Contacts of the strand formed by residues 111 - 118 (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 LEU 111 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E GLU* 3.5 4.0 - - - +
23E LEU* 2.9 50.3 + - + +
50E VAL* 4.1 12.8 - - + -
51E CYS 3.6 4.7 - - - +
52E LEU* 3.8 23.6 - - + +
61E HIS* 4.0 17.9 - - + -
63E VAL* 4.0 27.1 - - + -
81E LEU* 4.5 2.7 - - + -
104E LEU* 4.1 15.7 - - + -
109E GLY* 4.6 3.1 - - - -
110E PRO* 1.3 74.1 - - - +
112E TYR* 1.3 62.8 + - - +
113E ILE* 3.7 28.3 - - + -
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Residues in contact with TYR 112 (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* 5.1 4.0 - - + -
77A PRO* 3.7 49.1 - - + +
105A LYS* 3.2 29.1 + - + -
21E CYS 3.3 6.5 - - - +
22E GLU* 3.3 39.8 + - + -
50E VAL* 3.4 5.2 - - - +
51E CYS* 2.7 47.9 + - - +
52E LEU 4.3 3.6 - - - -
53E GLY* 3.7 24.4 - - - -
110E PRO* 3.9 17.2 - - + +
111E LEU* 1.3 72.5 - - - +
113E ILE* 1.3 64.0 + - - +
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Residues in contact with ILE 113 (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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76A VAL* 4.6 1.9 - - - +
77A PRO 5.1 1.1 - - - -
19E TRP* 4.1 7.0 - - + -
20E GLY* 3.1 23.2 - - - -
21E CYS* 2.9 28.1 + - - +
23E LEU* 4.1 6.7 - - + -
47E LEU* 4.0 30.3 - - + -
49E THR 3.5 9.4 - - - +
50E VAL* 4.3 11.9 - - + +
63E VAL* 4.3 8.7 - - + -
78E ILE* 6.3 0.7 - - + -
102E PHE* 3.9 34.5 - - + -
111E LEU* 3.7 23.1 - - + -
112E TYR* 1.3 79.7 - - - +
114E SER* 1.3 62.9 + - - +
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Residues in contact with SER 114 (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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76A VAL* 3.8 21.1 - - - -
77A PRO 4.0 6.1 - - - -
78A ILE* 4.2 9.5 - - - +
18E ILE* 5.0 3.8 - - - -
19E TRP* 3.4 9.4 - - - -
47E LEU* 3.6 4.5 - - - +
48E ARG* 2.7 33.7 + - - +
49E THR* 2.5 51.7 + - - +
113E ILE* 1.3 78.9 - - - +
115E GLY* 1.3 53.7 + - - +
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Residues in contact with GLY 115 (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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18E ILE* 3.7 2.8 - - - +
19E TRP* 2.7 54.7 + - - +
45E LEU* 4.5 1.3 - - - -
46E ALA 3.0 13.5 - - - -
47E LEU* 4.1 1.1 - - - -
48E ARG* 3.9 7.1 - - - +
114E SER* 1.3 77.7 - - - +
116E GLN* 1.3 66.2 + - - +
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Residues in contact with GLN 116 (chain E).
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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93A GLY 3.3 11.6 - - - +
94A ILE* 3.5 8.0 - - - -
95A GLU* 2.6 36.5 + - - +
96A LEU* 4.0 12.5 - - - +
16E ASP 3.8 24.9 + - - +
17E LEU 3.4 12.9 - - - +
18E ILE* 4.2 10.5 - - + -
19E TRP 4.7 0.4 - - - +
45E LEU* 3.5 5.4 - - - +
46E ALA* 2.7 40.6 + - - +
48E ARG* 2.7 39.9 + - + +
115E GLY* 1.3 80.4 - - - +
117E HIS* 1.3 61.2 + - - +
118E VAL* 3.4 0.7 + - + -
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Residues in contact with HIS 117 (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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16E ASP* 3.3 31.1 + - + +
17E LEU* 3.4 34.4 + - + +
18E ILE 5.4 0.6 + - - -
19E TRP* 4.1 21.9 - + + +
32E PHE* 3.4 40.8 - + - -
43E HIS* 5.0 16.9 + - + +
44E GLN 3.2 9.6 + - - +
45E LEU* 4.6 2.5 - - + +
116E GLN* 1.3 70.3 - - - +
118E VAL* 1.4 59.0 + - - +
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Residues in contact with VAL 118 (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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16E ASP* 4.8 11.0 - - - +
42E GLU 5.5 0.2 - - - +
43E HIS* 3.9 25.1 + - - +
44E GLN* 3.0 51.7 + - + +
46E ALA* 3.7 30.5 - - + -
48E ARG* 3.8 14.6 - - - +
95E GLU* 4.3 14.1 - - - +
116E GLN 3.4 1.7 + - - +
117E HIS* 1.4 73.2 - - - +
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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