Contacts of the helix formed by residues 167 - 177 (chain A) in PDB entry 3JTC
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 ASP 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A ARG* 5.7 1.6 + - - -
163A GLU* 2.9 38.9 + - + +
166A GLU* 1.3 92.0 - - - +
168A THR* 1.3 65.2 + - - +
169A CYS 3.4 0.7 - - - -
170A VAL* 3.9 1.0 - - - +
171A GLN* 3.0 43.9 + - - +
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Residues in contact with THR 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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163A GLU 3.0 8.3 + - - -
164A PHE* 3.4 26.1 - - + -
167A ASP* 1.3 79.3 - - - +
169A CYS* 1.4 63.2 - - - +
171A GLN* 3.5 7.8 + - - +
172A TYR* 3.1 21.8 + - - +
606A PTY 3.8 35.5 + - + +
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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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11A LEU* 3.8 21.5 - - - +
13A MET* 4.0 11.9 - - + -
100A GLY 4.2 1.3 - - - -
101A CYS* 2.1 51.1 - - - -
164A PHE* 2.8 16.6 + - + +
165A LEU* 3.2 16.4 - - - +
168A THR* 1.4 69.8 - - - +
170A VAL* 1.3 65.5 + - - +
172A TYR* 3.3 2.9 + - - +
173A VAL* 3.0 27.0 + - - +
606A PTY 3.1 16.4 - - + +
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Residues in contact with VAL 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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101A CYS* 4.0 11.2 - - + -
103A LEU* 4.1 16.8 - - + -
110A ALA* 3.5 28.9 - - + -
165A LEU 3.7 11.6 + - - +
166A GLU* 3.2 27.4 - - - +
167A ASP 3.5 1.5 + - - +
168A THR 3.3 0.4 - - - -
169A CYS* 1.3 76.3 - - - +
171A GLN* 1.3 60.0 + - + +
173A VAL* 3.2 3.6 + - - +
174A GLN* 2.9 45.6 + - - +
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Residues in contact with GLN 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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167A ASP* 3.0 35.8 + - - +
168A THR* 3.8 6.4 - - - +
170A VAL* 1.3 79.2 - - + +
172A TYR* 1.3 57.6 + - - +
174A GLN* 3.8 6.7 - - - +
175A LYS* 2.9 32.3 + - - +
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Residues in contact with TYR 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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11A LEU* 4.0 17.3 - - + -
33A LEU* 4.0 27.6 - - + -
39A HIS* 3.1 32.7 + + - -
56A LEU* 3.5 20.3 - - - +
57A GLN* 3.6 25.0 + - - -
168A THR 3.1 14.3 + - - +
169A CYS 3.4 8.3 - - - +
170A VAL 3.2 0.2 - - - -
171A GLN* 1.3 77.4 - - - +
173A VAL* 1.3 63.7 + - - +
175A LYS* 4.7 1.3 - - - -
176A HIS* 3.0 56.3 + + - +
606A PTY 3.7 28.7 - - + -
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Residues in contact with VAL 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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9A GLN* 3.6 38.6 - - + +
10A ARG 3.9 3.6 - - - +
11A LEU* 3.6 36.8 - - + +
33A LEU* 4.2 8.7 - - + -
101A CYS* 3.8 8.5 - - - -
103A LEU* 3.8 18.2 - - + -
169A CYS 3.0 14.7 + - - +
170A VAL 3.6 6.7 - - - +
172A TYR* 1.3 72.9 - - - +
174A GLN* 1.3 64.3 + - - +
175A LYS 3.3 0.7 + - - -
177A ILE* 3.3 26.5 + - + +
178A SER 3.8 4.7 + - - +
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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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9A GLN* 4.6 5.4 - - - +
103A LEU* 3.6 25.3 - - + +
170A VAL* 2.9 27.7 + - - +
171A GLN* 3.8 7.3 - - - +
172A TYR 3.3 0.2 - - - -
173A VAL* 1.3 75.8 - - - +
175A LYS* 1.3 57.4 + - - +
178A SER* 3.2 36.6 + - - +
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Residues in contact with LYS 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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171A GLN 2.9 17.5 + - - +
172A TYR* 4.0 2.7 - - - +
174A GLN* 1.3 80.8 - - - +
176A HIS* 1.3 86.9 + - + +
177A ILE 4.5 0.3 - - - +
178A SER* 4.4 9.4 + - - -
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Residues in contact with HIS 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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33A LEU* 4.0 22.3 - - + +
56A LEU* 2.9 53.6 + - + +
57A GLN* 3.8 10.2 - - + +
172A TYR* 3.0 61.3 + + + +
175A LYS* 1.3 106.0 + - + +
177A ILE* 1.3 65.9 + - - +
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Residues in contact with ILE 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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9A GLN* 2.9 40.8 - - + +
10A ARG 4.5 12.1 - - - +
33A LEU* 3.9 46.1 - - + +
34A GLY* 4.3 5.8 - - - +
173A VAL* 3.3 11.3 + - + +
175A LYS 4.5 0.6 - - - +
176A HIS* 1.3 81.7 - - - +
178A SER* 1.4 65.7 + - - +
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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