Contacts of the helix formed by residues 182 - 188 (chain A) in PDB entry 3TJF
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 HIS 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A VAL* 3.5 28.1 + - + +
179A ASP* 3.0 19.5 + - - -
180A LEU 3.4 14.6 + - - -
181A THR* 1.3 77.7 + - - +
183A GLN* 1.3 62.7 + - - +
184A ILE 3.3 2.9 - - - -
185A SER* 3.4 3.0 + - - -
186A LYS* 3.0 40.2 + - - +
191A TYR* 3.0 42.8 + + + -
196A GLY* 3.8 15.7 + - - -
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Residues in contact with GLN 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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78A LYS* 4.8 4.2 - - - +
179A ASP* 3.3 0.6 + - - +
181A THR* 3.2 20.1 + - - +
182A HIS* 1.3 77.8 - - - +
184A ILE* 1.3 60.3 + - + +
186A LYS* 4.1 19.3 + - - +
187A ASP* 3.0 62.8 + - - +
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Residues in contact with ILE 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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87A TYR 6.1 0.2 - - - -
88A TRP* 3.8 28.0 - - + -
89A GLU 3.8 22.2 - - - +
113A PHE* 4.0 11.2 - - + -
115A PHE* 3.9 20.0 - - + -
148A CYS* 4.8 0.4 - - - -
177A LEU* 3.8 26.0 - - + -
178A SER 4.5 4.9 - - - +
179A ASP* 3.0 25.2 + - + +
183A GLN* 1.3 78.1 - - + +
185A SER* 1.3 57.6 + - - +
187A ASP* 3.2 6.7 + - - +
188A TYR* 3.0 40.8 + - + +
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Residues in contact with SER 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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115A PHE* 3.9 8.3 - - - -
150A VAL* 4.0 6.2 + - - +
179A ASP* 2.6 23.9 + - - +
182A HIS* 3.7 4.7 - - - -
184A ILE* 1.3 76.9 - - - +
186A LYS* 1.3 57.6 - - - +
188A TYR 3.3 1.0 + - - -
189A GLY 3.1 7.6 + - - -
190A VAL* 3.0 37.3 + - - +
191A TYR* 3.7 19.1 - - - -
198A THR* 3.2 31.6 - - - +
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Residues in contact with LYS 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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76A LEU* 4.1 10.3 - - + +
77A SER* 4.0 9.4 - - - -
181A THR 4.9 3.4 + - - -
182A HIS* 3.0 34.6 + - - +
183A GLN* 3.8 20.5 + - - +
185A SER* 1.3 73.8 - - - +
187A ASP* 1.3 67.1 + - - +
189A GLY* 3.2 13.4 + - - +
191A TYR* 3.9 30.2 - - + -
193A GLU* 3.8 21.9 + - - -
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Residues in contact with ASP 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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78A LYS* 2.8 65.6 + - + +
79A ALA 3.4 6.2 + - - -
86A PRO* 3.9 16.7 - - + +
87A TYR 4.3 13.1 - - - +
183A GLN* 3.0 42.5 + - - +
184A ILE* 3.5 7.5 - - - +
186A LYS* 1.3 77.1 - - - +
188A TYR* 1.3 62.0 + - + +
189A GLY 3.3 0.2 - - - -
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Residues in contact with TYR 188 (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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77A SER* 3.9 7.5 + - - -
79A ALA* 4.2 8.2 - - + +
85A ALA* 3.5 16.5 - - + +
86A PRO* 2.7 50.4 + - + -
87A TYR 5.1 0.4 - - - -
88A TRP* 3.5 23.4 + + + -
103A LEU* 4.1 0.5 - - - +
113A PHE* 3.8 17.5 - + - -
115A PHE* 3.6 25.8 - + + -
184A ILE* 3.0 25.4 + - + +
185A SER 3.3 3.3 + - - +
186A LYS 3.2 0.2 - - - -
187A ASP* 1.3 80.8 - - + +
189A GLY* 1.3 62.3 + - - +
190A VAL* 3.3 2.5 + - + +
203A PHE* 3.4 57.6 - + + -
205A ILE* 3.9 6.7 - - + +
211A LEU* 5.4 0.9 - - + -
216A LEU* 5.3 0.9 - - - +
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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