Contacts of the helix formed by residues 162 - 165 (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 TRP 162 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C GLY* 3.6 32.8 - - - -
163C GLU* 3.9 15.5 - - - -
36D TYR* 3.8 15.3 - - - -
68D PHE* 4.1 11.7 - + - -
123D SER* 3.3 29.0 - - - +
124D GLY 3.5 19.5 - - - -
125D TRP* 4.0 5.4 - - - -
144D ASP* 3.0 30.1 + - - -
145D HIS* 3.4 28.3 - + - -
160D ASP* 3.1 18.0 + - - +
161D MET* 1.3 79.6 - - - +
163D GLU* 1.3 66.4 + - - +
164D HIS* 3.5 32.3 - + + +
165D ALA* 2.8 20.1 + - - +
166D PHE* 3.6 3.2 - - - -
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Residues in contact with GLU 163 (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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32C HIS* 3.9 8.5 - - - -
123C SER* 5.2 1.3 + - - -
162C TRP* 3.8 19.8 - - - -
163C GLU* 3.4 25.0 + - + +
164C HIS* 2.8 56.4 + - - +
123D SER* 5.4 1.8 + - - +
161D MET 3.5 1.9 + - - +
162D TRP* 1.3 70.0 - - - +
164D HIS* 1.3 59.3 + - - +
165D ALA 2.9 0.9 + - - -
166D PHE* 3.0 21.5 + - + -
167D TYR* 2.8 44.5 + - + +
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Residues in contact with HIS 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C GLU* 2.8 37.8 + - - +
167C TYR* 3.6 39.6 + - + -
24D ILE* 3.9 14.9 - - - +
28D HIS* 3.2 21.7 + + - +
32D HIS* 3.6 25.9 + + + +
36D TYR* 4.3 9.4 - - - -
76D HIS* 4.7 0.4 - - - -
160D ASP* 3.5 0.8 + - - -
162D TRP* 3.5 28.8 - + + +
163D GLU* 1.3 71.9 - - - +
165D ALA* 1.3 65.2 + - + +
166D PHE 3.3 0.7 + - - -
167D TYR 4.5 2.2 + - - +
168D LEU 5.6 0.5 + - - -
999D FE 2.1 32.2 - - - -
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Residues in contact with ALA 165 (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* 5.0 2.9 - - - +
24D ILE* 3.5 19.7 - - - +
28D HIS* 4.3 9.1 + - + -
79D TRP* 5.3 1.9 - - + -
160D ASP* 3.5 43.1 - - + +
162D TRP 2.8 15.8 + - - +
164D HIS* 1.3 83.7 - - - +
166D PHE* 1.3 60.3 + - + +
177D PHE* 3.9 18.5 - - + -
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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