Contacts of the helix formed by residues 47 - 58 (chain A) in PDB entry 1WZ0
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 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ILE* 3.7 18.2 - - + -
45A THR 3.5 2.2 + - - -
46A PRO* 1.3 69.8 - - - +
48A SER* 1.3 65.0 + - - +
49A LYS 3.1 0.2 - - - -
50A LEU* 2.6 44.7 + - + -
51A MET* 2.7 32.4 + - + +
74A ILE* 3.6 39.5 - - + -
75A ASN 4.7 2.7 - - - +
76A GLU 3.3 6.0 + - - +
78A ASP* 3.3 13.3 + - + +
79A THR 5.2 0.4 - - - -
80A PRO* 4.3 7.4 - - + -
83A LEU* 4.7 11.0 - - + -
85A MET* 4.1 22.7 - - + -
91A ILE* 6.1 0.4 - - + -
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Residues in contact with SER 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PRO* 2.6 26.8 + - - +
47A LEU* 1.3 72.3 - - - +
49A LYS* 1.3 78.4 + - - +
51A MET* 3.4 2.2 + - - +
52A LYS* 3.0 32.5 + - - +
62A MET* 4.3 0.2 - - - +
76A GLU* 3.1 46.1 + - - +
77A THR* 5.7 0.2 - - - -
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Residues in contact with LYS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ILE* 6.0 2.7 - - + -
42A LYS* 5.3 6.1 - - - +
45A THR* 3.3 32.6 + - + +
46A PRO* 3.3 11.0 + - + +
47A LEU 3.1 0.4 - - - -
48A SER* 1.3 91.7 + - - +
50A LEU* 1.3 64.7 + - - +
52A LYS* 3.4 8.2 + - + +
53A ALA* 3.0 24.5 + - - +
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.1 7.6 - - + -
29A VAL* 5.0 0.9 - - + -
39A PHE* 2.9 54.5 - - + -
41A ILE* 4.1 22.5 - - + +
46A PRO 4.4 0.4 + - - -
47A LEU* 2.6 42.0 + - + +
49A LYS* 1.3 76.1 - - - +
51A MET* 1.3 71.5 + - + +
53A ALA* 3.1 5.2 + - - +
54A TYR* 3.0 18.1 + - + -
67A PHE* 5.3 2.5 - - + -
91A ILE* 3.5 30.3 - - + -
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Residues in contact with MET 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 2.7 28.1 + - + +
50A LEU* 1.3 73.2 - - + +
52A LYS* 1.3 57.0 + - - +
54A TYR* 2.6 30.7 + - - +
55A CYS* 3.1 9.5 + - - -
62A MET* 3.6 13.9 - - + +
67A PHE* 3.3 50.0 - - + -
74A ILE* 3.7 37.2 - - + +
75A ASN 4.0 1.8 - - - -
76A GLU* 3.3 48.7 - - - +
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Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 3.6 32.2 + - - +
48A SER* 3.0 24.6 + - - +
49A LYS* 3.6 7.9 - - + +
51A MET* 1.3 74.1 - - - +
53A ALA* 1.3 61.8 + - - +
55A CYS* 3.0 20.3 + - - +
56A GLU* 3.2 11.4 + - - +
62A MET* 4.1 15.0 - - + +
76A GLU* 5.4 2.5 - - - +
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A PHE* 4.0 15.0 - - + -
49A LYS 3.0 13.1 + - - +
50A LEU* 3.4 10.1 - - - +
52A LYS* 1.3 76.6 - - - +
54A TYR* 1.3 62.7 + - - +
56A GLU* 3.2 23.0 - - + +
57A ARG* 3.1 26.0 + - - +
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Residues in contact with TYR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 3.3 24.7 - - + +
31A GLY* 4.2 6.6 + - - -
37A VAL* 4.1 14.1 - - + -
39A PHE* 3.5 33.4 - + + -
50A LEU* 3.0 8.6 + - + +
51A MET 2.6 16.8 + - - +
53A ALA* 1.3 72.4 - - - +
55A CYS* 1.3 59.2 + - - +
57A ARG* 3.8 4.7 - - - +
58A GLN* 3.7 17.2 + - + +
60A LEU* 5.2 2.9 - - + +
65A ILE* 3.4 24.7 - - + -
67A PHE* 3.6 15.7 - + + -
93A VAL* 3.4 31.4 - - + +
95A GLN* 2.9 43.8 + - + +
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Residues in contact with CYS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 4.9 4.9 - - - +
51A MET 3.1 16.3 + - - -
52A LYS* 3.0 11.7 + - - +
54A TYR* 1.3 74.9 - - - +
56A GLU* 1.3 56.2 + - - +
57A ARG 3.0 1.3 - - - -
58A GLN 2.8 4.2 + - - -
59A GLY 2.5 33.3 + - - -
60A LEU* 3.0 28.5 + - - +
61A SER 4.0 0.9 - - - -
62A MET* 3.5 34.1 - - - +
65A ILE* 3.7 21.8 - - - -
67A PHE* 4.9 0.2 - - - -
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLU 4.5 7.9 - - - +
12A LYS* 3.2 61.8 - - + +
14A LYS* 3.9 16.1 - - - +
52A LYS 3.2 3.6 + - - +
53A ALA* 3.2 30.9 - - - +
55A CYS* 1.3 78.0 - - - +
57A ARG* 1.3 71.1 + - - +
59A GLY* 3.0 14.6 + - - +
60A LEU 4.7 0.6 + - - -
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Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL 5.5 1.6 + - - -
37A VAL* 3.1 43.2 - - - +
38A GLN 5.6 0.6 + - - -
39A PHE* 4.9 4.1 - - + -
53A ALA 3.1 14.3 + - - +
54A TYR* 3.8 5.8 - - - +
55A CYS 3.0 0.2 - - - -
56A GLU* 1.3 87.3 - - + +
58A GLN* 1.3 82.5 + - - +
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Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLN* 4.4 12.9 + - - +
35A SER* 5.9 0.2 + - - -
37A VAL* 4.4 6.7 - - - +
54A TYR* 3.7 11.4 + - + +
55A CYS 2.8 6.6 + - - +
57A ARG* 1.3 105.2 + - + +
59A GLY* 1.3 64.9 + - - +
60A LEU* 3.3 30.5 + - + +
95A GLN* 3.3 34.0 - - - +
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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