Contacts of the strand formed by residues 100 - 106 (chain J) 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 VAL 100 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30J PHE 4.0 0.5 - - - +
31J GLU* 3.3 0.6 - - - -
32J PHE* 2.4 67.0 + - + +
45J LEU* 4.9 3.1 - - + -
65J ILE* 5.1 9.4 - - + -
66J VAL 4.6 4.3 - - - +
67J ASP* 5.5 6.3 - - + +
96J LEU* 3.9 37.0 - - + -
97J ASP 3.6 17.9 - - - +
98J PRO* 3.9 1.7 - - + +
99J PRO* 1.4 72.6 - - - +
101J THR* 1.3 62.1 + - - +
102J PHE* 4.0 21.1 - - + -
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Residues in contact with THR 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J THR* 5.2 9.9 - - + -
30J PHE 3.3 6.5 - - - +
31J GLU* 3.1 38.4 - - + +
65J ILE* 3.5 8.1 - - - +
66J VAL* 2.9 56.9 + - - +
100J VAL* 1.3 74.5 - - - +
102J PHE* 1.4 65.1 + - - +
103J ARG* 4.1 0.7 - - - -
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Residues in contact with PHE 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J TRP* 3.9 25.4 - + - -
21J CYS* 4.5 4.5 - - - -
23J LEU* 3.6 11.9 - - + +
29J THR* 3.5 3.5 + - - -
30J PHE* 3.0 39.0 + + - +
32J PHE* 4.6 4.7 - - + -
45J LEU* 4.0 8.5 - - + -
47J LEU* 4.0 28.3 - - + -
63J VAL* 4.4 4.0 - - + -
64J GLU 3.5 7.4 - - - +
65J ILE* 3.8 20.9 - - + -
78J ILE* 5.0 1.3 - - + -
96J LEU* 3.8 30.1 - - + -
100J VAL* 4.0 18.2 - - + -
101J THR* 1.4 73.2 - - - +
103J ARG* 1.3 58.8 + - - +
113J ILE* 3.8 31.0 - - + -
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Residues in contact with ARG 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J LEU* 4.2 3.1 - - - -
28J LYS* 3.3 17.0 - - + +
29J THR* 4.1 15.9 + - - +
63J VAL* 3.5 1.8 - - - -
64J GLU* 2.8 61.8 + - + +
66J VAL* 3.3 32.1 - - + +
73J GLU* 4.3 13.5 + - - -
75J VAL* 3.7 18.0 - - - +
101J THR* 4.1 1.6 + - - -
102J PHE* 1.3 72.4 - - - +
104J LEU* 1.3 69.2 + - - +
105J LYS* 2.9 11.0 + - - +
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Residues in contact with LEU 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J LEU* 3.8 13.4 - - + +
24J ASN* 3.6 37.9 - - - +
25J GLU* 5.3 0.2 - - - -
28J LYS* 2.7 39.9 + - + +
61J HIS* 4.5 4.3 - - + -
62J ILE 3.5 9.9 - - - +
63J VAL* 4.7 0.9 - - + +
103J ARG* 1.3 73.2 - - - +
105J LYS* 1.3 62.2 + - - +
106J ALA* 3.2 24.0 + - - +
107J GLY 3.5 17.3 - - - +
109J GLY* 3.8 11.4 - - - +
111J LEU* 3.8 33.9 - - + -
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Residues in contact with LYS 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112I TYR* 3.4 36.4 + - - -
28J LYS* 6.3 0.4 - - - -
62J ILE* 2.9 32.0 + - + +
64J GLU* 3.4 43.2 + - + +
75J VAL* 5.6 2.8 - - - +
77J PRO* 4.5 4.7 - - + -
103J ARG* 2.9 8.3 + - - +
104J LEU* 1.3 71.0 - - - +
106J ALA* 1.3 61.2 + - + +
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Residues in contact with ALA 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I ASP* 3.4 31.0 - - - +
60J PHE 3.8 9.9 - - - +
61J HIS* 3.4 2.3 - - - -
62J ILE* 3.1 33.1 + - + -
104J LEU* 3.2 11.1 + - - +
105J LYS* 1.3 80.2 - - + +
107J GLY* 1.3 67.6 + - - +
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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