Contacts of the strand formed by residues 44 - 52 (chain E) 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 GLN 44 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D LEU* 4.9 4.0 - - - +
32E PHE* 5.0 1.3 - - - -
42E GLU 4.4 6.1 - - - +
43E HIS* 1.3 74.7 - - - +
45E LEU* 1.3 62.1 + - - +
46E ALA 4.0 0.2 - - - -
95E GLU* 3.2 30.9 + - + +
96E LEU 3.3 21.8 - - - +
97E ASP* 3.6 29.8 + - - +
98E PRO* 4.5 2.7 - - - -
117E HIS* 3.2 8.4 + - - +
118E VAL* 3.0 44.9 + - + +
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Residues in contact with LEU 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E TRP* 3.6 43.3 - - + -
32E PHE* 3.8 42.5 - - + -
44E GLN* 1.3 71.9 - - - +
46E ALA* 1.3 59.7 + - - +
47E LEU* 3.9 14.2 + - + -
94E ILE 3.9 0.3 - - - +
95E GLU* 3.4 2.3 - - - -
96E LEU* 2.9 42.6 + - + +
100E VAL* 4.9 1.8 - - + -
102E PHE* 4.1 28.9 - - + -
115E GLY 4.5 0.4 - - - -
116E GLN 3.5 15.5 - - - +
117E HIS* 4.6 1.8 - - - +
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Residues in contact with ALA 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E GLN 4.0 1.2 + - - -
45E LEU* 1.3 70.7 - - - +
47E LEU* 1.3 62.5 + - - +
48E ARG* 3.5 34.6 - - - +
94E ILE 3.5 7.2 - - - +
95E GLU* 4.2 16.6 - - + +
115E GLY* 3.0 3.7 - - - -
116E GLN 2.7 42.2 + - - +
118E VAL* 3.7 14.3 - - + +
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Residues in contact with LEU 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E TRP* 4.2 10.1 - - + -
45E LEU* 3.9 12.0 + - + +
46E ALA* 1.3 74.0 - - - +
48E ARG* 1.3 68.6 + - - +
50E VAL* 5.9 0.4 - - + -
78E ILE* 3.7 30.3 - - + -
91E MET* 3.7 31.0 - - + +
92E VAL* 5.4 0.2 - - - -
93E GLY 5.5 0.9 + - - -
94E ILE* 3.1 36.1 + - + +
96E LEU* 4.5 7.6 - - + -
102E PHE* 3.9 31.0 - - + -
113E ILE* 4.0 23.1 - - + -
114E SER 3.6 4.7 - - - +
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Residues in contact with ARG 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A VAL 3.7 18.0 + - - +
93A GLY* 3.2 29.1 + - - -
94A ILE* 3.9 21.3 - - + +
95A GLU* 5.8 0.2 - - - +
18E ILE* 5.5 2.5 - - + -
46E ALA* 3.5 32.2 - - - +
47E LEU* 1.3 81.1 + - - +
49E THR* 1.3 68.3 + - + +
90E THR* 3.7 4.9 - - - +
91E MET* 2.9 30.1 + - - +
92E VAL* 6.4 0.2 - - - +
93E GLY 5.8 3.4 - - - +
95E GLU* 5.6 2.2 + - - +
114E SER* 2.7 22.3 + - - +
115E GLY* 3.9 15.5 - - - -
116E GLN* 2.7 30.1 + - + +
118E VAL* 3.8 14.8 - - - +
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Residues in contact with THR 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO 4.3 1.0 + - - -
78A ILE* 2.8 33.4 + - - +
91A MET* 4.4 23.8 - - + -
92A VAL 6.1 0.4 - - - +
94A ILE* 4.6 7.6 - - + -
48E ARG* 1.3 88.3 - - + +
50E VAL* 1.3 68.9 + - - +
51E CYS* 4.9 0.5 - - - -
88E MET* 4.4 4.9 - - + -
89E ALA 3.5 9.9 - - - +
90E THR* 4.5 3.1 - - + +
91E MET* 4.3 4.2 - - - +
113E ILE* 3.5 4.0 - - - +
114E SER* 2.5 51.3 + - - +
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Residues in contact with VAL 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E LEU* 5.9 0.2 - - + -
49E THR* 1.3 81.0 - - - +
51E CYS* 1.3 65.9 + - - +
63E VAL* 4.2 15.5 - - + -
78E ILE* 5.4 4.7 - - + -
79E ALA* 4.5 7.9 - - + -
81E LEU* 3.3 24.5 - - + -
88E MET* 3.1 3.8 - - - +
89E ALA 2.9 34.7 + - - +
91E MET* 4.3 21.1 - - + +
111E LEU* 4.1 18.6 - - + -
112E TYR 3.4 9.2 - - - +
113E ILE* 4.3 20.0 - - + -
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Residues in contact with CYS 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO* 4.1 25.4 - - - -
78A ILE 4.1 6.7 - - - +
79A ALA* 3.9 21.8 - - - -
80A THR* 3.7 20.0 - - - +
49E THR* 4.9 0.9 - - - -
50E VAL* 1.3 78.2 - - - +
52E LEU* 1.3 60.4 + - - +
81E LEU* 4.3 1.8 - - - -
87E PRO 3.6 4.9 - - - -
88E MET* 3.5 16.4 - - + +
111E LEU* 3.6 1.4 - - - +
112E TYR* 2.7 43.3 + - - +
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Residues in contact with LEU 52 (chain E).
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 2.8 - - - +
80A THR* 2.8 24.2 + - + +
51E CYS* 1.3 73.1 - - - +
53E GLY* 1.3 68.4 + - - +
56E ALA* 4.5 2.5 - - + -
61E HIS* 3.7 37.9 - - + +
81E LEU* 3.9 12.3 - - + -
82E LYS* 3.6 13.7 - - - +
83E PRO* 3.2 50.3 - - + -
87E PRO* 3.1 21.5 + - + +
110E PRO 3.5 6.3 - - - +
111E LEU* 3.8 18.8 - - + -
112E TYR* 4.3 4.6 - - - -
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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