Contacts of the helix formed by residues 173 - 181 (chain F) in PDB entry 1GN2
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 VAL 173 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170F TYR* 3.0 23.3 + - + +
171F LYS* 5.4 1.1 - - + -
172F ASN* 1.3 88.3 - - - +
174F LYS* 1.3 59.7 + - - +
175F VAL* 2.8 14.1 + - + +
176F ASP* 2.9 48.8 + - + +
177F PHE 3.6 2.1 + - - -
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Residues in contact with LYS 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F ALA 4.9 2.0 - - - -
118F THR* 3.0 38.1 + - + +
119F THR* 5.1 0.6 - - - +
120F VAL* 4.3 14.7 + - - +
161F MET* 3.8 16.5 - - + +
166F PHE* 3.5 38.0 - - + -
172F ASN 2.8 15.8 + - - +
173F VAL* 1.3 71.1 - - - +
175F VAL* 1.3 68.6 + - + +
176F ASP 3.2 0.2 - - - -
177F PHE* 3.4 5.3 + - - +
178F ALA* 3.1 23.9 + - - +
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Residues in contact with VAL 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F HIS* 3.8 19.5 + - + +
118F THR* 4.1 24.2 - - + -
173F VAL* 2.8 9.2 + - + +
174F LYS* 1.3 83.5 - - + +
176F ASP* 1.3 67.2 + - - +
178F ALA* 3.5 3.8 + - - +
179F LYS* 3.4 30.1 + - - +
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Residues in contact with ASP 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F TYR* 3.5 21.1 - - + -
173F VAL* 2.9 33.8 + - - +
175F VAL* 1.3 82.4 - - - +
177F PHE* 1.3 66.4 + - - +
179F LYS* 3.0 12.6 + - - +
180F ALA* 3.0 23.4 + - - +
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Residues in contact with PHE 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F HIS 5.0 0.7 - - - -
20F ILE* 4.2 26.2 - - + -
24F ILE* 6.2 0.4 - - + -
79F TRP* 4.0 14.8 - + - -
159F LEU* 3.5 21.5 - - + -
160F ASP 3.4 25.4 - - - -
161F MET* 4.0 11.2 - - + -
165F ALA* 3.6 20.2 - - + -
166F PHE* 3.5 33.4 - + + -
170F TYR* 3.7 37.6 - + + -
173F VAL 3.6 1.6 + - - -
174F LYS 3.4 7.1 + - - +
175F VAL 3.4 0.4 - - - -
176F ASP* 1.3 79.6 - - - +
178F ALA* 1.3 64.3 + - - +
180F ALA* 3.4 1.6 + - + +
181F PHE* 3.2 23.5 + - + +
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Residues in contact with ALA 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F HIS* 3.7 24.6 - - + -
117F ALA* 5.1 1.8 - - + -
118F THR* 3.8 12.8 - - + -
159F LEU* 4.2 21.0 - - + +
161F MET* 4.6 7.6 - - + -
174F LYS 3.1 14.1 + - - +
175F VAL 3.7 3.4 - - - +
176F ASP 3.1 0.8 - - - -
177F PHE* 1.3 85.2 - - - +
179F LYS* 1.3 58.6 + - - +
181F PHE* 3.8 8.8 - - - +
182F TRP* 3.6 18.9 + - - -
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Residues in contact with LYS 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F ARG* 5.3 0.2 + - - -
114F HIS* 4.0 29.7 + - + +
175F VAL* 3.4 21.1 + - + +
176F ASP* 3.0 15.7 + - - +
178F ALA* 1.3 76.6 - - - +
180F ALA* 1.3 65.9 + - - +
181F PHE 3.1 2.3 + - - -
182F TRP* 3.3 25.8 + - + +
183F ASN* 4.5 4.3 + - - +
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Residues in contact with ALA 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F HIS* 4.0 24.1 - - + +
20F ILE* 5.9 0.7 - - + -
170F TYR* 3.2 28.3 - - + +
176F ASP 3.0 13.0 + - - +
177F PHE* 3.6 5.6 - - + +
179F LYS* 1.3 77.2 - - - +
181F PHE* 1.3 63.2 + - - +
183F ASN* 3.0 31.1 + - - +
184F VAL 4.0 0.7 + - - -
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Residues in contact with PHE 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ILE* 5.7 4.9 - - + +
79F TRP* 3.9 22.9 - + - -
82F ASN* 5.2 0.9 - - + -
83F LEU* 4.0 18.8 - - + -
113F PHE* 4.2 8.7 - + - -
157F LEU* 3.9 17.0 - - + -
158F LEU 3.8 23.6 - - - -
159F LEU* 3.7 33.2 - - + -
177F PHE* 3.2 19.5 + - + +
178F ALA 3.8 6.7 - - - +
180F ALA* 1.3 76.8 - - - +
182F TRP* 1.3 80.4 + + - +
184F VAL* 2.8 28.9 + - + +
185F VAL* 3.3 33.2 + - + +
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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