Contacts of the helix formed by residues 84 - 89 (chain D) in PDB entry 2WJZ
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 CYS 84 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D GLY 3.2 12.6 - - - +
51D VAL* 4.7 2.5 - - + -
83D VAL* 1.3 74.8 - - - +
85D LEU* 1.3 69.4 - - - +
86D GLY 3.0 0.7 - - - -
87D MET* 2.8 21.1 + - - +
88D GLN* 3.5 3.1 + - - +
140D VAL 5.9 0.7 - - - -
175D PHE 2.8 17.6 + - - -
176D GLN* 3.8 25.7 + - - +
177D PHE 3.6 13.7 - - - -
178D HIS* 3.1 50.5 - - + +
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Residues in contact with LEU 85 (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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10D PRO* 4.5 11.9 - - + -
50D GLY* 3.1 23.9 + - - +
51D VAL* 4.1 4.7 - - - +
52D GLY 3.7 29.4 - - - +
53D HIS 4.0 14.8 - - - +
54D PHE* 3.9 14.4 - - + +
56D GLU 4.1 9.4 - - - +
57D GLY* 5.0 1.1 - - - -
84D CYS* 1.3 78.8 - - - +
86D GLY* 1.3 62.7 + - - +
88D GLN* 2.9 39.0 + - - +
89D LEU* 3.1 41.0 + - + +
96D GLU* 4.3 0.4 - - - +
176D GLN* 4.8 0.2 - - - +
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Residues in contact with GLY 86 (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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48D ILE* 3.1 33.4 - - - +
49D PRO 3.8 10.3 + - - -
82D GLY* 3.7 9.5 - - - -
83D VAL 3.0 4.6 + - - -
84D CYS 3.0 1.8 - - - -
85D LEU* 1.3 77.8 - - - +
87D MET* 1.3 60.3 + - - +
89D LEU* 3.5 18.3 + - - +
90D LEU* 3.6 12.8 - - - +
103D LEU* 5.3 0.2 - - - +
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Residues in contact with MET 87 (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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82D GLY 3.6 18.6 - - - +
84D CYS 2.8 13.8 + - - +
86D GLY* 1.3 74.4 - - - +
88D GLN* 1.3 64.8 + - - +
90D LEU* 3.1 29.9 + - + +
91D PHE* 3.5 9.8 - - + -
145D ALA* 3.8 23.1 - - + -
164D PRO 3.4 26.7 - - - +
165D SER 4.3 0.4 - - - +
166D ALA 4.5 0.9 - - - +
167D VAL* 3.9 20.9 - - + -
174D GLY* 3.5 29.4 - - - +
175D PHE 3.9 3.8 - - - +
176D GLN* 3.6 29.6 - - - +
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Residues in contact with GLN 88 (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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54D PHE* 3.0 23.9 - - + -
84D CYS 4.2 3.1 - - - +
85D LEU* 2.9 32.2 + - - +
87D MET* 1.3 78.0 - - + +
89D LEU* 1.3 61.2 + - - +
91D PHE* 3.2 21.9 + - - +
94D SER* 4.9 0.3 + - - -
96D GLU* 4.5 5.4 - - - +
110D VAL* 3.7 31.9 - - + +
141D HIS* 4.9 3.4 - - - +
143D TYR* 2.8 41.7 + - - +
144D ARG 5.4 2.2 - - - -
145D ALA* 5.5 1.8 - - + +
176D GLN* 3.7 24.4 + - - +
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Residues in contact with LEU 89 (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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48D ILE* 4.7 4.9 - - + -
49D PRO 5.1 3.1 - - - +
54D PHE* 3.5 33.0 - - + +
57D GLY* 4.5 13.0 - - - -
58D MET* 3.8 16.6 - - + -
61D LEU* 4.3 20.0 - - + -
85D LEU* 3.1 40.5 + - + +
86D GLY* 3.6 16.8 - - - +
87D MET 3.1 0.2 - - - -
88D GLN* 1.3 72.8 - - - +
90D LEU* 1.3 57.5 + - - +
91D PHE 3.0 7.1 + - - +
103D LEU* 2.8 47.6 + - + +
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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