Contacts of the helix formed by residues 166 - 171 (chain A) 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 PHE 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 4.2 7.9 - - - -
161A MET* 3.7 19.7 - - + -
162A TRP 3.6 18.8 - - - -
163A GLU* 3.8 18.4 - - + -
164A HIS 3.3 0.6 - - - -
165A ALA* 1.3 81.2 - - + +
167A TYR* 1.3 69.7 + + - +
168A LEU 3.4 2.5 - - - -
169A GLN* 3.1 4.9 + - - +
170A TYR* 2.8 36.2 + - + -
171A LYS 3.3 25.4 + - - -
172A ASN* 4.8 2.5 - - - -
174A LYS* 3.6 39.9 - - + -
177A PHE* 3.4 46.0 - + + -
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Residues in contact with TYR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLU* 2.8 35.9 + - + +
164A HIS 4.5 1.4 - - - -
166A PHE* 1.3 77.2 - + - +
168A LEU* 1.3 58.8 + - - +
171A LYS* 2.8 62.8 + - + +
172A ASN* 3.9 4.4 + - - +
24B ILE* 6.2 0.7 - - + -
27B LEU* 4.0 15.3 - - + +
32B HIS* 2.8 33.5 + + - -
164B HIS* 3.4 39.9 + - + +
167B TYR* 4.4 22.7 - - + -
168B LEU* 3.9 29.4 - - + +
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Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER* 5.6 0.2 - - - +
23A GLN* 3.8 32.3 - - + +
24A ILE* 4.0 19.2 - - + +
27A LEU* 3.8 30.1 - - + -
164A HIS 5.6 0.4 + - - -
166A PHE 3.2 1.2 + - - -
167A TYR* 1.3 75.7 - - - +
169A GLN* 1.3 58.5 + - - +
171A LYS* 3.0 22.3 + - - -
167B TYR* 3.8 28.1 - - + +
168B LEU* 3.9 20.2 - - + +
171B LYS* 3.6 25.4 - - + +
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Residues in contact with GLN 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PRO 3.0 27.9 + - - -
19A HIS 3.1 9.5 + - - -
20A ILE* 3.5 3.3 - - - -
21A SER* 2.7 38.6 + - - +
24A ILE* 3.6 17.7 - - + +
166A PHE 3.1 1.2 + - - -
168A LEU* 1.3 80.3 - - - +
170A TYR* 1.3 90.0 + - + +
171A LYS* 3.5 11.5 + - - +
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Residues in contact with TYR 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PRO 4.1 1.0 + - - -
19A HIS* 2.7 26.3 + - - -
20A ILE* 5.3 0.4 - - - -
24A ILE* 5.9 0.4 - - + -
166A PHE* 2.8 17.2 + - + +
169A GLN* 1.3 108.2 + - + +
171A LYS* 1.3 75.8 - - - +
173A VAL* 3.0 33.7 + - + +
176A ASP* 3.7 35.0 - - + -
177A PHE* 3.7 36.8 - + + -
180A ALA* 3.2 16.8 - - + +
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Residues in contact with LYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A PHE* 3.3 24.2 + - - -
167A TYR* 2.8 36.1 + - + +
168A LEU 3.0 29.0 + - - -
169A GLN 3.5 9.8 + - - +
170A TYR* 1.3 82.2 - - - +
172A ASN* 1.3 71.9 + - - +
173A VAL* 3.4 1.1 + - + -
23B GLN* 4.5 10.1 + - - +
27B LEU* 3.5 28.3 - - + -
168B LEU* 3.6 21.5 - - + +
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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
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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