Contacts of the strand formed by residues 75 - 81 (chain A) 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 SER 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A GLU* 3.0 25.1 - - - -
65A ILE 3.4 6.7 - - - -
66A VAL* 4.0 4.7 - - - +
73A GLU* 4.6 3.6 - - - +
74A LYS* 1.3 74.6 - - - +
76A VAL* 1.3 61.0 + - - +
77A PRO* 3.7 7.1 - - - +
103A ARG* 2.7 30.0 + - - -
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLU* 3.7 2.5 - - - -
65A ILE 2.9 35.0 + - - +
74A LYS* 4.1 15.5 - - + -
75A SER* 1.3 74.8 - - - +
77A PRO* 1.3 65.7 - - + +
78A ILE* 3.6 4.4 - - + +
18E ILE* 4.0 29.4 - - + -
19E TRP 3.6 21.1 - - - +
20E GLY* 3.7 28.7 - - - +
113E ILE 4.6 1.1 - - - +
114E SER* 3.8 20.9 - - - -
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Residues in contact with PRO 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ILE* 4.1 10.8 - - + -
63A VAL 3.5 7.0 - - - +
64A GLU* 3.7 14.6 - - + +
75A SER 3.7 10.8 - - - +
76A VAL* 1.3 91.0 - - + +
78A ILE* 1.3 61.3 + - - +
105A LYS* 4.2 9.9 - - + -
49E THR* 4.3 0.7 + - - -
51E CYS* 4.1 11.6 - - - -
112E TYR* 3.7 60.5 - - + +
113E ILE 5.0 0.5 - - - +
114E SER* 4.0 7.8 + - - -
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 3.8 23.6 - - + -
50A VAL* 5.4 3.4 - - + -
63A VAL* 2.9 33.5 + - + +
65A ILE* 3.6 40.6 - - + -
76A VAL* 3.6 10.1 - - + +
77A PRO* 1.3 79.1 - - - +
79A ALA* 1.3 66.8 + - + +
91A MET* 4.5 8.0 - - - +
94A ILE* 4.3 13.9 - - + -
102A PHE* 4.8 4.3 - - + -
113A ILE* 5.9 0.7 - - + -
18E ILE* 4.6 3.1 - - + -
49E THR* 2.8 34.8 + - - +
51E CYS* 4.1 4.1 - - - -
88E MET* 3.7 3.3 - - - +
114E SER* 4.2 15.7 - - - +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A VAL* 4.7 17.5 - - + -
61A HIS 4.5 0.2 - - - -
62A ILE* 3.4 6.9 - - - +
63A VAL* 3.0 45.7 + - + -
77A PRO 3.8 0.6 - - - -
78A ILE* 1.3 82.6 - - + +
80A THR* 1.3 61.6 + - - +
81A LEU* 5.0 2.9 - - + -
89A ALA* 5.5 0.2 - - + -
91A MET* 4.7 4.5 - - + -
51E CYS* 3.9 4.6 - - - -
88E MET* 3.6 18.8 - - + -
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Residues in contact with THR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PHE* 3.8 28.0 - - + -
61A HIS 3.3 9.9 - - - +
62A ILE* 3.4 15.1 - - + +
79A ALA* 1.3 71.7 - - - +
81A LEU* 1.3 74.0 + - - +
51E CYS* 3.7 10.3 - - - +
52E LEU* 2.8 28.8 + - + +
53E GLY 5.5 0.9 - - - +
87E PRO* 3.8 29.2 - - + +
88E MET* 3.5 17.2 - - - +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A VAL* 3.3 44.6 - - + +
51A CYS* 4.1 8.3 - - - +
52A LEU* 4.1 25.8 - - + -
59A GLU 3.7 0.2 - - - +
60A PHE* 3.3 6.8 - - - -
61A HIS* 2.7 34.5 + - + +
63A VAL* 6.0 0.2 - - + -
79A ALA* 5.0 1.8 - - + -
80A THR* 1.3 84.7 - - - +
82A LYS* 1.3 63.3 + - - +
86A LEU* 3.3 23.8 - - + +
87A PRO 4.3 0.4 - - - +
88A MET* 3.6 27.4 - - - +
89A ALA* 4.0 8.5 - - + +
111A LEU* 4.4 3.6 - - + -
87E PRO* 4.9 2.5 - - - -
88E MET* 4.1 2.9 - - - -
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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