Contacts of the helix formed by residues 167 - 177 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B GLU* 2.8 24.7 + - + +
165B LEU 3.4 0.2 - - - -
166B GLU* 1.3 80.0 - - + +
168B THR* 1.3 66.5 + - - +
169B CYS 3.4 0.7 - - - -
170B VAL* 3.9 0.6 - - - +
171B GLN* 2.8 54.6 + - - +
607B PTY 6.1 0.7 - - - -
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Residues in contact with THR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLU 3.2 3.8 + - - -
164B PHE* 3.3 35.3 - - + -
167B ASP* 1.3 83.7 + - - +
169B CYS* 1.3 58.9 - - - +
171B GLN* 3.8 4.3 - - - +
172B TYR* 2.9 28.2 + - - +
607B PTY 3.8 33.9 + - + +
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Residues in contact with CYS 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.9 22.9 - - - -
13B MET* 4.3 8.3 - - + -
100B GLY 4.0 3.4 - - - -
101B CYS* 2.1 58.2 - - - -
164B PHE* 2.8 16.2 + - + +
165B LEU* 3.1 17.7 - - + +
167B ASP 3.4 0.2 - - - -
168B THR* 1.3 70.5 - - - +
170B VAL* 1.3 63.8 + - - +
172B TYR* 3.2 4.3 + - - +
173B VAL* 3.0 21.1 + - - +
607B PTY 3.3 15.4 - - + +
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B CYS* 4.0 11.9 - - + -
103B LEU* 3.8 25.1 - - + -
110B ALA* 3.5 26.9 - - + -
165B LEU 3.6 12.3 + - - +
166B GLU* 3.3 29.8 - - - +
167B ASP 3.5 1.5 + - - +
168B THR 3.3 0.2 - - - -
169B CYS* 1.3 79.9 - - - +
171B GLN* 1.3 59.3 + - + +
173B VAL* 3.4 5.7 + - - +
174B GLN* 3.0 40.8 + - - +
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Residues in contact with GLN 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ASP* 2.8 38.3 + - - +
168B THR* 3.8 4.0 - - - +
170B VAL* 1.3 75.9 - - + +
172B TYR* 1.3 66.0 + - - +
174B GLN* 3.2 6.7 + - - +
175B LYS* 3.0 26.8 + - - +
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Residues in contact with TYR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.9 18.6 - - + -
33B LEU* 4.0 25.4 - - + -
39B HIS* 3.2 32.8 + + - -
56B LEU* 3.3 20.1 - - - +
57B GLN* 3.5 28.5 + - - -
168B THR 2.9 14.4 + - - +
169B CYS 3.3 10.3 - - - +
171B GLN* 1.3 76.3 - - - +
173B VAL* 1.3 58.2 + - - +
175B LYS* 3.2 1.6 + - - -
176B HIS* 2.9 61.9 + + - +
607B PTY 3.8 27.8 - - + -
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLN* 3.8 18.8 - - + +
10B ARG* 3.6 2.9 - - - -
11B LEU* 3.5 38.6 - - + +
33B LEU* 4.0 9.6 - - + -
101B CYS* 3.9 8.1 - - - -
103B LEU* 3.7 21.3 - - + -
169B CYS 3.0 16.5 + - - +
170B VAL* 3.6 7.4 - - - +
171B GLN 3.4 0.2 - - - -
172B TYR* 1.3 73.8 - - - +
174B GLN* 1.3 64.5 + - - +
177B ILE* 2.9 49.8 + - + +
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Residues in contact with GLN 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLN* 4.7 7.1 - - - +
103B LEU* 3.4 23.7 - - + +
170B VAL* 3.0 32.2 + - - +
171B GLN* 3.2 6.8 + - - +
173B VAL* 1.3 77.4 - - - +
175B LYS* 1.3 62.2 + - - +
177B ILE* 4.6 10.3 - - - +
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Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B GLN 3.0 16.7 + - - +
172B TYR* 3.8 2.9 - - - +
174B GLN* 1.3 80.6 - - - +
176B HIS* 1.3 84.2 + - + +
177B ILE 3.8 0.2 - - - -
178B SER* 4.4 8.3 + - - -
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Residues in contact with HIS 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 3.7 20.7 - - + +
56B LEU* 2.9 46.2 + - + +
57B GLN* 3.9 10.2 - - + +
172B TYR* 2.9 58.1 + + - +
175B LYS* 1.3 105.1 + - + +
177B ILE* 1.3 64.4 + - - +
178B SER* 3.1 3.4 - - - -
179B ALA* 3.0 24.5 + - - +
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Residues in contact with ILE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU 5.1 1.3 - - - +
9B GLN* 3.4 44.0 - - + +
10B ARG 4.6 2.2 - - - +
33B LEU* 3.7 23.8 - - + +
34B GLY* 5.0 5.4 - - - +
173B VAL* 2.9 49.1 + - + +
174B GLN* 4.6 9.2 - - - +
175B LYS 3.8 0.4 - - - -
176B HIS* 1.3 71.1 - - - +
178B SER* 1.3 85.8 + - - +
180B GLU* 2.9 29.4 + - - +
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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