Contacts of the helix formed by residues 173 - 181 (chain D) in PDB entry 1GN6
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D TYR* 3.0 28.3 + - + +
171D LYS* 4.6 1.6 - - + -
172D ASN* 1.3 90.0 - - - +
174D LYS* 1.3 62.9 + - - +
175D VAL* 3.2 9.8 + - + -
176D ASP* 3.3 41.2 + - + +
177D PHE 3.6 6.4 + - - -
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Residues in contact with LYS 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ALA 5.3 0.8 + - - -
118D THR* 3.2 31.6 + - - -
120D VAL* 3.8 20.0 + - - +
122D GLY 5.8 0.8 + - - -
161D MET* 3.8 20.4 - - + +
166D PHE* 3.6 35.7 - - + -
172D ASN 2.8 14.1 + - - +
173D VAL* 1.3 71.5 - - - +
175D VAL* 1.3 66.2 + - + +
177D PHE* 3.2 4.8 + - - +
178D ALA* 2.9 28.3 + - - +
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Residues in contact with VAL 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D HIS* 3.9 13.2 - - + +
118D THR* 4.0 27.4 - - + +
173D VAL* 3.2 11.0 - - + -
174D LYS* 1.3 82.1 - - + +
176D ASP* 1.3 72.1 + - - +
178D ALA* 3.3 1.9 + - - +
179D LYS* 2.8 38.4 + - + +
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Residues in contact with ASP 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D TYR* 3.7 23.4 - - + -
173D VAL* 3.3 25.5 + - + +
174D LYS 3.3 0.6 - - - -
175D VAL* 1.3 86.2 - - - +
177D PHE* 1.3 57.0 + - - +
179D LYS* 3.1 11.4 + - - +
180D ALA* 2.9 28.9 + - - +
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Residues in contact with PHE 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D HIS 5.1 0.7 - - - -
20D ILE* 4.2 25.1 - - + -
79D TRP* 4.2 11.7 - + - -
159D LEU* 3.8 22.2 - - + -
160D ASP 3.4 25.6 - - - -
161D MET* 3.8 10.8 - - - -
165D ALA* 3.9 20.6 - - + -
166D PHE* 3.4 33.9 - + + -
170D TYR* 3.7 35.8 - + + -
173D VAL 3.6 2.5 + - - +
174D LYS 3.2 10.7 + - - +
175D VAL 3.2 0.4 - - - -
176D ASP* 1.3 76.9 - - - +
178D ALA* 1.3 65.8 + - - +
180D ALA* 3.2 2.6 + - + +
181D PHE* 3.2 24.8 + - + +
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Residues in contact with ALA 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D HIS* 3.8 23.5 + - + +
117D ALA* 4.8 1.8 - - + -
118D THR* 3.9 12.6 - - + -
159D LEU* 4.2 22.4 - - + +
161D MET* 4.6 5.8 - - - -
174D LYS 2.9 16.6 + - - +
175D VAL 3.3 2.7 + - - +
177D PHE* 1.3 81.1 - - - +
179D LYS* 1.3 62.1 + - - +
181D PHE* 3.7 9.9 - - - +
182D TRP* 3.7 17.7 + - - -
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Residues in contact with LYS 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D HIS* 4.1 19.1 - - + +
175D VAL* 2.8 24.6 + - + +
176D ASP* 3.7 11.2 - - - +
177D PHE 3.1 0.4 - - - -
178D ALA* 1.3 77.7 - - - +
180D ALA* 1.3 64.0 + - - +
181D PHE 3.2 1.1 + - - -
182D TRP* 3.4 23.1 + - + +
183D ASN* 4.2 4.4 + - - -
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Residues in contact with ALA 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D HIS* 4.0 23.2 - - + +
20D ILE* 5.9 1.1 - - + -
170D TYR* 3.2 28.0 - - + +
176D ASP 2.9 13.5 + - - +
177D PHE* 3.2 7.4 + - + +
179D LYS* 1.3 75.9 - - - +
181D PHE* 1.3 63.6 + - - +
183D ASN* 3.0 32.3 + - - +
184D VAL* 4.0 1.7 + - - +
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Residues in contact with PHE 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ILE* 5.7 4.9 - - + +
79D TRP* 3.7 26.9 - + - -
82D ASN* 5.4 1.3 - - + -
83D LEU* 4.0 18.2 - - + -
113D PHE* 3.9 20.0 - + - -
157D LEU* 3.9 20.6 - - + -
158D LEU 3.9 9.0 - - - -
159D LEU* 3.8 31.4 - - + -
177D PHE* 3.2 15.1 + - + +
178D ALA 3.7 10.5 - - - +
179D LYS 3.2 0.2 - - - -
180D ALA* 1.3 76.9 - - - +
182D TRP* 1.3 86.2 + + - +
183D ASN 2.9 1.0 + - - -
184D VAL* 3.0 22.3 + - + +
185D VAL* 3.3 31.0 - - + +
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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