Contacts of the helix formed by residues 173 - 181 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170H TYR* 3.0 23.7 + - + +
171H LYS* 5.4 1.1 - - + -
172H ASN* 1.3 88.7 - - - +
174H LYS* 1.3 60.2 + - - +
175H VAL* 2.8 14.9 + - + +
176H ASP* 2.9 48.9 + - + +
177H PHE 3.6 2.1 + - - -
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Residues in contact with LYS 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H ALA 4.9 1.8 - - - -
118H THR* 3.0 39.4 + - + +
119H THR* 5.1 0.2 - - - +
120H VAL* 4.3 14.5 + - - +
161H MET* 3.8 16.6 - - + +
166H PHE* 3.5 38.9 - - + -
172H ASN 2.8 15.1 + - - +
173H VAL* 1.3 69.8 - - - +
175H VAL* 1.3 69.0 + - + +
176H ASP 3.2 0.2 - - - -
177H PHE* 3.4 4.9 + - - +
178H ALA* 3.1 23.2 + - - +
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Residues in contact with VAL 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H HIS* 3.8 20.0 + - + +
118H THR* 4.1 24.2 - - + -
173H VAL* 2.8 9.0 + - + +
174H LYS* 1.3 82.1 - - + +
176H ASP* 1.3 68.3 + - - +
178H ALA* 3.5 3.6 + - - +
179H LYS* 3.4 30.1 + - - +
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Residues in contact with ASP 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H TYR* 3.5 20.8 - - + -
173H VAL* 2.9 33.4 + - + +
175H VAL* 1.3 81.8 - - - +
177H PHE* 1.3 66.1 + - - +
179H LYS* 3.0 12.3 + - - +
180H ALA* 3.0 22.7 + - - +
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Residues in contact with PHE 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H HIS 5.0 0.4 - - - -
20H ILE* 4.2 25.8 - - + -
24H ILE* 6.2 0.4 - - + -
79H TRP* 4.0 15.3 - + - -
159H LEU* 3.5 21.8 - - + -
160H ASP 3.4 25.4 - - - -
161H MET* 4.0 11.2 - - + -
165H ALA* 3.6 19.5 - - + -
166H PHE* 3.5 31.9 - + + -
170H TYR* 3.7 36.9 - + + -
173H VAL 3.6 1.6 + - - -
174H LYS 3.4 6.6 + - - +
175H VAL 3.4 0.4 - - - -
176H ASP* 1.3 80.0 - - - +
178H ALA* 1.3 64.4 - - - +
180H ALA* 3.4 2.1 + - + +
181H PHE* 3.2 23.3 + - + +
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Residues in contact with ALA 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H HIS* 3.7 24.7 - - + -
117H ALA* 5.1 1.8 - - + -
118H THR* 3.8 12.1 - - + -
159H LEU* 4.2 21.4 - - + +
161H MET* 4.6 7.6 - - + -
174H LYS 3.1 15.2 + - - +
175H VAL 3.7 3.1 - - - +
176H ASP 3.1 0.8 - - - -
177H PHE* 1.3 84.8 - - - +
179H LYS* 1.3 58.1 + - - +
181H PHE* 3.8 8.3 - - - +
182H TRP* 3.6 18.9 + - - -
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Residues in contact with LYS 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H ARG* 5.3 0.3 + - - -
114H HIS* 4.0 29.5 + - + +
175H VAL* 3.4 20.9 + - + +
176H ASP* 3.0 15.5 + - - +
178H ALA* 1.3 77.1 - - - +
180H ALA* 1.3 66.5 + - - +
181H PHE 3.1 2.9 + - - -
182H TRP* 3.3 26.1 + - + +
183H ASN* 4.5 3.8 + - - +
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Residues in contact with ALA 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H HIS* 4.0 24.7 - - + +
20H ILE* 5.9 0.7 - - + -
170H TYR* 3.2 27.1 - - + +
176H ASP 3.0 13.2 + - - +
177H PHE* 3.6 6.5 - - + +
179H LYS* 1.3 76.5 - - - +
181H PHE* 1.3 62.9 + - - +
183H ASN* 3.0 31.8 + - - +
184H VAL 4.0 0.5 + - - -
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Residues in contact with PHE 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H ILE* 5.7 3.6 - - - +
79H TRP* 3.9 23.3 - + - -
82H ASN* 5.2 0.9 - - + -
83H LEU* 4.0 18.6 - - + -
113H PHE* 4.2 9.0 - + - -
157H LEU* 3.9 16.8 - - + -
158H LEU 3.8 23.8 - - - -
159H LEU* 3.7 32.3 - - + -
177H PHE* 3.2 19.5 + - + +
178H ALA 3.8 7.2 - - - +
179H LYS 3.1 0.4 - - - -
180H ALA* 1.3 76.1 - - - +
182H TRP* 1.3 80.5 + + - +
184H VAL* 2.8 28.8 + - + +
185H VAL* 3.3 32.8 + - + +
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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
------------------------------------------------------------
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