Contacts of the helix formed by residues 175 - 185 (chain C) in PDB entry 1CJT
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 ALA 175 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C ALA* 4.0 17.9 - - + -
106C ILE* 5.0 0.4 - - + -
163C TYR* 4.2 8.1 - - + -
171C LEU* 3.9 31.4 - - + -
172C ILE* 3.3 16.8 + - - +
173C ASP 3.2 3.5 - - - +
174C CYS* 1.3 81.3 - - - +
176C GLN* 1.3 64.0 + - - +
178C PHE* 4.1 1.3 - - - +
179C LEU* 3.1 33.9 + - + +
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Residues in contact with GLN 176 (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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154C TRP* 4.2 13.4 - - + -
160C ARG* 4.0 18.5 + - - -
163C TYR* 3.3 36.1 + - + +
173C ASP 4.6 3.1 + - - +
174C CYS 3.4 0.4 - - - -
175C ALA* 1.3 76.7 - - - +
177C TYR* 1.3 66.6 + - - +
180C ASP* 3.2 42.2 + - - +
299C GLU* 4.9 14.6 + - - -
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Residues in contact with TYR 177 (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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173C ASP 5.3 0.6 + - - -
174C CYS* 3.3 13.4 + - - +
176C GLN* 1.3 80.7 - - - +
178C PHE* 1.3 83.0 + + - +
180C ASP* 3.9 7.5 + - - +
181C LYS* 3.4 35.6 + - + +
193C SER* 4.0 1.0 + - - -
195C GLN* 3.3 35.6 - - + +
196C ASP* 2.6 31.2 + - - -
199C ARG* 3.6 51.8 - - + +
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Residues in contact with PHE 178 (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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95C ILE* 3.4 34.1 - - + -
98C ASN* 3.9 22.4 - - + -
99C LEU* 3.9 23.3 - - + +
174C CYS* 3.1 50.8 + - + +
175C ALA* 4.3 1.6 - - - +
177C TYR* 1.3 93.1 - + - +
179C LEU* 1.3 59.8 + - - +
180C ASP 3.2 2.0 - - - -
181C LYS* 3.0 32.5 + - + +
182C ILE* 3.4 1.7 + - - +
185C ILE* 3.8 12.3 - - + +
196C ASP* 3.7 29.8 - - + -
199C ARG* 4.0 7.2 - - + -
200C CYS* 3.9 8.3 - - - -
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Residues in contact with LEU 179 (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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99C LEU* 3.3 25.6 - - + +
102C ALA* 4.4 6.5 - - + -
103C ILE* 4.2 26.7 - - + +
106C ILE* 4.0 15.7 - - + -
150C ALA* 5.6 1.1 - - + +
151C LYS* 6.0 0.3 - - - +
154C TRP* 3.4 63.1 - - + -
175C ALA 3.1 23.3 + - - +
176C GLN 4.3 0.2 - - - +
178C PHE* 1.3 75.2 - - - +
180C ASP* 1.3 60.5 + - - +
181C LYS 3.2 0.9 + - - -
182C ILE* 3.3 29.7 + - + +
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Residues in contact with ASP 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C TRP* 2.9 25.1 + - - +
160C ARG* 4.1 7.8 + - - -
176C GLN* 3.2 38.1 + - - +
177C TYR* 4.1 5.1 - - - +
178C PHE 3.2 0.8 - - - -
179C LEU* 1.3 75.8 - - - +
181C LYS* 1.3 60.1 + - + +
182C ILE 3.7 0.7 - - - -
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Residues in contact with LYS 181 (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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177C TYR* 3.4 44.7 + - + +
178C PHE* 3.0 16.1 + - + +
180C ASP* 1.3 78.9 - - + +
182C ILE* 1.3 61.9 + - - +
183C ASP* 3.2 4.3 - - - +
184C VAL* 3.1 43.0 + - + +
185C ILE* 3.2 20.8 + - + +
193C SER* 4.3 6.1 + - - -
196C ASP* 3.2 27.0 + - - +
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Residues in contact with ILE 182 (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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99C LEU* 4.2 13.0 - - + -
147C TYR* 3.7 39.4 - - + +
150C ALA* 4.0 12.3 - - + +
151C LYS* 3.7 41.3 - - + +
154C TRP* 5.0 2.2 - - + -
178C PHE 4.0 2.7 - - - +
179C LEU* 3.3 39.7 + - + +
180C ASP 3.7 1.4 - - - -
181C LYS* 1.3 76.8 - - - +
183C ASP* 1.3 62.9 + - - +
184C VAL 3.1 0.2 + - - -
185C ILE* 3.2 6.0 + - - +
186C LYS* 2.9 30.3 + - + +
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Residues in contact with ASP 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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151C LYS* 3.5 38.9 + - - +
181C LYS* 3.2 1.3 - - - -
182C ILE* 1.3 75.8 - - - +
184C VAL* 1.3 61.3 + - + +
186C LYS* 3.3 41.1 + - - +
187C GLN* 3.5 18.4 + - - +
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Residues in contact with VAL 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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181C LYS* 3.1 40.1 + - + +
182C ILE 3.0 0.6 - - - -
183C ASP* 1.3 82.9 - - + +
185C ILE* 1.3 63.2 + - + +
186C LYS 3.4 0.4 + - - -
187C GLN* 3.8 11.8 + - - +
190C TYR* 3.2 37.7 - - + +
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Residues in contact with ILE 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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95C ILE* 3.7 24.5 - - + +
96C LYS* 3.9 37.1 - - + -
99C LEU* 4.5 13.2 - - + -
147C TYR* 4.4 9.2 - - + -
178C PHE* 3.8 30.3 - - + +
181C LYS* 3.2 18.5 + - + +
182C ILE* 3.2 7.0 + - - +
184C VAL* 1.3 75.9 - - + +
186C LYS* 1.3 64.7 + - - +
187C GLN 3.2 9.4 + - - +
190C TYR* 3.9 36.5 - - + +
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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