Contacts of the strand formed by residues 44 - 50 (chain E) in PDB entry 3VXR
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 GLU 44 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35E TYR* 3.2 7.3 - - - -
36E ARG* 2.6 74.9 + - + +
37E GLN* 5.9 1.1 - - - -
38E THR* 4.7 10.3 + - - -
41E GLN* 5.1 5.2 + - - +
42E GLY 3.8 10.2 - - - +
43E PRO* 1.3 75.3 - - - +
45E PHE* 1.3 66.7 + - - +
46E LEU* 3.5 1.5 + - + -
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Residues in contact with PHE 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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99D LYS* 3.4 49.4 - - + -
100D LEU 4.7 1.6 - - - +
33E TYR* 4.6 4.7 - + - -
34E TRP 3.8 6.1 - - - -
35E TYR* 3.5 25.4 - + + -
44E GLU* 1.3 73.9 - - - +
46E LEU* 1.3 67.9 + - - +
47E THR* 3.4 39.0 - - - -
48E TYR* 3.5 18.2 - + + -
56E GLU* 3.5 29.2 - - + -
58E SER* 3.2 35.9 + - - -
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Residues in contact with LEU 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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34E TRP* 2.9 24.6 + - + +
35E TYR* 3.5 35.2 - - - +
36E ARG* 3.8 23.6 - - + +
44E GLU* 4.5 1.8 - - + +
45E PHE* 1.3 79.5 - - - +
47E THR* 1.3 66.2 + - + +
57E LYS* 3.6 0.7 - - - +
58E SER* 2.9 28.7 + - - -
61E LEU* 3.9 31.1 - - + +
65E PHE* 5.0 6.3 - - + -
77E LEU* 4.4 11.4 - - + -
90E TYR* 3.8 23.1 - - + -
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Residues in contact with THR 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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33E TYR* 3.7 0.2 - - - -
34E TRP* 2.8 42.8 + - + -
45E PHE* 3.4 8.0 - - - -
46E LEU* 1.3 84.8 - - + +
48E TYR* 1.3 66.9 + - - +
49E PHE* 4.2 4.5 - - + -
54E GLN* 2.9 25.6 + - - +
56E GLU 3.2 15.1 + - - -
57E LYS* 3.5 7.8 - - - +
61E LEU* 5.1 6.3 - - + -
67E ALA* 3.6 30.7 - - + -
77E LEU* 5.2 2.5 - - + -
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Residues in contact with TYR 48 (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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65A GLY 4.7 1.6 + - - -
69A ALA* 4.3 1.4 - - - +
98D TYR* 3.1 44.9 - + + -
99D LYS 5.3 1.6 - - - -
31E ARG* 4.1 16.3 + - + -
32E LEU 3.3 10.5 - - - +
33E TYR* 3.7 29.4 - + + -
45E PHE* 3.8 9.0 - + + -
47E THR* 1.3 77.5 + - - +
49E PHE* 1.3 93.6 + - - +
50E GLN* 4.0 3.6 - - + -
54E GLN* 3.4 7.6 - - - +
55E LEU* 3.1 49.1 + - + +
56E GLU* 3.0 49.5 + - + -
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Residues in contact with PHE 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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31E ARG* 3.2 5.9 - - - -
32E LEU* 2.9 44.4 + - + +
34E TRP* 4.3 3.4 - + - -
47E THR* 4.2 10.5 - - + -
48E TYR* 1.3 87.1 - - - +
50E GLN* 1.3 60.4 + - - +
51E ASN 3.8 12.6 - - - +
52E GLU 3.9 10.1 - - - -
53E ALA 3.0 5.2 - - - +
54E GLN* 3.6 35.0 - - + -
67E ALA* 3.6 17.9 - - + -
68E GLU* 3.4 28.3 - - - -
69E ARG* 3.4 36.7 + - + +
75E SER* 3.7 14.1 - - - -
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Residues in contact with GLN 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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69A ALA* 3.2 24.9 - - - +
72A GLN* 3.4 12.0 + - + +
73A THR* 3.2 37.6 + - - +
30E ASN* 3.8 20.3 + - - +
31E ARG* 3.1 36.7 + - + +
48E TYR* 4.0 3.5 - - + -
49E PHE* 1.3 70.7 - - - +
51E ASN* 1.3 75.5 + - - +
52E GLU 3.0 0.3 + - - -
53E ALA* 2.9 32.8 + - - +
55E LEU* 3.7 14.6 - - + +
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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