Contacts of the strand formed by residues 74 - 81 (chain B) in PDB entry 2VTX
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 LYS 74 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A LEU* 5.5 8.7 - - + +
18A ILE* 4.4 6.7 + - + +
19A TRP* 3.8 30.3 - - - +
20A GLY 3.8 25.7 + - - +
65B ILE 3.9 0.5 - - - +
66B VAL* 3.8 1.6 - - - +
67B ASP 2.9 39.0 + - - +
68B GLN 4.8 5.8 - - - +
73B GLU* 1.3 76.0 - - - +
75B SER* 1.3 64.0 + - - +
76B VAL* 4.1 14.4 - - + +
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Residues in contact with SER 75 (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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64B GLU* 3.0 32.0 + - - -
65B ILE 3.1 12.3 - - - -
66B VAL* 3.8 13.7 - - - -
73B GLU* 4.8 1.4 + - - -
74B LYS* 1.3 77.0 - - - +
76B VAL* 1.3 66.3 + - - +
77B PRO* 3.5 9.1 - - - +
103B ARG* 3.6 9.7 + - - -
105B LYS* 5.3 1.4 + - - -
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Residues in contact with VAL 76 (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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18A ILE* 4.0 26.7 - - + -
19A TRP 3.5 22.0 - - - +
20A GLY* 3.8 26.0 - - - +
113A ILE 4.7 0.4 - - - +
114A SER* 3.6 21.5 - - - -
64B GLU* 3.8 2.2 - - - -
65B ILE* 3.0 30.0 + - + +
74B LYS* 4.1 17.3 - - + +
75B SER* 1.3 79.0 - - - +
77B PRO* 1.3 69.8 - - + +
78B ILE* 3.3 5.4 + - + +
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Residues in contact with PRO 77 (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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49A THR* 4.4 0.5 + - - -
51A CYS* 4.1 8.2 - - - -
112A TYR* 3.7 57.7 - - + +
113A ILE 4.8 0.7 - - - -
114A SER* 3.7 8.7 + - - -
62B ILE* 4.1 14.1 - - + -
63B VAL 3.8 6.3 - - - +
64B GLU* 3.8 16.4 - - + +
75B SER 3.5 11.7 - - - +
76B VAL* 1.3 90.5 - - + +
78B ILE* 1.4 61.2 + - - +
105B LYS* 4.3 10.8 - - + +
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Residues in contact with ILE 78 (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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18A ILE* 4.8 3.6 - - + -
49A THR* 2.7 39.8 + - + +
51A CYS* 4.1 4.4 - - - -
88A MET* 3.9 2.4 - - - +
114A SER* 4.1 16.4 - - - +
47B LEU* 3.8 28.7 - - + -
50B VAL* 5.4 2.7 - - + -
63B VAL* 3.1 33.3 + - + +
64B GLU* 4.7 0.9 - - - -
65B ILE* 3.9 30.1 - - + -
76B VAL* 3.5 16.4 - - + +
77B PRO* 1.4 72.4 - - - +
79B ALA* 1.4 60.9 + - + +
91B MET* 4.4 11.0 - - - +
94B ILE* 4.9 7.4 - - + -
102B PHE* 4.9 2.5 - - + -
113B ILE* 6.4 0.2 - - + -
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Residues in contact with ALA 79 (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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51A CYS* 3.9 4.4 - - - -
88A MET* 3.6 19.7 - - + -
50B VAL* 4.2 17.3 - - + -
62B ILE* 3.4 7.3 - - - +
63B VAL* 3.2 42.5 + - + +
78B ILE* 1.4 82.8 - - + +
80B THR* 1.3 62.2 + - - +
81B LEU* 4.2 4.3 - - + -
89B ALA* 5.1 0.2 - - + -
91B MET* 4.4 8.5 - - + -
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Residues in contact with THR 80 (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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51A CYS* 3.6 11.3 - - - +
52A LEU* 2.6 31.5 + - + +
53A GLY 5.3 1.3 - - - +
87A PRO* 3.7 30.1 - - + +
88A MET* 3.4 20.3 - - - +
60B PHE* 3.8 28.5 - - + -
61B HIS 3.4 9.0 - - - +
62B ILE* 3.7 13.7 - - + +
79B ALA* 1.3 73.2 + - - +
81B LEU* 1.3 72.2 + - - +
86B LEU* 4.0 0.2 - - - +
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Residues in contact with LEU 81 (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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87A PRO* 4.8 2.5 - - - -
88A MET* 4.1 1.6 - - - -
50B VAL* 3.4 42.4 - - + +
51B CYS 4.2 1.1 - - - +
52B LEU* 4.0 26.2 - - + -
59B GLU 3.8 0.2 - - - +
60B PHE* 3.4 5.8 - - - -
61B HIS* 2.8 34.8 + - - +
79B ALA* 4.8 2.2 - - + -
80B THR* 1.3 84.5 - - - +
82B LYS* 1.4 64.0 + - - +
86B LEU* 3.3 19.5 - - + +
87B PRO 4.1 9.4 - - - +
88B MET 3.5 27.8 - - - +
89B ALA* 3.9 11.9 - - + +
111B LEU* 4.5 4.3 - - + -
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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