Contacts of the strand formed by residues 45 - 52 (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 LEU 45 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19J TRP* 3.8 44.0 - - + -
32J PHE* 3.9 38.1 - - + -
44J GLN* 1.3 72.1 - - - +
46J ALA* 1.3 65.6 + - - +
47J LEU* 4.0 4.8 + - + +
94J ILE 3.8 1.0 - - - +
95J GLU* 3.5 2.4 - - - -
96J LEU* 2.7 49.7 + - + +
98J PRO* 4.9 1.0 - - - +
100J VAL* 4.9 2.0 - - + -
102J PHE* 4.0 20.0 - - + -
115J GLY* 4.0 0.9 - - - -
116J GLN* 3.3 33.4 - - - +
117J HIS* 4.6 2.9 - - + +
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Residues in contact with ALA 46 (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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44J GLN 4.0 1.2 - - - -
45J LEU* 1.3 73.0 - - - +
47J LEU* 1.3 60.4 + - - +
48J ARG* 3.2 33.5 + - - +
94J ILE 3.3 7.0 - - - +
95J GLU* 3.8 20.6 - - + +
115J GLY* 3.0 3.1 - - - -
116J GLN 2.7 42.3 + - - +
118J VAL* 4.4 11.8 - - + +
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Residues in contact with LEU 47 (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* 4.5 1.1 - - + -
45J LEU* 4.0 13.2 - - + +
46J ALA* 1.3 76.2 - - - +
48J ARG* 1.3 71.7 + - - +
50J VAL* 6.1 0.2 - - + -
78J ILE* 4.0 25.1 - - + -
91J MET* 3.5 33.5 - - + +
92J VAL* 5.3 0.3 - - - -
93J GLY 5.4 0.3 + - - -
94J ILE* 3.2 40.6 + - + +
96J LEU* 4.4 5.6 - - + -
102J PHE* 4.0 33.0 - - + -
113J ILE* 4.0 20.9 - - + -
114J SER 3.8 6.1 - - - +
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Residues in contact with ARG 48 (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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18J ILE* 6.1 2.0 - - + -
46J ALA* 3.2 30.5 - - - +
47J LEU* 1.3 78.8 + - - +
49J THR* 1.3 67.4 + - - +
90J THR* 3.7 6.1 - - - +
91J MET* 2.8 28.8 + - - +
93J GLY 5.9 3.0 - - - +
95J GLU* 6.0 0.4 - - - -
114J SER* 3.1 17.4 + - - +
115J GLY* 4.0 13.9 - - - +
116J GLN* 3.0 37.4 + - + +
118J VAL* 4.1 13.1 - - - +
92K VAL 3.7 15.8 + - - +
93K GLY* 3.1 27.0 + - - -
94K ILE* 3.6 26.2 - - + -
95K GLU 5.1 0.2 - - - +
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Residues in contact with THR 49 (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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48J ARG* 1.3 79.2 - - - +
50J VAL* 1.3 66.7 + - - +
51J CYS* 4.7 1.6 - - - -
88J MET* 4.1 11.0 - - + -
89J ALA 3.6 8.7 - - - -
90J THR* 4.6 6.7 - - + +
91J MET* 4.4 4.5 - - - +
112J TYR 6.0 0.2 - - - -
113J ILE* 3.5 5.0 - - - +
114J SER* 2.6 55.5 + - - +
77K PRO 4.2 1.0 + - - -
78K ILE* 3.0 33.9 + - - +
91K MET* 4.1 20.6 - - - -
94K ILE* 4.4 8.5 - - + -
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Residues in contact with VAL 50 (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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47J LEU* 6.1 0.4 - - + -
49J THR* 1.3 77.5 - - - +
51J CYS* 1.3 69.6 + - - +
63J VAL* 4.4 12.3 - - + -
78J ILE* 5.5 3.8 - - + -
79J ALA* 4.4 11.0 - - + -
81J LEU* 3.0 28.7 - - + -
88J MET* 3.2 0.7 - - - +
89J ALA* 2.9 33.7 + - + +
91J MET* 4.2 27.1 - - + -
111J LEU* 4.2 15.0 - - + -
112J TYR 3.4 10.3 - - - +
113J ILE* 4.7 13.5 - - + -
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Residues in contact with CYS 51 (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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49J THR* 4.7 1.3 - - - -
50J VAL* 1.3 85.1 - - - +
52J LEU* 1.3 59.4 + - - +
81J LEU* 4.0 2.0 - - - -
87J PRO 3.5 4.9 - - - -
88J MET* 3.4 18.4 - - + -
111J LEU* 3.6 2.3 - - - +
112J TYR* 2.7 46.2 + - - -
77K PRO* 4.4 23.3 - - - -
78K ILE* 4.1 19.5 - - - +
79K ALA* 4.1 3.1 - - - -
80K THR* 3.4 24.0 - - - +
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Residues in contact with LEU 52 (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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51J CYS* 1.3 75.4 - - - +
53J GLY* 1.3 67.2 + - - +
54J ASP 3.8 0.2 + - - -
56J ALA* 4.3 1.6 - - + -
61J HIS* 3.6 37.2 - - + +
81J LEU* 4.0 17.5 - - + -
82J LYS* 3.9 7.4 - - - +
83J PRO* 3.5 44.6 - - + -
87J PRO* 3.0 23.5 + - + +
110J PRO 3.5 4.3 - - - +
111J LEU* 3.8 23.3 - - + -
112J TYR* 4.0 3.6 - - - -
62K ILE* 4.0 2.6 - - - +
80K THR* 2.9 24.6 + - - +
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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