Contacts of the helix formed by residues 83 - 94 (chain B) in PDB entry 2W5X
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 ASP 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A TYR* 5.0 5.4 - - + -
82B THR* 1.3 90.7 + - - +
84B SEP 1.3 71.9 + - - +
85B ALA 3.5 2.7 + - - -
86B SER* 3.0 27.4 + - - -
87B GLY* 3.1 10.0 + - - -
99B ASN* 3.1 19.7 + - + +
100B ALA* 3.1 30.9 + - - +
148B ARG* 2.9 22.3 + - - +
302B HIS* 4.3 5.2 - - - -
337B HIS* 3.8 7.9 - - + -
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Residues in contact with SEP 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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43B ASP* 3.1 8.4 + - - +
83B ASP* 1.3 74.2 - - - +
85B ALA* 1.3 60.5 + - - -
87B GLY 3.9 0.4 - - - -
88B ALA* 3.0 31.9 + - - +
135B GLU* 3.7 11.3 + - - -
136B ALA* 4.0 15.2 - - - +
137B THR* 4.2 3.9 + - - -
148B ARG* 2.8 35.9 + - - -
259B ASP* 2.6 10.9 + - - -
260B TRP* 5.2 2.6 + - - -
301B ASP* 3.3 12.8 - - - +
337B HIS* 3.0 13.3 + - - -
1377B ZN 2.0 42.3 - - - -
1378B ZN 2.1 39.2 - - - -
1379B MG 4.4 0.7 - - - -
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Residues in contact with ALA 85 (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 ASP* 3.2 6.2 + - - +
84B SEP 1.3 76.6 + - - +
86B SER* 1.3 60.6 + - - +
88B ALA 3.3 0.7 + - - -
89B THR* 2.9 33.3 + - - -
100B ALA* 3.5 26.7 - - - +
101B ALA 3.1 19.7 - - - +
102B ILE* 3.7 16.2 - - + -
136B ALA* 3.9 13.3 - - + +
140B SER* 3.5 2.8 + - - -
148B ARG* 4.1 2.5 - - + -
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Residues in contact with SER 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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76B SER* 3.7 4.3 - - - -
82B THR* 2.8 18.6 + - - -
83B ASP* 3.0 5.3 + - - -
85B ALA* 1.3 78.5 - - - +
87B GLY* 1.3 56.1 + - - +
89B THR* 3.4 1.0 + - - -
90B ALA* 3.0 28.2 + - - +
95B ILE 4.9 0.5 - - - +
96B LYS* 6.0 0.2 - - - -
97B THR* 3.5 33.2 + - - +
98B TYR 3.3 24.7 - - - -
99B ASN* 2.8 22.2 + - - -
100B ALA 4.3 0.2 - - - +
101B ALA 3.7 0.4 + - - -
360B ASN* 4.9 0.6 + - - -
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Residues in contact with GLY 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B THR* 3.8 7.4 - - - -
83B ASP 3.1 14.1 + - - -
84B SEP 4.1 0.7 - - - -
86B SER* 1.3 84.6 + - - +
88B ALA* 1.3 59.3 + - - +
90B ALA* 3.5 14.4 - - - +
91B PHE* 3.7 18.2 + - - -
301B ASP* 4.4 18.4 - - - -
360B ASN* 4.2 12.4 + - - -
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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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84B SEP 3.0 20.6 + - - +
87B GLY* 1.3 74.6 - - - +
89B THR* 1.3 60.4 + - - +
90B ALA 3.2 0.2 - - - -
91B PHE* 3.2 14.6 + - + +
92B SER* 2.9 28.2 + - - -
137B THR* 3.9 28.7 - - + +
140B SER* 3.7 21.2 - - - +
141B PHE* 4.1 4.6 - - + -
301B ASP* 4.6 3.5 - - + +
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Residues in contact with THR 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 ALA 2.9 19.7 + - - -
86B SER 3.4 4.2 + - - -
88B ALA* 1.3 73.6 - - - +
90B ALA* 1.3 61.5 + - - +
92B SER* 3.4 7.2 - - - -
93B CYS* 2.8 36.4 + - + +
94B GLY 3.4 4.0 + - - -
95B ILE* 4.1 8.1 - - + +
97B THR* 3.9 21.8 - - + -
101B ALA 3.3 4.5 + - - -
103B GLY* 2.9 39.1 + - - +
104B VAL 4.2 6.7 - - - +
140B SER* 3.3 6.3 + - - -
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Residues in contact with ALA 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 SER 3.0 12.6 + - - +
87B GLY 3.5 12.1 - - - +
88B ALA 3.2 0.4 - - - -
89B THR* 1.3 76.3 - - - +
91B PHE* 1.3 57.4 + - - +
94B GLY* 2.8 28.4 + - - -
95B ILE 3.4 17.9 + - - +
96B LYS* 5.5 1.6 - - + -
360B ASN* 3.5 35.2 - - + +
361B ASN* 3.4 17.5 - - - +
364B PHE* 3.8 0.2 - - - +
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Residues in contact with PHE 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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39B LEU* 4.5 8.9 - - + +
41B ILE* 3.7 27.1 - - + -
72B ILE* 3.6 20.2 - - + -
87B GLY 3.7 15.0 - - - -
88B ALA* 3.2 9.5 + - - +
90B ALA* 1.3 77.7 - - - +
92B SER* 1.3 61.4 + - - +
114B ILE* 4.8 2.9 - - - +
141B PHE* 4.0 14.0 - - + -
299B THR* 3.9 15.7 - - + -
300B SER 3.4 27.1 - - - -
301B ASP* 4.0 13.7 - - + -
360B ASN* 3.5 29.8 - - + -
363B ILE* 3.8 23.7 - - + +
364B PHE* 3.3 21.5 + - - +
367B ILE* 5.3 3.3 - - - +
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Residues in contact with SER 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ALA 2.9 17.7 + - - -
89B THR* 3.4 9.4 - - - -
91B PHE* 1.3 77.5 - - - +
93B CYS* 1.3 65.4 + - - +
113B SER* 3.3 4.0 - - - -
114B ILE* 2.8 33.1 + - - -
140B SER 2.7 28.7 + - - -
141B PHE* 3.7 31.9 - - - -
364B PHE* 3.3 4.7 - - - -
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Residues in contact with CYS 93 (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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89B THR* 2.8 14.9 + - + +
92B SER* 1.3 90.7 - - - +
94B GLY* 1.3 64.3 + - - +
95B ILE* 3.5 9.1 + - + +
103B GLY* 3.9 17.9 - - - -
111B VAL* 3.6 40.4 - - + +
112B LYS 4.0 8.0 - - - +
113B SER* 3.8 18.4 - - - -
140B SER 4.5 0.9 - - - -
144B HIS* 5.1 0.4 - - - -
364B PHE* 3.6 20.5 - - - -
365B HIS* 5.0 0.5 + - - -
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Residues in contact with GLY 94 (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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89B THR 3.4 0.6 + - - -
90B ALA 2.8 18.8 + - - -
93B CYS* 1.3 78.7 - - - +
95B ILE* 1.3 63.2 + - - +
361B ASN* 3.1 22.1 + - - -
364B PHE* 3.3 23.8 - - - -
365B HIS* 2.9 20.0 + - - -
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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