Contacts of the helix formed by residues 182 - 188 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B LEU* 3.2 27.1 + - - +
181B THR 4.7 1.2 + - - -
182B HIS* 3.2 29.2 + + - -
150C VAL* 3.4 27.7 + - + +
179C ASP* 2.9 20.9 + - - -
180C LEU 3.3 9.3 + - - -
181C THR* 1.3 77.7 + - - +
183C GLN* 1.3 63.3 + - - +
184C ILE 3.2 2.6 + - - -
185C SER* 3.4 2.4 + - - -
186C LYS* 3.1 38.4 + - - +
191C TYR* 3.1 40.8 + + + -
196C GLY 3.8 7.5 + - - -
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Residues in contact with GLN 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C LYS* 4.5 5.5 - - - +
179C ASP* 3.4 0.4 + - - +
181C THR* 3.2 20.8 + - - +
182C HIS* 1.3 77.3 - - - +
184C ILE* 1.3 59.8 + - + +
186C LYS* 3.5 19.3 + - - +
187C ASP* 3.0 63.8 + - - +
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Residues in contact with ILE 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C TRP* 3.9 31.4 - - + -
89C GLU 3.7 23.8 - - - +
90C GLY* 5.1 0.2 - - - -
113C PHE* 4.1 10.8 - - + -
115C PHE* 3.9 20.2 - - + -
148C CYS* 4.8 1.1 - - - -
177C LEU* 4.1 18.2 - - + -
178C SER 4.5 7.0 - - - +
179C ASP* 3.0 25.6 + - + +
183C GLN* 1.3 77.7 - - + +
185C SER* 1.3 59.2 + - - +
187C ASP* 3.2 6.0 + - - +
188C TYR* 2.9 36.6 + - + -
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Residues in contact with SER 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C PHE* 3.8 7.3 - - - -
150C VAL* 4.0 6.1 + - - +
179C ASP* 2.6 26.7 + - - +
182C HIS* 3.4 4.7 + - - -
184C ILE* 1.3 72.2 - - - +
186C LYS* 1.3 57.0 + - - +
188C TYR 3.3 1.4 + - - -
189C GLY 3.0 7.3 + - - -
190C VAL* 3.0 36.9 + - - +
191C TYR* 3.8 19.7 - - - -
198C THR* 3.1 32.0 - - - +
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Residues in contact with LYS 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B LYS* 5.4 7.7 - - - +
76C LEU 4.3 3.5 - - - +
77C SER* 4.2 8.5 - - - -
181C THR 5.0 3.4 + - - -
182C HIS* 3.1 33.5 + - - +
183C GLN* 3.9 21.9 + - - +
185C SER* 1.3 73.9 - - - +
187C ASP* 1.3 66.6 + - - +
189C GLY* 3.2 12.9 + - - +
191C TYR* 3.9 30.9 - - + +
193C GLU* 3.8 22.7 + - - +
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Residues in contact with ASP 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C LYS* 2.8 70.5 + - + +
79C ALA 3.4 6.2 + - - -
86C PRO* 3.9 9.2 - - + +
87C TYR 4.4 11.8 - - - +
183C GLN* 3.0 43.5 + - - +
184C ILE* 3.5 7.7 - - - +
186C LYS* 1.3 76.5 - - - +
188C TYR* 1.3 66.2 + - + +
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Residues in contact with TYR 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C SER* 3.8 7.9 + - - -
79C ALA* 4.2 6.7 - - + +
85C ALA* 3.5 16.7 - - + +
86C PRO* 2.7 49.3 + - + -
87C TYR 5.0 0.4 - - - -
88C TRP* 3.5 24.8 + + + -
103C LEU* 4.2 0.3 - - - +
113C PHE* 3.7 16.6 - + - -
115C PHE* 3.6 21.3 - + + -
184C ILE* 2.9 28.6 + - + +
185C SER 3.9 2.7 - - - +
186C LYS 3.2 0.2 - - - -
187C ASP* 1.3 83.0 - - + +
189C GLY* 1.3 60.6 + - - +
190C VAL* 3.3 2.0 - - + +
203C PHE* 3.4 57.8 - + + -
205C ILE* 4.0 6.5 - - + +
211C LEU* 5.4 1.3 - - + -
216C LEU* 5.5 0.7 - - - +
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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