Contacts of the helix formed by residues 174 - 183 (chain C) in PDB entry 1G2D
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 THR 174 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A C 3.9 11.0 + - + -
7A T 3.9 25.1 + - + +
152C GLN* 4.2 21.5 - - + +
155C ARG* 4.0 10.5 - - - +
163C PHE* 3.5 10.3 - - - -
172C PHE* 4.1 2.4 - - - +
173C ALA* 1.3 88.0 - - + +
175C LEU* 1.3 64.9 + - - +
176C HIS* 4.2 3.6 + - - +
177C THR* 2.8 32.0 + - - -
178C ARG* 3.3 21.0 + - - +
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Residues in contact with LEU 175 (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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24B T 3.8 10.3 - - + -
25B A 3.5 58.3 - - + +
26B T 4.1 6.3 - - + +
155C ARG* 5.1 0.2 - - - +
163C PHE* 3.6 31.4 - - + -
174C THR* 1.3 73.7 - - - +
176C HIS* 1.3 59.6 + - - +
178C ARG* 3.3 33.1 + - - +
179C ASP* 3.0 45.3 + - - +
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Residues in contact with HIS 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A C 4.4 1.1 - - - +
7A T 5.2 0.4 - - - +
26B T 3.5 32.0 + + + +
27B A 3.1 55.4 + + - +
28B G 3.3 19.1 + - - -
174C THR* 3.5 3.9 + - - +
175C LEU* 1.3 75.0 - - - +
177C THR* 1.3 62.0 + - - +
179C ASP* 3.1 8.7 + - + +
180C ARG* 2.8 55.6 + - + +
183C LYS* 6.3 2.2 - - - -
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Residues in contact with THR 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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4A C 3.8 24.7 - - + +
5A G 4.0 12.3 - - + +
6A C 3.1 24.3 + - - -
172C PHE* 3.7 26.2 - - + -
173C ALA 5.7 0.4 - - - +
174C THR* 2.8 27.3 + - - -
175C LEU 3.4 0.2 - - - -
176C HIS* 1.3 77.8 - - - +
178C ARG* 1.3 57.8 + - - +
180C ARG* 4.0 12.9 + - - +
181C HIS* 3.1 28.2 + - - +
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Residues in contact with ARG 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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163C PHE* 3.6 31.2 - - + +
164C ALA 3.0 33.7 + - - +
165C CYS* 4.1 3.1 - - - +
166C ASP 5.4 0.4 - - - +
172C PHE* 3.5 28.7 - - + +
174C THR 3.3 10.2 + - - +
175C LEU* 3.3 28.1 + - - +
176C HIS 3.1 0.2 - - - -
177C THR* 1.3 77.5 - - - +
179C ASP* 1.3 89.7 + - - +
181C HIS* 3.2 4.7 + - - +
182C THR* 3.2 35.4 + - - -
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Residues in contact with ASP 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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25B A 5.3 1.7 + - - +
26B T 4.6 5.0 - - - +
175C LEU* 3.0 39.1 + - - +
176C HIS* 3.7 11.2 - - - +
178C ARG* 1.3 105.6 + - - +
180C ARG* 1.3 62.2 + - - +
181C HIS 3.6 0.2 + - - -
182C THR* 3.7 12.0 + - - -
183C LYS* 3.6 22.9 + - - +
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Residues in contact with ARG 180 (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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4A C 3.6 28.9 - - + +
5A G 2.9 40.7 + - - -
6A C 3.5 8.0 - - - +
28B G 2.8 27.8 + - - -
29B C 3.5 9.9 - - - +
176C HIS* 2.8 35.7 + - + +
177C THR* 4.0 13.7 + - - +
179C ASP* 1.3 74.0 - - - +
181C HIS* 1.3 67.1 + - - +
183C LYS* 3.3 32.7 + - + +
184C ILE* 4.2 5.4 + - - +
187C ARG* 5.0 3.1 + - - +
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Residues in contact with HIS 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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4A C 3.0 42.7 + - + +
165C CYS* 3.6 6.7 - - + -
168C CYS* 3.3 9.6 - - - -
170C ARG* 4.2 4.7 - - - -
172C PHE* 3.2 34.0 - + + -
177C THR* 3.1 20.2 + - + +
178C ARG 3.2 4.4 + - - +
180C ARG* 1.3 76.9 - - - +
182C THR* 1.3 63.4 + - - +
184C ILE* 2.9 46.8 + - + +
185C HIS* 3.4 2.2 + + - -
303C ZN 2.2 36.2 - - - -
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Residues in contact with THR 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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165C CYS* 3.6 15.0 - - - +
166C ASP* 4.8 5.1 + - + +
167C ILE* 4.0 23.1 - - + -
178C ARG* 3.2 20.4 + - - -
179C ASP* 3.8 11.3 - - - -
180C ARG 3.4 0.4 - - - -
181C HIS* 1.3 78.1 - - - +
183C LYS* 1.3 59.9 + - + +
184C ILE 3.3 1.0 + - - -
185C HIS* 3.3 27.2 + - - +
186C LEU* 4.1 10.7 - - + +
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Residues in contact with LYS 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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176C HIS* 6.3 2.2 - - - -
179C ASP* 3.6 22.1 + - - +
180C ARG* 3.4 23.1 - - + +
181C HIS 2.9 0.6 + - - -
182C THR* 1.3 76.3 - - + +
184C ILE* 1.3 63.6 + - - +
185C HIS 3.2 0.4 - - - -
186C LEU* 3.3 29.7 + - + +
187C ARG* 3.9 26.6 + - - +
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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