Contacts of the helix formed by residues 162 - 165 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C TYR* 3.8 15.3 - - - -
68C PHE* 4.1 11.4 - + - -
123C SER* 3.3 31.0 - - - +
124C GLY 3.5 19.7 - - - -
125C TRP* 4.0 5.2 - - - -
144C ASP* 3.0 29.3 + - - -
145C HIS* 3.4 29.4 - + - -
160C ASP* 3.1 17.6 + - - +
161C MET* 1.3 80.1 - - - +
163C GLU* 1.3 64.5 + - - +
164C HIS* 3.5 32.1 - + + +
165C ALA* 2.8 20.4 + - - +
166C PHE* 3.6 2.8 - - - -
122D GLY* 3.6 29.8 - - - -
163D GLU* 3.8 15.9 - - - -
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Residues in contact with GLU 163 (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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123C SER* 5.4 1.8 + - - +
161C MET 3.5 1.7 + - - +
162C TRP* 1.3 70.7 - - - +
164C HIS* 1.3 58.7 + - - +
165C ALA 2.9 1.4 + - - -
166C PHE* 3.0 21.7 + - + -
167C TYR* 2.8 45.6 + - + +
32D HIS* 3.9 9.4 + - - -
123D SER* 5.3 1.7 + - - -
162D TRP* 3.9 18.1 - - - -
163D GLU* 3.4 24.7 + - + +
164D HIS* 2.8 56.1 + - - +
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Residues in contact with HIS 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ILE* 3.9 14.9 - - - +
28C HIS* 3.2 22.8 + + - +
32C HIS* 3.6 24.7 + + + +
36C TYR* 4.3 10.1 - - - -
76C HIS* 4.7 0.4 - - - -
160C ASP* 3.5 1.0 + - - -
162C TRP* 3.5 27.9 - + + +
163C GLU* 1.3 71.8 - - - +
165C ALA* 1.3 66.2 + - + +
166C PHE 3.3 0.4 + - - -
167C TYR 4.5 1.9 + - - +
168C LEU 5.6 0.5 + - - -
999C FE 2.1 31.9 - - - -
163D GLU* 2.8 33.7 + - - +
167D TYR* 3.5 44.3 + - + -
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Residues in contact with ALA 165 (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* 5.0 2.9 - - - +
24C ILE* 3.5 19.5 - - - +
28C HIS* 4.3 8.9 + - + -
79C TRP* 5.3 2.4 - - + -
160C ASP* 3.5 43.5 - - + +
162C TRP 2.8 15.0 + - - +
164C HIS* 1.3 83.6 - - - +
166C PHE* 1.3 60.3 + - + +
177C PHE* 3.9 17.0 - - + -
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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