Contacts of the helix formed by residues 166 - 171 (chain F) 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 PHE 166 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ILE* 4.0 10.5 - - - -
161F MET* 3.6 24.5 - - + -
162F TRP 3.2 21.8 - - - -
163F GLU* 3.1 17.2 + - + -
164F HIS 3.3 1.6 + - - -
165F ALA* 1.3 81.1 - - + +
167F TYR* 1.3 80.3 + + - +
168F LEU 3.3 2.7 - - - -
169F GLN* 3.1 3.5 + - - -
170F TYR* 2.8 31.4 + - + -
171F LYS 3.5 21.7 + - - -
172F ASN* 5.0 2.0 - - - -
174F LYS* 3.5 35.0 - - + -
177F PHE* 3.5 41.7 - + + -
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Residues in contact with TYR 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E ILE* 6.3 0.4 - - + -
27E LEU* 3.7 20.8 - - + +
32E HIS* 2.5 44.3 + + - -
163E GLU 6.3 0.2 - - - -
164E HIS* 4.0 25.4 + - + +
167E TYR* 5.0 13.7 - - + -
168E LEU* 4.0 36.3 - - + +
163F GLU* 2.9 30.1 + - + +
164F HIS 4.6 1.0 - - - -
166F PHE* 1.3 85.9 - + - +
168F LEU* 1.3 59.9 + - - +
171F LYS* 2.8 61.3 + - - +
172F ASN* 3.7 4.8 + - - +
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Residues in contact with LEU 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E TYR* 4.1 24.0 - - + +
168E LEU* 3.8 42.3 - - + +
171E LYS* 4.5 8.7 - - + -
21F SER* 5.7 0.9 - - - +
23F GLN* 3.9 26.5 - - + +
24F ILE* 4.2 21.4 - - + +
27F LEU* 3.7 29.8 - - + -
164F HIS 5.8 0.4 + - - -
166F PHE 3.3 1.2 - - - -
167F TYR* 1.3 78.3 - - - +
169F GLN* 1.3 59.5 + - + +
171F LYS* 3.8 13.7 + - - -
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Residues in contact with GLN 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F PRO 3.0 22.3 + - - -
19F HIS 3.3 2.6 + - - -
20F ILE* 3.7 1.9 - - - -
21F SER* 2.8 38.8 + - - -
24F ILE* 3.8 13.8 - - + +
166F PHE 3.1 3.2 + - - -
168F LEU* 1.3 80.5 - - - +
170F TYR* 1.3 104.4 + - + +
171F LYS* 3.4 15.1 + - - +
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Residues in contact with TYR 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F PRO 4.3 0.2 + - - -
19F HIS* 2.8 25.7 + - - -
20F ILE* 5.4 0.4 - - - -
24F ILE* 5.7 1.1 - - + -
166F PHE* 2.8 24.2 + - + +
169F GLN* 1.3 106.6 + - + +
171F LYS* 1.3 72.9 + - - +
173F VAL* 3.0 33.9 + - + +
176F ASP* 3.5 33.7 - - + -
177F PHE* 3.7 35.4 - + + -
180F ALA* 3.2 15.2 - - + +
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Residues in contact with LYS 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E GLN* 4.3 21.6 - - - +
27E LEU* 3.8 27.4 - - + -
168E LEU* 4.5 8.1 - - + -
166F PHE* 3.5 13.4 + - - -
167F TYR* 2.8 47.1 + - + +
168F LEU 3.8 19.9 + - - -
169F GLN 3.4 14.8 + - - -
170F TYR* 1.3 80.3 - - - +
172F ASN* 1.3 70.0 + - - +
173F VAL* 3.4 1.1 + - + -
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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