Contacts of the strand formed by residues 45 - 52 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I TRP* 3.8 37.0 - - + -
32I PHE* 3.4 48.9 - - + -
43I HIS 4.4 0.2 + - - -
44I GLN* 1.3 72.5 - - - +
46I ALA* 1.4 57.5 - - - +
47I LEU* 4.0 7.8 + - + -
94I ILE 4.0 0.7 - - - +
95I GLU* 3.4 2.8 - - - -
96I LEU* 2.7 49.1 + - + +
98I PRO* 4.6 0.4 - - - +
100I VAL* 4.7 3.8 - - + -
102I PHE* 4.1 27.4 - - + -
115I GLY* 4.6 1.1 - - - -
116I GLN 3.8 20.9 - - - +
117I HIS* 4.4 2.9 - - + +
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Residues in contact with ALA 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I GLN 4.0 1.8 + - - -
45I LEU* 1.4 71.4 - - - +
47I LEU* 1.3 65.7 + - - +
48I ARG* 3.4 32.8 - - - +
94I ILE 3.5 7.6 - - - +
95I GLU* 4.2 15.3 - - + -
115I GLY* 3.1 2.5 - - - -
116I GLN 2.9 41.0 + - - +
118I VAL* 4.0 13.4 - - + +
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Residues in contact with LEU 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I TRP* 4.1 8.3 - - + -
45I LEU* 4.0 8.9 + - + -
46I ALA* 1.3 77.5 - - - +
48I ARG* 1.3 72.9 + - - +
50I VAL* 5.7 0.4 - - + -
78I ILE* 3.8 29.6 - - + -
91I MET* 3.8 29.0 - - + +
92I VAL* 5.3 0.3 - - - -
93I GLY 5.5 0.3 + - - -
94I ILE* 3.1 36.2 + - + +
96I LEU* 4.4 7.2 - - + -
102I PHE* 4.0 33.0 - - + -
113I ILE* 4.0 14.6 - - + -
114I SER 3.7 13.0 - - - +
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Residues in contact with ARG 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I ILE* 5.4 2.5 - - + -
46I ALA* 3.4 36.8 - - - +
47I LEU* 1.3 82.5 + - - +
49I THR* 1.3 66.1 + - + +
90I THR* 3.6 4.3 - - - +
91I MET* 2.7 36.6 + - - +
93I GLY* 5.6 5.7 - - - +
94I ILE 5.6 0.2 + - - -
114I SER* 3.0 18.3 + - - +
115I GLY* 4.0 13.7 - - - +
116I GLN* 3.0 23.1 + - + +
118I VAL* 4.3 9.9 - - - +
92J VAL 3.7 18.0 + - - +
93J GLY* 2.8 33.6 + - - -
94J ILE* 3.9 20.6 - - + -
95J GLU* 5.4 1.2 + - - -
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Residues in contact with THR 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I ARG* 1.3 89.2 - - + +
50I VAL* 1.3 67.4 + - - +
51I CYS* 4.8 0.7 - - - -
88I MET* 4.2 12.6 - - + -
89I ALA 3.4 11.2 - - - +
90I THR* 4.6 5.8 - - + +
91I MET* 4.1 4.4 - - - +
113I ILE* 3.7 0.5 - - - +
114I SER* 2.7 43.7 + - - +
77J PRO 4.3 0.9 + - - -
78J ILE* 3.2 32.2 + - + +
91J MET* 4.3 17.3 - - + -
92J VAL 6.1 0.4 - - - +
94J ILE* 4.4 6.7 - - + -
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Residues in contact with VAL 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47I LEU* 5.7 0.7 - - + -
49I THR* 1.3 78.7 - - - +
51I CYS* 1.3 67.2 + - - +
63I VAL* 4.2 20.6 - - + -
78I ILE* 5.4 4.5 - - + -
79I ALA* 4.3 10.8 - - + -
81I LEU* 3.6 22.2 - - + -
88I MET* 3.2 2.6 - - - +
89I ALA* 3.0 34.5 + - + +
91I MET* 4.4 19.1 - - + -
111I LEU* 4.1 17.9 - - + -
112I TYR 3.5 2.9 - - - -
113I ILE* 4.0 25.6 - - + -
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Residues in contact with CYS 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49I THR* 4.8 2.0 - - - -
50I VAL* 1.3 77.8 - - - +
52I LEU* 1.3 64.3 + - - +
81I LEU* 4.3 2.5 - - - -
87I PRO 3.5 4.9 - - - -
88I MET* 3.5 15.0 - - + +
111I LEU* 3.5 3.5 - - - +
112I TYR* 2.8 46.5 + - - +
77J PRO* 4.1 18.6 - - - -
78J ILE 3.9 6.7 - - - -
79J ALA* 3.7 25.1 - - - -
80J THR* 3.3 17.9 - - - +
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Residues in contact with LEU 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I CYS* 1.3 75.5 - - - +
53I GLY* 1.3 69.3 + - - +
56I ALA* 4.4 1.6 - - + -
61I HIS* 3.6 41.1 - - + +
81I LEU* 4.0 9.9 - - + -
82I LYS* 3.8 13.9 - - - +
83I PRO* 3.4 46.4 - - + -
87I PRO* 3.0 21.0 + - + +
110I PRO 3.6 8.7 - - - +
111I LEU* 4.1 14.8 - - + -
112I TYR* 4.4 2.6 - - - -
62J ILE* 3.9 3.5 - - - +
80J THR* 2.5 31.7 + - + +
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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