Contacts of the helix formed by residues 177 - 187 (chain A) in PDB entry 1OQY
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 ARG 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A TYR* 4.5 1.5 + - - -
167A LEU* 3.6 22.6 - - + +
171A MET* 3.2 33.2 - - - +
176A GLU* 1.3 84.8 - - + +
178A GLU* 1.3 68.0 + - + +
179A ARG 3.3 0.9 - - - -
180A VAL* 3.4 1.9 + - - -
181A VAL* 3.3 20.6 + - - +
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Residues in contact with GLU 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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163A TYR* 5.7 0.7 - - - -
176A GLU* 3.6 10.6 + - - +
177A ARG* 1.3 82.2 - - + +
179A ARG* 1.3 61.8 + - - +
181A VAL* 3.0 27.0 - - + +
182A ALA* 3.2 10.2 + - - +
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Residues in contact with ARG 179 (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 GLU* 3.8 38.2 + - + +
177A ARG 3.3 0.4 - - - -
178A GLU* 1.3 76.5 - - + +
180A VAL* 1.3 61.9 + - + +
182A ALA* 3.5 8.0 - - + +
183A ALA* 3.0 26.0 + - - +
198A LEU* 4.0 6.6 - - + +
202A ILE* 4.0 22.5 - - + +
203A PRO 4.6 2.6 + - - -
204A GLY* 3.5 30.9 + - - -
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Residues in contact with VAL 180 (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 LEU* 3.3 22.2 - - + -
170A ILE* 3.2 25.6 - - + -
171A MET* 3.9 5.8 - - - +
175A TYR* 3.5 23.1 - - + -
176A GLU 2.7 34.3 - - - +
177A ARG 3.7 0.7 - - - +
178A GLU 3.3 0.2 - - - -
179A ARG* 1.3 75.6 - - + +
181A VAL* 1.3 53.3 + - - +
183A ALA* 2.6 5.7 + - - +
184A LEU* 2.6 57.0 + - + +
198A LEU* 4.0 7.2 - - + -
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Residues in contact with VAL 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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163A TYR* 2.9 55.9 - - + +
167A LEU* 3.5 2.6 - - - +
177A ARG 3.3 5.1 + - - +
178A GLU* 3.0 28.9 - - + +
180A VAL* 1.3 77.2 - - - +
182A ALA* 1.3 70.5 + - + +
184A LEU* 2.8 11.3 + - + -
185A ARG* 2.7 36.9 + - + +
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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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178A GLU 3.2 15.5 + - - +
179A ARG* 3.5 9.4 - - + +
180A VAL 3.1 0.2 - - - -
181A VAL* 1.3 82.9 - - + +
183A ALA* 1.3 62.5 + - - +
185A ARG* 3.2 19.7 + - - +
186A ALA* 3.3 17.3 + - - +
197A TYR* 4.4 1.4 + - - -
202A ILE* 4.7 4.5 - - + -
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Residues in contact with ALA 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 ARG 3.0 5.5 + - - +
180A VAL 2.6 13.5 + - - +
182A ALA* 1.3 73.8 - - - +
184A LEU* 1.3 56.3 + - + -
185A ARG 3.2 0.2 - - - -
187A SER* 3.0 33.1 + - - -
194A ALA* 3.5 3.8 - - + -
197A TYR* 3.9 6.5 - - - +
198A LEU* 3.0 45.3 - - + -
202A ILE* 3.3 20.4 - - + +
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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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163A TYR* 4.9 6.1 - - + +
166A MET* 3.3 54.3 - - + +
167A LEU* 4.4 4.9 - - + +
170A ILE* 3.3 16.8 - - + -
180A VAL* 2.6 56.7 + - + +
181A VAL* 2.8 12.7 + - + +
183A ALA* 1.3 74.7 - - + +
185A ARG* 1.3 56.0 + - - +
189A ASN* 2.7 48.7 + - + +
194A ALA* 3.6 11.4 - - + -
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Residues in contact with ARG 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 VAL* 2.7 19.3 + - + +
182A ALA* 3.2 11.8 + - - +
184A LEU* 1.3 78.2 - - - +
186A ALA* 1.3 63.0 + - - +
188A TYR* 4.9 2.0 - - - -
189A ASN 5.2 0.2 - - - -
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Residues in contact with ALA 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 ALA 3.3 8.5 + - - +
185A ARG* 1.3 84.4 - - + +
187A SER* 1.3 59.1 + - - +
188A TYR 3.6 0.2 - - - -
197A TYR* 3.4 30.7 - - + +
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Residues in contact with SER 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 ALA 3.0 20.7 + - - -
186A ALA* 1.3 81.0 - - - +
188A TYR* 1.3 68.6 + - - +
193A ARG* 2.5 65.7 + - - +
194A ALA 3.3 1.1 - - - -
197A TYR* 3.0 20.7 - - - +
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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