Contacts of the helix formed by residues 173 - 181 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170G TYR* 3.0 22.6 + - + +
171G LYS* 5.4 0.9 - - + -
172G ASN* 1.3 87.4 - - - +
174G LYS* 1.3 60.8 + - - +
175G VAL* 2.8 14.6 + - + +
176G ASP* 2.9 48.6 + - + +
177G PHE 3.6 1.9 + - - -
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Residues in contact with LYS 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G ALA 4.9 1.6 - - - -
118G THR* 3.0 39.9 + - + +
119G THR* 5.1 0.4 - - - +
120G VAL* 4.3 14.3 + - - +
161G MET* 3.8 16.9 - - + +
166G PHE* 3.5 39.0 - - + -
172G ASN 2.8 14.5 + - - +
173G VAL* 1.3 70.2 - - - +
175G VAL* 1.3 68.5 + - + +
177G PHE* 3.4 5.7 + - - +
178G ALA* 3.1 23.2 + - - +
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Residues in contact with VAL 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114G HIS* 3.8 19.9 + - + +
118G THR* 4.1 23.8 - - + -
173G VAL* 2.8 9.2 + - + +
174G LYS* 1.3 82.7 - - + +
176G ASP* 1.3 68.7 + - - +
178G ALA* 3.5 4.2 + - - +
179G LYS* 3.4 29.7 + - - +
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Residues in contact with ASP 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170G TYR* 3.5 21.7 - - + -
173G VAL* 2.9 34.1 + - - +
175G VAL* 1.3 82.3 - - - +
177G PHE* 1.3 66.1 + - - +
179G LYS* 3.0 13.4 + - - +
180G ALA* 3.0 22.7 + - - +
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Residues in contact with PHE 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G HIS 5.0 0.4 - - - -
20G ILE* 4.2 26.2 - - + -
24G ILE* 6.2 0.4 - - + -
79G TRP* 4.0 15.7 - + - -
159G LEU* 3.5 22.2 - - + -
160G ASP 3.4 25.8 - - - -
161G MET* 4.0 11.2 - - + -
165G ALA* 3.6 20.6 - - + -
166G PHE* 3.5 33.9 - + + -
170G TYR* 3.7 36.0 - + + -
173G VAL 3.6 1.6 + - - -
174G LYS 3.4 6.7 + - - +
175G VAL 3.4 0.6 - - - -
176G ASP* 1.3 79.8 - - - +
178G ALA* 1.3 64.1 + - - +
180G ALA* 3.4 2.6 + - + +
181G PHE* 3.2 23.9 + - + +
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Residues in contact with ALA 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G HIS* 3.7 24.0 - - + -
117G ALA* 5.1 1.6 - - + -
118G THR* 3.8 13.0 - - + -
159G LEU* 4.2 20.6 - - + +
161G MET* 4.6 7.6 - - + -
174G LYS 3.1 14.1 + - - +
175G VAL 3.7 3.6 - - - +
176G ASP 3.1 0.6 - - - -
177G PHE* 1.3 84.2 - - - +
179G LYS* 1.3 57.5 + - - +
181G PHE* 3.8 8.5 - - - +
182G TRP* 3.6 18.5 + - - -
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Residues in contact with LYS 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G ARG* 5.3 0.3 + - - -
114G HIS* 4.0 30.3 + - + +
175G VAL* 3.4 19.6 + - + +
176G ASP* 3.0 15.8 + - - +
178G ALA* 1.3 76.8 - - - +
180G ALA* 1.3 64.8 - - - +
181G PHE 3.1 2.9 + - - -
182G TRP* 3.3 25.9 + - + +
183G ASN* 4.5 4.0 + - - -
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Residues in contact with ALA 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G HIS* 4.0 24.6 - - + +
20G ILE* 5.9 0.7 - - + -
170G TYR* 3.2 27.4 - - + +
176G ASP 3.0 13.4 + - - +
177G PHE* 3.4 6.7 + - + +
179G LYS* 1.3 77.6 - - - +
181G PHE* 1.3 63.6 + - - +
183G ASN* 3.0 31.5 + - - +
184G VAL 4.0 0.5 + - - -
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Residues in contact with PHE 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ILE* 5.7 4.7 - - + +
79G TRP* 3.9 22.7 - + - -
82G ASN* 5.2 0.9 - - + -
83G LEU* 4.0 19.1 - - + -
113G PHE* 4.2 9.6 - + - -
157G LEU* 3.9 17.5 - - + -
158G LEU 3.8 24.0 - - - -
159G LEU* 3.7 31.2 - - + -
177G PHE* 3.2 19.3 + - + +
178G ALA 3.8 6.5 - - - +
179G LYS 3.1 0.4 - - - -
180G ALA* 1.3 77.2 - - - +
182G TRP* 1.3 81.6 + + - +
184G VAL* 2.8 28.8 + - + +
185G VAL* 3.3 32.5 + - + -
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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
------------------------------------------------------------
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