Contacts of the helix formed by residues 168 - 177 (chain A) in PDB entry 3ROU
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 THR 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A ILE* 1.3 83.6 - - - +
169A ARG* 1.3 63.1 + - - +
170A GLN* 3.4 12.8 + - - +
171A GLU* 3.0 37.7 + - + +
172A ILE* 3.1 22.2 + - - +
201A LYS* 3.7 42.0 - - + +
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Residues in contact with ARG 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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168A THR* 1.3 72.4 - - - +
170A GLN* 1.3 58.0 + - - +
172A ILE* 3.3 2.7 + - - +
173A GLY* 2.8 26.3 + - - -
180A ARG* 3.4 42.6 + - + +
181A GLU* 5.0 7.3 - - - +
183A VAL* 3.5 25.1 - - + +
184A GLY* 3.5 28.4 + - - +
187A LEU* 4.5 11.5 - - + +
201A LYS* 5.6 2.2 - - - +
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Residues in contact with GLN 170 (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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168A THR* 3.1 11.2 + - - +
169A ARG* 1.3 81.5 - - - +
171A GLU* 1.3 58.6 + - - +
174A GLN* 2.8 44.4 + - - +
180A ARG* 3.4 36.6 + - - +
302A CMP 3.1 35.5 + - - +
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Residues in contact with GLU 171 (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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60A ILE* 4.6 1.5 - - + +
63A TYR* 3.3 21.1 + - - +
89A LYS* 4.2 13.9 + - - -
167A ILE* 2.9 38.7 - - + +
168A THR* 3.0 34.5 + - + +
170A GLN* 1.3 74.0 - - + +
172A ILE* 1.3 65.5 + - - +
174A GLN* 3.1 16.6 + - - +
175A ILE* 2.9 28.9 + - - +
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Residues in contact with ILE 172 (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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143A ILE* 4.0 26.0 - - + -
146A THR* 5.2 10.1 - - + -
147A LEU* 3.9 20.0 - - + -
150A LEU* 5.6 0.4 - - + -
167A ILE* 3.5 33.4 - - + +
168A THR 3.1 13.3 + - - +
169A ARG 3.6 5.8 - - - +
171A GLU* 1.3 77.3 - - - +
173A GLY* 1.3 63.7 + - - +
175A ILE* 3.0 11.2 + - - +
176A VAL* 3.0 25.3 + - + +
183A VAL* 3.7 30.5 - - + -
187A LEU* 4.2 8.3 - - + -
203A ILE* 4.0 9.0 - - + -
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Residues in contact with GLY 173 (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 ARG 2.8 16.2 + - - -
170A GLN 3.2 3.3 + - - -
172A ILE* 1.3 73.2 - - - +
174A GLN* 1.3 56.9 + - - +
177A GLY* 2.8 26.7 + - - -
178A CYS* 3.0 28.2 + - - +
183A VAL* 3.5 15.9 - - - +
302A CMP 3.3 10.8 - - - +
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Residues in contact with GLN 174 (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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50A LEU* 6.0 1.2 - - - +
58A GLU* 3.1 43.1 + - - +
59A MET* 2.6 30.1 - - - +
60A ILE* 3.1 42.0 + - + +
87A ARG* 5.0 4.6 - - - +
170A GLN* 2.8 30.8 + - - +
171A GLU* 3.1 21.3 + - - +
173A GLY* 1.3 79.2 - - - +
175A ILE* 1.3 52.0 + - - +
302A CMP 3.5 21.9 + - - -
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Residues in contact with ILE 175 (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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59A MET* 3.0 6.9 - - - +
60A ILE* 4.4 21.1 - - + +
63A TYR* 4.2 23.6 - - + +
130A LYS* 2.8 40.1 + - - +
134A LEU* 4.9 2.8 - - - +
146A THR* 3.7 39.9 - - + +
150A LEU* 5.3 8.3 - - + -
167A ILE* 5.1 7.2 - - + -
171A GLU 2.9 20.4 + - - +
172A ILE* 3.0 8.3 + - - +
174A GLN* 1.3 78.6 - - - +
176A VAL* 1.3 55.7 + - + +
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Residues in contact with VAL 176 (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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59A MET* 3.7 2.9 - - - -
134A LEU* 3.5 10.3 - - - +
139A VAL* 4.2 5.5 - - + +
142A ARG* 3.0 55.5 + - + +
143A ILE* 3.8 18.8 - - + +
146A THR* 3.3 28.3 - - - +
172A ILE* 3.0 19.6 + - + +
173A GLY* 4.1 0.4 - - - +
175A ILE* 1.3 79.8 - - + +
177A GLY* 1.3 58.1 + - - +
178A CYS* 3.5 31.4 - - - -
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Residues in contact with GLY 177 (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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59A MET* 3.2 10.8 - - - +
139A VAL* 5.6 0.2 - - - +
142A ARG* 4.5 4.5 + - - -
173A GLY 2.8 9.3 + - - -
176A VAL* 1.3 81.0 - - - +
178A CYS* 1.3 60.8 + - - +
302A CMP 3.0 44.1 + - - -
135B ALA* 3.9 10.6 - - - +
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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