.6 + - - -
196A ILE* 6.3 1.8 - - - -
278A SER 4.5 0.2 + - - -
279A GLU* 2.6 50.9 + - - +
282A GLY* 3.8 20.0 + - - -
283A ILE* 3.2 18.9 - - - +
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Residues in contact with TYR 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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180A ILE 3.1 9.3 + - - +
181A LEU* 3.1 10.1 + - - +
183A ARG* 1.3 77.1 - - - +
185A LYS* 1.3 61.1 + - - +
187A GLY* 3.2 12.5 + - - -
189A MET* 3.5 28.6 - - + +
198A LEU* 3.5 32.8 - - + -
199A GLU 4.8 7.8 + - - -
200A LYS 5.5 1.7 + - - -
206A MET* 3.5 46.0 - - + -
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Residues in contact with LYS 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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181A LEU* 3.2 14.1 + - - +
182A GLU* 3.6 31.2 + - - +
183A ARG 3.2 0.2 - - - -
184A TYR* 1.3 77.1 - - - +
186A GLN* 1.3 61.4 + - + +
187A GLY* 3.4 0.7 + - - -
206A MET* 3.6 37.5 - - + -
207A GLU* 5.4 6.3 + - - -
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Residues in contact with GLN 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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182A GLU* 3.0 21.3 + - - +
183A ARG* 3.2 18.9 + - - +
185A LYS* 1.3 77.6 - - + +
187A GLY* 1.3 60.7 + - - +
188A ARG* 2.8 47.2 + - + +
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Residues in contact with GLY 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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183A ARG 3.0 4.0 + - - -
184A TYR 3.2 10.0 + - - -
185A LYS 3.2 4.8 - - - -
186A GLN* 1.3 78.9 - - - +
188A ARG* 1.3 57.9 + - - +
189A MET* 3.8 6.1 + - - -
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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