Contacts of the helix formed by residues 170 - 178 (chain A) in PDB entry 2G4C
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 PHE 170 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A VAL* 5.3 2.9 - - + -
152A THR* 5.4 2.5 - - - -
153A LEU* 4.9 6.5 - - + -
156A ILE* 3.2 44.6 - - + -
166A GLN* 3.2 19.9 + - - +
167A LEU* 4.3 9.9 - - + -
169A THR* 1.3 72.9 - - - +
171A LEU* 1.3 81.3 + - + +
172A GLU 2.6 4.8 + - - -
173A ASN* 2.5 50.1 + - + +
174A VAL* 3.3 31.9 + - + -
171C LEU* 4.0 10.8 - - + -
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Residues in contact with LEU 171 (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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167A LEU 4.4 11.4 - - - +
168A VAL* 4.6 2.0 - - - +
169A THR 3.4 1.0 - - - +
170A PHE* 1.3 108.7 - - + +
172A GLU* 1.3 57.8 + - - +
173A ASN 3.3 0.4 - - - -
174A VAL* 4.0 12.7 - - + +
175A LEU* 3.7 28.6 + - - +
153C LEU* 4.5 17.3 - - + +
156C ILE* 4.5 9.2 - - + -
157C LEU* 3.7 33.4 - - + +
167C LEU* 4.8 6.3 - - + -
170C PHE* 4.0 27.4 - - + -
171C LEU* 4.0 17.7 - - + -
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Residues in contact with GLU 172 (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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168A VAL 5.3 0.2 - - - +
169A THR* 3.1 25.6 + - - +
170A PHE 2.6 4.6 + - - -
171A LEU* 1.3 75.2 - - - +
173A ASN* 1.3 61.1 + - - +
174A VAL 3.5 0.2 - - - -
175A LEU* 4.5 6.5 - - + +
176A LYS* 3.3 45.6 + - + +
157C LEU* 4.1 16.6 - - + +
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Residues in contact with ASN 173 (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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169A THR 3.7 2.6 + - - +
170A PHE* 2.5 34.5 + - + +
172A GLU* 1.3 71.6 - - - +
174A VAL* 1.3 51.2 + - - +
176A LYS* 3.3 1.9 + - - -
177A THR* 2.6 73.6 + - - +
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Residues in contact with VAL 174 (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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146A ARG* 4.7 9.4 - - + -
148A VAL* 4.3 24.0 - - + -
170A PHE* 3.3 37.1 + - + -
171A LEU* 4.1 11.9 - - + +
173A ASN* 1.3 76.8 - - - +
175A LEU* 1.3 58.2 + - - +
176A LYS 2.7 13.0 + - - -
177A THR* 2.7 17.7 + - - -
178A SER* 2.9 25.3 + - - +
153C LEU* 3.2 30.5 - - + -
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Residues in contact with LEU 175 (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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138A LEU* 5.2 3.3 - - - +
139A LEU 5.0 4.7 - - - +
146A ARG* 3.1 39.0 + - - +
171A LEU 3.7 20.3 + - - +
172A GLU* 4.7 7.2 - - + +
174A VAL* 1.3 81.5 - - - +
176A LYS* 1.3 62.0 + - + +
178A SER 5.0 0.3 + - - +
150C ALA* 4.0 27.1 - - + +
153C LEU* 3.6 39.7 - - + +
154C ARG* 5.1 11.9 - - + +
157C LEU* 4.4 12.3 - - + -
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Residues in contact with LYS 176 (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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137A PRO* 3.5 24.7 - - - +
138A LEU 3.8 12.2 + - - +
139A LEU 6.0 0.2 - - - -
172A GLU* 3.3 41.3 + - + +
173A ASN* 3.3 3.2 + - - +
174A VAL 2.7 4.8 + - - -
175A LEU* 1.3 80.5 - - + +
177A THR* 1.3 64.6 + - + +
178A SER 3.8 0.7 - - - -
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Residues in contact with THR 177 (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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136A GLY* 4.2 13.7 - - - +
137A PRO* 4.4 15.1 - - + +
173A ASN* 2.6 58.7 + - - +
174A VAL* 2.7 5.3 + - - -
176A LYS* 1.3 82.1 - - + +
178A SER* 1.3 61.8 + - - -
179A GLY 4.1 0.3 + - - -
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Residues in contact with SER 178 (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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136A GLY 3.6 9.5 - - - +
138A LEU* 3.8 10.0 + - - +
146A ARG* 3.6 33.3 + - - +
147A LEU 3.7 15.8 + - - -
148A VAL* 4.5 6.1 - - - +
174A VAL* 2.9 30.8 + - - +
176A LYS 3.8 0.9 - - - -
177A THR* 1.3 81.8 + - - +
179A GLY* 1.3 64.0 + - - +
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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