Contacts of the strand formed by residues 60 - 68 (chain E) in PDB entry 2V8W
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 60 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46E TRP* 4.1 23.5 - - + -
47E PHE 3.6 10.3 - - - +
48E PHE* 4.2 17.9 - - + -
56E TRP* 3.5 44.9 - - + +
57E GLN 3.6 15.8 - - - +
58E ALA* 3.3 1.9 - - - +
59E ASN* 1.3 77.6 - - - +
61E ARG* 1.3 68.0 + - - +
90E ASP* 6.1 0.2 - - + -
92E SER* 5.0 5.4 - - - +
100E PRO* 4.1 26.9 - - + -
101E MET* 3.6 17.7 - - + -
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Residues in contact with ARG 61 (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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46E TRP* 3.2 8.2 - - - -
47E PHE* 2.8 43.4 + - + +
49E LYS* 6.4 1.3 - - + -
54E LYS* 5.5 6.7 - - - +
58E ALA 4.4 13.1 + - - -
59E ASN 4.4 6.7 - - - +
60E LEU* 1.3 85.0 - - - +
62E LEU* 1.3 65.3 + - - +
63E ILE* 3.6 1.8 + - + -
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Residues in contact with LEU 62 (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 ALA* 3.4 24.5 - - + -
45E LEU 3.4 19.5 - - - +
46E TRP* 3.4 39.9 - - + -
61E ARG* 1.3 75.0 - - - +
63E ILE* 1.3 66.0 + - - +
64E SER* 3.6 16.2 - - - +
65E LYS* 3.9 24.5 - - + +
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Residues in contact with ILE 63 (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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45E LEU* 2.7 42.4 + - + +
47E PHE* 3.8 32.3 - - + +
61E ARG* 4.4 1.6 - - + +
62E LEU* 1.3 77.2 - - - +
64E SER* 1.3 62.5 + - - +
75E LEU* 3.6 24.9 - - + -
78E HIS* 5.2 4.5 - - - +
79E ILE* 4.3 13.2 - - + -
91E TYR* 3.9 12.1 - - + -
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Residues in contact with SER 64 (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 ALA* 3.4 3.1 - - - -
45E LEU* 3.0 27.0 + - - +
62E LEU* 3.6 4.4 - - - +
63E ILE* 1.3 83.3 + - - +
65E LYS* 1.3 70.9 + - - +
66E PHE* 4.8 0.3 - - - -
75E LEU* 3.8 33.3 - - - +
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Residues in contact with LYS 65 (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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42E ARG* 3.5 40.8 + - - +
43E TRP 3.2 11.7 - - - +
44E ALA* 3.9 11.0 - - + -
62E LEU* 3.9 26.5 - - + +
64E SER* 1.3 86.8 + - - +
66E PHE* 1.3 64.9 + - - +
71E ASP* 5.5 0.3 - - - +
96E ASP* 2.4 33.5 + - - +
97E GLY 4.7 2.8 - - - +
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Residues in contact with PHE 66 (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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39E LEU* 3.7 24.7 - - + -
41E ASN 4.3 0.2 - - - +
42E ARG* 3.5 7.8 - - - +
43E TRP* 2.9 51.8 + - + -
45E LEU 5.0 1.3 - - - -
65E LYS* 1.3 78.4 - - - +
67E ASP* 1.3 61.7 + - - +
68E THR 3.8 2.2 - - - -
71E ASP* 3.6 26.9 - - + +
72E PHE* 3.5 45.3 - + + -
75E LEU* 3.8 29.4 - - + -
93E LEU* 3.6 23.6 - - + -
138E ILE* 3.9 8.1 - - + -
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Residues in contact with ASP 67 (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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38E PRO* 3.6 2.9 - - - +
39E LEU* 2.9 29.8 + - + +
41E ASN 4.0 17.9 - - - +
42E ARG* 4.0 26.3 + - + +
66E PHE* 1.3 75.9 - - - +
68E THR* 1.3 72.5 + - - +
71E ASP* 4.7 4.0 + - - +
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Residues in contact with THR 68 (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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36E LYS* 3.8 26.5 - - + +
37E HIS 3.1 14.4 - - - +
38E PRO* 4.3 7.0 - - + -
39E LEU* 3.8 13.2 - - - +
66E PHE* 3.8 2.1 - - - -
67E ASP* 1.3 91.7 - - - +
69E VAL* 1.3 64.6 + - - +
70E GLU 3.7 1.7 + - - -
71E ASP* 2.7 39.7 + - - +
72E PHE* 3.1 16.8 + - - +
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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