Contacts of the helix formed by residues 173 - 181 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C TYR* 3.0 22.9 + - + +
171C LYS* 5.4 0.9 - - + -
172C ASN* 1.3 88.5 - - - +
174C LYS* 1.3 61.3 + - - -
175C VAL* 2.8 14.7 + - + +
176C ASP* 2.9 49.1 + - + +
177C PHE 3.6 1.7 + - - -
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Residues in contact with LYS 174 (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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117C ALA 4.9 2.0 - - - -
118C THR* 3.0 38.8 + - + +
119C THR* 5.1 0.6 - - - +
120C VAL 4.3 14.7 + - - +
161C MET* 3.8 17.2 - - + +
166C PHE* 3.5 37.4 - - + -
172C ASN 2.8 15.1 + - - +
173C VAL* 1.3 69.7 - - - +
175C VAL* 1.3 68.0 + - + +
176C ASP 3.2 0.4 - - - -
177C PHE* 3.4 5.9 + - - +
178C ALA* 3.1 23.0 + - - +
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Residues in contact with VAL 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C HIS* 3.8 19.1 + - + +
118C THR* 4.1 25.4 - - + +
173C VAL* 2.8 8.5 + - + -
174C LYS* 1.3 82.6 - - + +
176C ASP* 1.3 67.2 + - - +
178C ALA* 3.5 4.0 + - - +
179C LYS* 3.4 29.7 + - - +
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Residues in contact with ASP 176 (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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170C TYR* 3.5 21.1 - - + -
173C VAL* 2.9 33.3 + - - +
175C VAL* 1.3 82.5 - - - +
177C PHE* 1.3 66.6 + - - +
179C LYS* 3.0 12.0 + - - +
180C ALA* 3.0 23.2 + - - +
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Residues in contact with PHE 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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19C HIS 5.0 0.7 - - - -
20C ILE* 4.2 26.7 - - + -
24C ILE* 6.2 0.7 - - + -
79C TRP* 4.0 15.3 - + - -
159C LEU* 3.5 21.5 - - + -
160C ASP 3.4 25.1 - - - -
161C MET* 4.0 10.3 - - + -
165C ALA* 3.6 20.6 - - + -
166C PHE* 3.5 33.9 - + + -
170C TYR* 3.7 36.9 - + + -
173C VAL 3.6 1.4 + - - -
174C LYS 3.4 7.1 + - - +
175C VAL 3.4 0.4 - - - -
176C ASP* 1.3 79.8 - - - +
178C ALA* 1.3 65.0 + - - +
180C ALA* 3.4 2.0 + - + +
181C PHE* 3.2 23.4 + - + +
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Residues in contact with ALA 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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114C HIS* 3.7 23.6 - - + -
117C ALA* 5.1 2.0 - - + -
118C THR* 3.8 13.2 - - + -
159C LEU* 4.2 21.1 - - + +
161C MET* 4.6 7.2 - - + -
174C LYS 3.1 14.7 + - - +
175C VAL 3.7 2.9 - - - +
176C ASP 3.1 0.8 - - - -
177C PHE* 1.3 84.8 - - - +
179C LYS* 1.3 58.8 + - - +
181C PHE* 3.8 8.0 - - - +
182C TRP* 3.6 18.5 + - - -
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Residues in contact with LYS 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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110C ARG* 5.3 0.2 + - - -
114C HIS* 4.0 30.7 + - + +
175C VAL* 3.4 19.8 + - + +
176C ASP* 3.0 15.0 + - - +
178C ALA* 1.3 76.8 - - - +
180C ALA* 1.3 65.3 + - - +
181C PHE 3.1 2.9 + - - -
182C TRP* 3.3 26.4 + - + +
183C ASN* 4.5 4.2 + - - +
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Residues in contact with ALA 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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19C HIS* 4.0 23.8 - - + +
20C ILE* 5.9 0.7 - - + -
170C TYR* 3.2 27.8 - - + +
176C ASP 3.0 13.4 + - - +
177C PHE* 3.6 7.0 - - + +
179C LYS* 1.3 77.0 - - - +
181C PHE* 1.3 63.6 + - - +
183C ASN* 3.0 30.7 + - - +
184C VAL* 4.0 0.9 + - - +
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Residues in contact with PHE 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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20C ILE* 5.7 4.3 - - + -
79C TRP* 3.9 23.1 - + - -
82C ASN* 5.2 0.9 - - + -
83C LEU* 4.0 18.4 - - + -
113C PHE* 4.2 8.7 - + - -
157C LEU* 3.9 17.0 - - + -
158C LEU 3.8 23.6 - - - -
159C LEU* 3.7 33.0 - - + -
177C PHE* 3.2 18.9 + - + +
178C ALA 3.8 7.0 - - - +
179C LYS 3.1 0.2 - - - -
180C ALA* 1.3 76.9 - - - +
182C TRP* 1.3 79.8 + + - +
184C VAL* 2.8 29.1 + - + +
185C 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