Contacts of the helix formed by residues 82 - 92 (chain B) in PDB entry 2W9M
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 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ALA* 3.9 13.2 - - + -
17B LEU* 3.6 28.7 - - + -
20B THR* 3.3 17.0 - - - -
37B TYR* 4.2 5.4 - + - -
72B GLU* 3.8 30.5 - - + -
73B LEU* 4.3 5.6 - - + -
76B PHE* 3.6 43.6 - + + -
81B THR* 1.3 72.7 - - - +
83B ALA* 1.3 67.7 + - - +
84B PRO* 3.1 30.1 - - + -
85B LEU* 3.1 39.4 + - + +
86B GLU* 3.1 17.7 + - - +
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLU* 4.8 12.3 + - + +
75B ASP* 5.0 10.4 + - + +
81B THR* 3.7 8.7 + - - -
82B PHE* 1.3 71.6 - - - +
84B PRO* 1.3 74.5 - - + +
86B GLU* 3.0 18.4 + - - +
87B ALA* 3.0 14.0 + - - +
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Residues in contact with PRO 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B THR* 4.3 11.7 - - + +
37B TYR* 4.0 18.2 - - + +
72B GLU* 4.0 19.1 - - + +
82B PHE* 3.1 37.2 - - + -
83B ALA* 1.3 93.5 - - + +
85B LEU* 1.3 59.4 + - - +
87B ALA* 3.6 3.0 + - + +
88B ALA* 3.2 19.1 + - - +
370B TYR* 3.3 35.2 - - + +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 5.6 3.1 - - - +
16B ALA* 3.4 31.2 - - + +
19B ARG* 4.3 18.2 - - + +
20B THR* 3.1 36.8 - - + +
23B LEU* 4.2 19.1 - - + -
82B PHE* 3.1 25.3 + - + +
84B PRO* 1.3 76.7 - - - +
86B GLU* 1.3 66.2 + - - +
88B ALA* 3.4 4.0 + - - +
89B ALA* 3.1 26.2 + - - +
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Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B GLY 5.2 0.2 - - - +
81B THR* 3.1 42.3 + - + +
82B PHE* 3.3 17.7 - - - +
83B ALA* 3.0 7.8 + - - +
85B LEU* 1.3 76.5 - - - +
87B ALA* 1.3 66.9 + - - +
89B ALA* 3.3 19.4 + - - +
90B GLY* 3.4 8.0 + - - -
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ALA 3.0 11.2 + - - +
84B PRO* 3.6 10.8 - - + +
86B GLU* 1.3 76.2 - - - +
88B ALA* 1.3 62.5 + - - +
90B GLY* 3.1 11.6 + - - -
91B GLN* 3.2 31.2 + - - +
370B TYR* 3.7 16.8 - - + -
428B HIS 4.4 1.7 - - - +
429B SER* 6.4 2.2 - - - +
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 3.6 31.9 - - + -
84B PRO 3.2 11.5 + - - +
85B LEU 3.7 7.2 - - - +
86B GLU 3.3 0.2 - - - -
87B ALA* 1.3 77.5 - - - +
89B ALA* 1.3 65.5 + - - +
91B GLN* 4.4 0.7 - - - +
92B LEU* 2.9 34.6 + - + +
97B LEU* 5.1 0.2 - - - -
370B TYR* 4.0 26.9 - - + -
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LEU 3.1 14.2 + - - +
86B GLU* 3.6 18.2 - - - +
87B ALA 3.3 0.4 - - - -
88B ALA* 1.3 75.7 - - - +
90B GLY* 1.3 60.2 + - - +
91B GLN 3.7 0.2 + - - -
92B LEU 4.3 2.9 - - - +
97B LEU* 3.6 31.9 - - + +
461B LEU* 5.0 0.9 - - - +
465B ARG* 2.9 17.9 + - - +
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Residues in contact with GLY 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLU 3.4 5.4 + - - -
87B ALA 3.1 6.9 + - - -
88B ALA 3.1 0.6 - - - -
89B ALA* 1.3 81.5 - - - +
91B GLN* 1.3 55.5 + - - +
92B LEU 4.8 1.9 - - - +
428B HIS* 3.2 38.3 + - - +
431B PHE* 4.1 14.0 - - - -
465B ARG* 3.2 15.2 + - - +
494B ARG* 5.8 1.0 + - - -
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ALA* 3.2 31.8 + - - +
88B ALA* 3.1 5.0 + - - +
90B GLY* 1.3 79.8 - - - +
92B LEU* 1.3 66.9 + - - +
93B PRO* 3.8 1.0 - - - +
339B ASP* 4.3 2.3 - - - +
364B HIS* 4.4 7.6 - - - -
367B ALA 3.9 12.3 + - - -
368B ALA* 3.1 15.2 - - + -
369B TYR* 2.9 8.7 + - - +
370B TYR* 2.8 37.5 + - + -
371B ALA* 4.0 21.3 - - + +
403B ASP* 5.4 0.6 + - - +
428B HIS* 3.4 35.1 + - + +
429B SER* 5.4 6.1 - - - -
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 3.5 41.1 - - + -
27B LEU* 4.1 10.5 - - + -
88B ALA* 2.9 24.2 + - + +
89B ALA 4.3 3.1 - - - +
90B GLY 3.8 1.4 - - - +
91B GLN* 1.3 80.7 - - - +
93B PRO* 1.3 75.1 - - + +
94B PRO* 3.7 2.4 - - - +
96B LEU* 3.6 23.8 - - + -
97B LEU* 3.8 32.0 - - + +
100B LEU* 4.4 1.6 - - + -
370B TYR* 3.2 29.2 - - + +
371B ALA* 4.5 2.7 - - - -
461B LEU* 5.4 2.1 - - - +
494B ARG* 4.7 6.5 + - - -
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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
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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