Contacts of the helix formed by residues 82 - 87 (chain W) in PDB entry 6FF7
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 GLY 82 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80W GLY 3.7 0.8 - - - -
81W GLU* 1.3 77.3 - - - +
83W LEU* 1.3 64.8 + - - +
84W ASP 3.3 2.7 - - - -
85W GLN* 3.0 26.8 + - - +
86W ALA* 3.6 5.8 + - - +
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Residues in contact with LEU 83 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57W LEU 5.8 2.7 - - - +
80W GLY* 4.3 14.1 + - - +
81W GLU 3.4 4.4 + - - -
82W GLY* 1.3 75.5 - - - +
84W ASP* 1.3 57.6 + - - +
86W ALA* 3.2 6.0 + - - +
87W LEU* 2.9 34.0 + - + +
108W PRO 5.3 7.9 - - - +
111W SER* 6.5 0.2 - - - -
112W LEU* 5.8 7.0 - - + -
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Residues in contact with ASP 84 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81W GLU 5.2 0.4 + - - -
82W GLY 3.2 1.4 + - - -
83W LEU* 1.3 77.1 - - - +
85W GLN* 1.3 59.6 + - - +
87W LEU 3.9 9.0 - - - +
88W PRO* 3.3 27.0 - - + +
111W SER* 3.0 39.5 - - - +
112W LEU* 4.4 6.9 - - - +
113W LYS* 5.0 1.8 - - + +
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Residues in contact with GLN 85 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62W LEU* 4.7 8.3 - - - +
82W GLY* 3.0 16.0 + - - +
84W ASP* 1.3 77.6 - - - +
86W ALA* 1.3 59.2 + - - +
88W PRO* 5.2 0.4 - - - -
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Residues in contact with ALA 86 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60W PHE* 3.4 22.4 - - + +
61W PRO 3.1 24.5 - - - +
62W LEU* 4.0 5.6 - - + +
63W LEU 2.8 29.6 + - - +
82W GLY 3.6 5.7 + - - +
83W LEU* 3.2 8.1 + - - +
85W GLN* 1.3 79.1 - - - +
87W LEU* 1.3 59.1 + - + +
88W PRO 4.0 1.3 - - - -
49m ARG 3.4 4.4 - - - -
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Residues in contact with LEU 87 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60W PHE* 5.8 2.5 - - + -
63W LEU 4.1 8.7 - - - +
66W LEU* 5.3 7.4 - - + +
83W LEU* 2.9 18.2 + - + +
84W ASP* 3.6 8.2 - - - +
86W ALA* 1.3 80.3 - - + +
88W PRO* 1.3 61.5 - - - +
89W ASP 3.4 3.2 + - - -
90W LEU* 3.5 26.1 + - + +
112W LEU* 5.6 2.8 - - - +
49m ARG 5.5 1.1 - - - -
63m GLU* 5.4 12.1 - - + +
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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