Contacts of the helix formed by residues 81 - 91 (chain B) in PDB entry 5VBL
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 THR 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77B THR 3.9 6.5 - - - +
78B PHE* 2.7 29.9 + - - -
80B VAL* 1.4 78.2 - - + +
82B LEU* 1.4 62.2 + - - +
83B PRO 3.5 0.7 - - - -
84B LEU* 3.3 27.0 + - + +
85B TRP* 3.2 21.3 + - - -
104B LEU* 6.0 2.2 - - + -
105B SER* 3.4 28.1 + - - +
108B LEU* 3.8 30.9 - - + +
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Residues in contact with LEU 82 (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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35B TYR* 3.7 41.8 - - + +
38B VAL* 3.8 29.2 - - + -
39B PHE* 4.4 1.3 - - + +
78B PHE* 3.5 23.3 + - + +
79B VAL* 3.2 31.0 + - + +
81B THR* 1.4 74.9 + - - +
83B PRO* 1.4 62.2 - - + +
85B TRP* 2.9 10.8 + - + +
86B ALA* 2.8 28.8 + - - +
299B TYR* 3.8 32.1 - - + +
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Residues in contact with PRO 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B MET* 3.7 29.5 - - + +
39B PHE* 3.7 35.2 - - + -
79B VAL 3.7 8.3 - - - +
80B VAL 3.2 17.0 - - - +
81B THR 3.6 0.7 - - - -
82B LEU* 1.4 90.1 - - + +
84B LEU* 1.4 58.2 + - + +
86B ALA* 3.5 3.1 + - + +
87B THR* 3.0 27.9 + - - -
97B PHE* 4.9 0.4 - - - -
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL 4.6 4.9 - - - +
81B THR* 3.4 31.2 - - + +
82B LEU 3.1 0.6 - - - -
83B PRO* 1.4 76.5 - - + +
85B TRP* 1.4 59.0 + - - +
87B THR 3.5 1.0 + - - -
88B TYR* 3.3 18.5 + - - +
95B TRP* 3.9 18.0 - - + -
97B PHE* 3.3 56.3 - - + -
101B PHE* 4.9 18.6 - - + -
105B SER* 4.0 13.0 - - - +
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Residues in contact with TRP 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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16A PRO 5.0 0.9 - - - -
17A 200 3.3 33.3 - + + +
35B TYR* 4.3 8.1 - - + -
78B PHE* 5.2 5.2 - + - -
81B THR* 3.2 28.3 + - - -
82B LEU* 2.9 14.8 + - + +
84B LEU* 1.4 75.6 - - - +
86B ALA* 1.4 54.0 + - - +
88B TYR* 3.4 32.7 + + - +
89B THR* 2.8 37.1 + - - -
95B TRP* 3.6 20.6 - + - -
105B SER* 2.8 28.8 + - - -
106B SER* 3.4 28.9 - - - -
109B ILE* 3.5 31.2 - - + +
168B ARG* 4.0 9.0 - - - -
181B CYS* 3.9 11.4 - - + -
299B TYR* 5.5 2.9 - + + -
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Residues in contact with ALA 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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32B PRO* 3.5 40.4 - - + +
35B TYR* 3.8 18.5 - - + -
36B MET* 4.2 9.6 - - + -
82B LEU 2.8 14.8 + - - +
83B PRO* 3.6 11.7 - - + +
85B TRP* 1.4 73.9 - - - +
87B THR* 1.4 61.7 + - - +
89B THR* 3.6 1.1 + - - -
90B TYR* 3.4 19.1 + - - +
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Residues in contact with THR 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 PRO 3.0 12.4 + - - -
84B LEU 3.6 9.2 - - - -
85B TRP 3.3 0.4 - - - -
86B ALA* 1.4 75.7 - - - +
88B TYR* 1.4 57.3 + - - +
90B TYR* 3.5 5.3 + - - +
91B ARG* 3.0 57.0 + - + +
96B PRO* 4.5 3.4 - - + -
97B PHE* 3.7 24.2 - - + -
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Residues in contact with TYR 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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16A PRO* 4.6 14.3 - - + +
17A 200 3.7 10.8 - - + -
84B LEU 3.3 12.0 + - - +
85B TRP* 3.5 33.0 - + + +
87B THR* 1.4 79.6 - - - +
89B THR* 1.4 57.5 + - - +
91B ARG 3.6 2.1 + - - -
93B TYR* 3.0 60.1 + + - +
94B ASP 3.5 39.0 + - - -
95B TRP* 3.5 30.5 - + + -
96B PRO* 5.6 0.4 - - - -
97B PHE* 5.0 0.2 - - - -
180B GLN* 3.4 22.9 + - - +
181B CYS* 3.4 29.6 + - + -
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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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17A 200 3.0 17.6 - - + +
26B SER* 3.3 21.4 + - - +
27B SER* 5.7 1.8 - - - +
28B GLY 5.8 0.2 - - - +
31B ILE* 4.1 27.4 - - + -
32B PRO* 4.3 11.7 - - + -
35B TYR* 3.8 8.7 - - - -
85B TRP 2.8 17.0 + - - -
86B ALA* 3.9 5.8 - - - -
87B THR 3.4 0.2 - - - -
88B TYR* 1.4 76.6 - - - +
90B TYR* 1.4 61.4 + - - +
92B ASP* 3.3 12.3 + - - -
93B TYR* 4.0 26.8 + - + +
292B PRO* 5.7 1.6 - - + -
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Residues in contact with TYR 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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26B SER* 3.7 13.4 - - - -
28B GLY* 3.7 26.7 - - - -
29B ALA* 3.9 19.8 - - + +
32B PRO* 3.9 13.9 - - + +
86B ALA 3.4 14.4 + - - +
87B THR* 4.1 4.0 - - - +
89B THR* 1.4 74.0 - - - +
91B ARG* 1.3 57.7 + - + +
92B ASP* 3.1 13.8 + - - +
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Residues in contact with ARG 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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1A LYS* 5.1 3.2 - - - +
2A PHE* 3.6 39.7 - - + +
87B THR* 3.0 36.1 + - + +
88B TYR 4.1 1.3 - - - +
89B THR 3.3 0.8 - - - -
90B TYR* 1.3 75.3 - - + +
92B ASP* 1.4 76.2 + - - +
93B TYR 3.3 2.1 + - - -
94B ASP* 3.2 57.5 + - + +
96B PRO* 3.6 27.1 - - - +
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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