Contacts of the strand formed by residues 42 - 48 (chain B) in PDB entry 6WC2
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 42 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE 3.8 0.9 - - - +
47A ILE* 3.4 3.3 - - - -
48A PHE* 2.9 43.9 + - + +
49A ASN 5.0 1.6 - - - +
52A ASN* 3.7 5.5 + - - -
41B CYS* 1.3 74.9 - - - +
43B ILE* 1.3 60.3 + - - +
59B SER* 3.5 5.6 - - - -
60B THR* 4.0 18.6 - - + +
64B LYS* 3.2 33.9 + - - +
65B VAL* 4.5 10.9 - - + +
68B LYS* 2.4 37.4 + - - -
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 4.5 1.3 - - + -
45A LEU* 3.6 28.7 - - + -
46A ILE 3.2 5.8 - - - +
47A ILE* 4.1 11.7 - - + -
32B ALA* 3.5 38.8 - - + +
35B LEU* 3.9 27.8 - - + -
36B SER* 4.0 11.0 - - - +
41B CYS* 4.1 9.9 - - - -
42B GLU* 1.3 79.3 - - - +
44B ALA* 1.3 64.4 + - - +
57B TYR* 4.4 8.5 - - + -
58B ALA* 3.2 5.7 - - - +
59B SER* 2.9 35.3 + - - +
60B THR 4.7 0.3 + - - -
65B VAL* 4.9 4.9 - - - +
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ALA 3.9 0.8 - - - +
45A LEU* 3.4 5.4 - - - +
46A ILE* 2.9 41.5 + - + +
43B ILE* 1.3 75.1 - - - +
45B LEU* 1.3 60.8 + - - +
46B ILE* 4.3 2.5 - - + -
57B TYR 3.5 5.6 - - - -
58B ALA* 4.3 2.0 - - + +
62B MET* 3.6 28.9 - - - -
65B VAL* 3.7 24.0 - - + +
66B LEU* 5.1 0.4 - - + -
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ALA* 5.4 0.4 - - + -
43A ILE* 3.7 22.2 - - + -
44A ALA 3.4 13.7 - - - +
45A LEU* 4.2 21.5 - - + -
28B LEU* 3.9 34.5 - - + +
29B MET* 4.0 29.4 - - + -
32B ALA* 4.8 4.7 - - + -
43B ILE* 5.0 0.4 - - + -
44B ALA* 1.3 72.7 - - - +
46B ILE* 1.3 62.0 + - - +
47B ILE* 4.2 12.1 - - + -
55B PHE 4.1 0.2 - - - +
56B GLN* 3.3 7.3 - - - +
57B TYR* 2.8 51.9 + - + +
62B MET* 4.3 0.2 - - - +
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ILE* 3.1 8.5 - - - +
44A ALA* 2.9 36.8 + - + +
46A ILE* 5.9 0.9 - - + -
65A VAL* 3.7 23.8 - - + -
66A LEU* 3.8 27.8 - - + -
69A TYR* 3.7 35.4 - - + -
44B ALA* 5.4 2.2 - - + -
45B LEU* 1.3 78.3 - - - +
47B ILE* 1.3 63.6 + - - +
48B PHE* 3.7 18.8 - - + -
54B LEU* 3.8 10.1 - - + -
55B PHE 3.9 2.7 - - - -
56B GLN* 4.7 1.8 - - + +
62B MET* 4.0 15.9 - - + -
66B LEU* 4.6 7.6 - - + -
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 4.3 14.1 - - + -
41A CYS* 4.2 3.6 - - + -
42A GLU 3.7 2.7 - - - -
43A ILE* 4.1 20.2 - - + -
21B PHE* 3.9 30.1 - - + -
25B LYS* 4.0 27.4 - - + +
28B LEU* 4.3 4.3 - - + -
29B MET* 4.4 7.2 - - + -
45B LEU* 4.2 26.7 - - + -
46B ILE* 1.3 78.3 - - - +
48B PHE* 1.3 71.6 + - - +
49B ASN 4.5 0.2 - - - +
53B LYS 3.5 1.0 - - - +
54B LEU* 3.4 4.0 - - - +
55B PHE* 2.8 45.6 + - + +
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Residues in contact with PHE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A CYS* 3.2 7.3 - - - +
42A GLU* 2.9 41.3 + - + +
65A VAL* 3.7 21.8 - - + -
68A LYS* 3.6 54.7 - - + -
69A TYR* 3.6 11.9 - - - -
72A TYR* 3.8 16.8 - + - -
46B ILE* 3.7 20.6 - - + -
47B ILE* 1.3 73.3 - - - +
49B ASN* 1.3 65.9 + - - +
52B ASN* 3.7 21.1 - - - +
53B LYS 3.2 8.3 - - - -
54B LEU* 3.8 27.6 - - + -
10I ARG* 5.1 0.2 + - - -
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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