Contacts of the helix formed by residues 65 - 76 (chain B) in PDB entry 1MQ0
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 CYS 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A CYS* 3.6 15.0 - - - -
61A PRO* 4.0 2.5 - - - -
53B CYS 3.9 1.3 - - - -
64B ILE* 1.3 80.2 - - - +
66B ALA* 1.3 63.5 + - - +
67B GLU* 3.4 0.9 - - - +
68B ARG* 3.5 16.3 + - - +
69B THR* 3.0 27.7 + - - -
102B CYS* 3.2 14.1 - - - -
147B ZN 2.5 34.3 - - - -
149B BRD 3.1 31.0 - - - +
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Residues in contact with ALA 66 (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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38B VAL* 3.4 46.2 - - + +
39B GLY 3.8 7.0 - - - -
40B ALA* 3.8 2.9 - - + +
52B GLY* 3.6 12.7 - - - +
53B CYS* 3.3 18.4 - - - -
54B ASN 3.7 2.0 - - - +
65B CYS* 1.3 70.3 - - - +
67B GLU* 1.3 67.2 + - - +
69B THR* 3.2 3.6 + - - -
70B ALA* 3.1 19.6 + - - +
149B BRD 2.9 7.7 + - - -
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Residues in contact with GLU 67 (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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40B ALA* 3.9 9.6 - - + +
65B CYS* 3.7 1.4 - - - +
66B ALA* 1.3 81.4 + - - +
68B ARG* 1.3 63.5 + - - +
70B ALA* 3.2 3.1 + - - +
71B ILE* 3.0 31.7 + - + +
85B ILE* 4.0 13.2 - - + +
87B ILE* 3.8 30.4 - - + +
98B PRO* 3.2 30.0 - - - +
102B CYS* 3.6 22.0 - - + -
106B MET* 4.0 15.0 - - + -
147B ZN 4.0 0.3 - - - -
149B BRD 2.9 28.4 + - - -
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Residues in contact with ARG 68 (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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61A PRO* 3.9 18.8 - - - +
62A LEU* 4.9 2.2 - - - +
64B ILE* 3.6 31.3 - - + +
65B CYS* 3.5 26.4 + - - +
66B ALA 3.3 0.4 - - - -
67B GLU* 1.3 79.8 - - - +
69B THR* 1.3 56.6 + - - +
71B ILE* 4.6 5.6 - - - -
72B GLN* 2.9 59.5 + - - +
99B CYS* 4.5 0.8 - - - -
101B ALA* 3.7 26.8 - - - +
102B CYS* 3.2 29.7 - - - +
105B VAL* 3.4 34.1 - - + +
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Residues in contact with THR 69 (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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51B LYS 4.6 2.4 - - - +
52B GLY* 3.9 13.5 - - - -
53B CYS* 3.0 22.4 + - - +
55B ILE* 4.3 13.9 - - + +
64B ILE* 3.4 17.0 - - - +
65B CYS 3.0 16.3 + - - -
66B ALA 3.2 5.3 + - - -
68B ARG* 1.3 76.1 - - - +
70B ALA* 1.3 57.6 + - - +
72B GLN* 4.0 9.7 + - - +
73B LYS* 3.0 27.7 + - + +
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Residues in contact with ALA 70 (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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40B ALA* 4.3 9.0 - - + +
42B LEU* 4.1 13.5 - - + +
50B PHE* 3.7 24.8 - - - +
51B LYS 4.0 8.7 - - - -
52B GLY* 3.9 9.8 - - - +
66B ALA 3.1 11.7 + - - +
67B GLU* 3.2 7.8 + - - +
69B THR* 1.3 76.6 - - - +
71B ILE* 1.3 59.3 - - - +
73B LYS* 3.2 3.0 + - - +
74B ALA* 2.9 31.4 + - - +
85B ILE* 5.0 1.8 - - + -
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Residues in contact with ILE 71 (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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42B LEU* 3.7 20.2 - - + -
67B GLU* 3.0 20.5 + - + +
68B ARG* 4.0 3.4 - - - +
70B ALA* 1.3 75.2 - - - +
72B GLN* 1.3 59.4 + - + +
74B ALA* 3.2 1.4 + - - +
75B VAL* 2.8 37.0 + - + +
82B PHE* 3.9 18.4 - - + -
85B ILE* 4.7 7.9 - - + -
102B CYS 4.9 0.7 - - - +
105B VAL* 3.8 31.2 - - + -
106B MET* 3.7 35.0 - - + +
109B PHE* 3.9 14.1 - - + -
113B TRP* 4.4 7.6 - - + -
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Residues in contact with GLN 72 (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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64B ILE* 4.2 16.7 - - - +
68B ARG* 2.9 47.5 + - + +
69B THR* 4.1 8.0 - - - +
71B ILE* 1.3 77.7 - - + +
73B LYS* 1.3 64.0 + - - +
75B VAL* 4.0 5.2 - - - +
76B SER* 3.1 25.1 + - - -
105B VAL* 5.2 5.5 - - + +
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Residues in contact with LYS 73 (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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50B PHE* 4.0 11.9 - - + -
51B LYS 4.7 7.6 - - - +
69B THR* 3.0 21.8 + - + +
70B ALA* 3.2 6.5 + - - +
72B GLN* 1.3 76.1 - - - +
74B ALA* 1.3 62.6 + - - +
76B SER* 2.6 23.1 + - - -
77B GLU* 3.0 15.5 - - + +
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Residues in contact with ALA 74 (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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42B LEU* 3.9 15.3 - - + -
50B PHE* 3.5 35.8 - - + -
70B ALA 2.9 16.6 + - - +
71B ILE 3.6 3.4 - - - +
73B LYS* 1.3 78.4 - - - +
75B VAL* 1.3 57.6 + - - +
77B GLU* 2.9 19.1 + - - +
79B TYR* 3.0 27.6 + - + +
82B PHE* 4.1 4.5 - - + -
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Residues in contact with VAL 75 (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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71B ILE* 2.8 28.4 + - + +
72B GLN* 4.1 5.8 - - - +
74B ALA* 1.3 72.1 - - - +
76B SER* 1.3 61.1 + - - +
77B GLU 3.0 0.2 - - - -
78B GLY* 3.2 13.5 + - - -
79B TYR 3.4 15.5 - - - +
80B LYS* 4.2 16.4 - - + +
82B PHE* 4.0 9.9 - - + -
109B PHE* 3.7 35.2 - - + -
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Residues in contact with SER 76 (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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72B GLN 3.1 16.3 + - - -
73B LYS* 2.6 25.1 + - - -
75B VAL* 1.3 76.0 - - - +
77B GLU* 1.3 68.9 + - - +
78B GLY 3.4 0.4 - - - -
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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