Contacts of the strand formed by residues 46 - 51 (chain E) in PDB entry 2WJZ
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 46 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5E ARG* 2.9 41.5 + - - -
6E ILE 3.7 2.0 + - - -
7E ILE* 3.6 22.7 - - + +
8E ALA 3.1 13.3 + - - -
44E ILE* 2.9 20.0 - - - +
45E ASP* 1.3 88.1 - - - +
47E LEU* 1.3 65.3 + - - +
48E VAL* 5.6 1.6 - - - +
75E ILE* 4.4 2.0 - - - -
76E PRO* 3.5 29.7 - - + +
78E THR* 4.3 8.5 + - - -
99E LYS* 3.6 26.2 + - - -
167E GLU* 5.0 0.3 - - - +
122F GLY* 6.0 0.5 - - - -
123F TRP* 4.8 2.1 + - - +
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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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8E ALA* 3.5 5.6 - - + -
10E LEU* 3.9 24.0 - - + -
36E GLY* 3.6 31.0 - - - +
39E TYR* 4.0 25.6 - - + -
44E ILE* 4.2 1.3 - - + -
46E GLU* 1.3 81.8 - - - +
48E VAL* 1.3 68.3 + - - +
49E PHE* 3.8 26.0 - - + -
73E ILE* 4.3 13.0 - - + -
75E ILE* 3.8 19.5 - - + -
76E PRO 3.1 7.5 + - - -
77E PHE* 3.3 6.9 - - + -
78E THR* 3.0 24.1 + - - -
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Residues in contact with VAL 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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7E ILE* 3.5 25.6 - - + -
8E ALA 2.9 10.9 + - - +
9E CYS* 3.3 6.4 - - - -
10E LEU* 2.7 33.5 + - - +
46E GLU* 5.6 2.0 - - - +
47E LEU* 1.3 80.9 - - - +
49E PHE* 1.3 59.2 + - - +
50E LEU* 3.7 25.6 - - + -
78E THR* 3.4 22.9 - - + +
101E SER* 5.9 0.7 - - - -
169E LEU* 4.7 12.8 - - + -
199E ILE* 5.7 4.3 - - + -
222E LEU* 3.7 19.7 - - + -
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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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10E LEU* 3.3 37.2 - - + +
12E VAL* 4.8 16.2 - - + -
32E PRO* 4.3 17.0 - - + -
36E GLY* 4.8 2.0 - - - -
47E LEU* 3.8 26.9 - - + -
48E VAL* 1.3 73.3 - - - +
50E LEU* 1.3 62.7 + - - +
51E ASP* 4.0 0.6 + - - -
65E LEU* 6.2 4.9 - - + -
69E VAL* 3.8 29.8 - - + -
73E ILE* 5.2 0.7 - - + -
77E PHE* 3.7 44.6 - + + -
78E THR 2.7 13.8 + - - +
79E VAL* 3.5 14.9 - - + +
80E GLY 3.0 26.7 + - - +
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Residues in contact with LEU 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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9E CYS* 3.6 25.1 - - - -
10E LEU 2.9 11.9 + - - +
11E ASP* 3.6 16.0 - - - +
12E VAL* 2.9 26.4 + - - +
48E VAL* 3.7 19.4 + - + -
49E PHE* 1.3 80.5 - - - +
51E ASP* 1.3 62.5 + - - +
52E ILE* 4.0 5.8 + - + +
80E GLY* 3.6 20.0 - - - +
81E GLY* 5.3 2.9 - - - +
101E SER* 5.2 6.5 - - - +
169E LEU* 5.7 8.1 - - + -
222E LEU* 6.1 0.2 - - + -
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Residues in contact with ASP 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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12E VAL* 3.1 23.0 - - + +
14E ASP 4.1 1.7 + - - -
15E GLY 4.8 0.9 + - - -
49E PHE 4.0 1.2 + - - -
50E LEU* 1.3 73.7 - - - +
52E ILE* 1.3 66.5 + - - +
53E THR* 2.8 41.2 + - - +
58E LYS* 4.3 2.3 - - - +
61E THR* 4.3 6.3 - - - +
62E MET* 3.3 43.8 - - + +
79E VAL* 6.5 0.9 - - + -
80E GLY 3.1 9.7 + - - +
81E GLY* 3.8 20.1 - - - +
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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