Contacts of the helix formed by residues 57 - 70 (chain V) in PDB entry 5A0Q
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 ASP 57 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103O TYR* 4.0 15.4 - - + -
52V THR 5.0 0.3 - - - +
53V GLN* 3.1 28.5 + - - +
54V ALA 4.9 0.7 - - - +
55V VAL 2.8 7.9 + - - +
56V ALA* 1.3 76.0 - - - +
58V ALA* 1.3 54.8 + - - +
60V THR* 3.2 12.0 + - - +
61V TYR* 2.9 26.3 + - - +
81W ARG* 5.2 14.8 + - - +
84W LYS* 4.5 16.8 + - + -
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Residues in contact with ALA 58 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103O TYR* 3.9 21.3 - - + +
54V ALA 3.5 21.5 + - - +
55V VAL* 4.7 0.7 - - - -
56V ALA 3.2 0.4 - - - +
57V ASP* 1.3 76.0 - - - +
59V VAL* 1.3 64.4 + - - +
61V TYR* 3.4 4.6 - - + +
62V GLN* 3.1 38.1 + - - +
86V MET* 4.1 20.2 - - + -
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Residues in contact with VAL 59 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37V ILE* 4.1 11.0 - - + -
55V VAL 5.1 0.2 - - - -
56V ALA 3.2 13.7 + - - +
58V ALA* 1.3 77.0 - - - +
60V THR* 1.4 49.3 + - - +
62V GLN* 3.4 7.1 + - - +
63V LEU* 2.8 44.3 + - + +
79V ALA 4.0 11.7 - - - +
82V LEU* 4.1 23.8 - - + -
83V PHE* 3.7 47.3 - - + -
86V MET* 4.1 18.6 - - + -
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Residues in contact with THR 60 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102O LYS* 6.1 4.9 - - + -
36V PRO 4.3 2.5 + - - +
37V ILE* 3.1 46.0 - - - +
38V HIS* 5.2 1.1 - - - -
56V ALA 2.6 27.1 + - - -
57V ASP* 3.2 16.2 + - - +
59V VAL* 1.4 68.0 - - - +
61V TYR* 1.3 60.2 + - - +
64V GLY* 2.9 28.0 + - - +
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Residues in contact with TYR 61 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96O TYR* 3.9 19.2 + - - -
99O ALA* 3.1 46.8 - - + +
100O ASN* 3.4 22.6 + - - +
103O TYR* 3.2 39.9 - + + -
57V ASP 2.9 13.3 + - - +
58V ALA* 3.4 9.4 - - + +
60V THR* 1.3 75.8 - - - +
62V GLN* 1.3 77.1 + - + +
64V GLY 4.1 0.3 - - - -
65V PHE* 3.0 37.3 + + - +
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Residues in contact with GLN 62 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102U PHE* 5.6 4.1 - - + -
58V ALA* 3.1 28.4 + - - +
59V VAL* 3.8 3.9 - - - +
61V TYR* 1.3 91.7 - - + +
63V LEU* 1.3 51.3 + - - +
65V PHE* 3.4 11.5 - - + +
66V HIS* 2.7 31.6 + - - +
82V LEU* 3.6 40.0 - - + +
86V MET* 4.5 15.2 - - - +
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Residues in contact with LEU 63 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37V ILE* 3.7 25.8 - - + +
38V HIS* 4.1 6.7 - - + -
41V ILE* 3.7 19.3 - - + -
59V VAL* 2.8 20.8 + - + +
60V THR 4.1 1.8 - - - +
62V GLN* 1.3 73.8 - - - +
64V GLY* 1.3 59.7 + - - +
65V PHE 3.2 1.6 - - - -
66V HIS* 3.0 22.3 - - + +
67V SER 3.1 8.1 + - - -
74V PRO* 3.2 39.5 - - + +
78V THR* 4.4 4.7 - - + -
79V ALA* 3.5 44.2 - - + +
82V LEU* 4.2 9.2 - - + -
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Residues in contact with GLY 64 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37V ILE 5.2 1.5 + - - -
38V HIS* 5.4 6.3 - - - -
60V THR* 2.9 19.9 + - - -
61V TYR 4.1 0.4 - - - -
63V LEU* 1.3 74.9 - - - +
65V PHE* 1.3 53.6 + - - +
66V HIS 3.3 1.3 - - - -
67V SER* 3.8 9.1 - - - -
68V ILE* 3.3 33.7 + - - +
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Residues in contact with PHE 65 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92O GLN* 4.2 12.3 - - - -
95O ARG* 3.9 33.2 - - + -
96O TYR* 4.7 18.6 - + + -
99O ALA* 4.6 15.0 - - + -
61V TYR* 3.0 29.8 + + - +
62V GLN* 3.4 11.0 - - + +
64V GLY* 1.3 73.8 - - - +
66V HIS* 1.3 60.2 + - - +
68V ILE* 4.7 5.6 - - + -
69V GLU* 2.8 60.0 - - - +
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Residues in contact with HIS 66 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98U PHE* 4.7 1.5 - + - -
102U PHE* 3.9 22.2 - + + -
104U TYR* 3.7 28.6 + + - -
62V GLN 2.7 15.1 + - - +
63V LEU* 3.0 19.7 - - + +
65V PHE* 1.3 77.1 - - - +
67V SER* 1.3 58.8 + - - +
68V ILE 3.5 0.4 - - - -
69V GLU 3.9 0.6 + - - -
70V LEU* 2.9 59.9 + - + +
72V GLU* 5.4 1.6 - - + -
73V PRO 5.4 0.4 - - - -
74V PRO* 3.3 34.6 - - + +
75V LEU 4.3 4.0 - - - -
78V THR* 3.8 18.6 - - + +
82V LEU* 5.9 0.4 - - + -
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Residues in contact with SER 67 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71O LYS* 4.8 6.5 + - - -
38V HIS* 4.2 10.4 - - - -
63V LEU 3.1 15.0 + - - -
64V GLY* 3.8 10.5 - - - -
66V HIS* 1.3 77.0 - - - +
68V ILE* 1.3 61.3 + - - +
71V ASN* 2.9 28.2 + - - -
72V GLU 3.3 21.1 + - - -
73V PRO* 4.5 0.2 - - - +
74V PRO* 3.7 16.7 - - - +
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Residues in contact with ILE 68 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71O LYS* 3.0 52.0 - - - +
72O ILE 4.1 5.2 - - - +
73O THR* 4.1 24.0 - - + -
74O GLU* 4.5 7.0 - - + +
95O ARG* 3.6 21.5 + - + +
99O ALA* 6.1 3.6 - - + -
64V GLY 3.3 21.0 + - - +
65V PHE* 4.7 7.6 - - + -
66V HIS 3.5 0.8 - - - -
67V SER* 1.3 77.0 - - - +
69V GLU* 1.3 65.3 + - - +
71V ASN* 2.8 27.2 + - - +
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Residues in contact with GLU 69 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92O GLN* 3.7 26.0 - - - +
95O ARG* 3.7 18.3 + - - +
109U LYS* 5.1 4.0 - - - -
110U HIS* 4.2 22.4 + - + +
113U ASP* 5.5 2.8 - - - +
114U ARG* 5.2 1.6 + - - -
65V PHE* 2.8 58.7 - - - +
66V HIS 3.9 0.6 + - - +
67V SER 3.4 0.2 - - - -
68V ILE* 1.3 92.2 - - - +
70V LEU* 1.3 72.1 + - + +
71V ASN* 3.3 10.6 + - - -
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Residues in contact with LEU 70 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98U PHE* 4.3 4.5 - - + -
104U TYR* 2.4 32.5 - - - +
107U PRO* 3.9 18.6 - - + -
109U LYS* 3.4 26.6 + - + +
110U HIS* 4.2 22.4 - - + +
66V HIS* 2.9 50.7 + - + +
67V SER 4.7 0.2 - - - +
69V GLU* 1.3 87.0 - - + +
71V ASN* 1.3 66.9 + - - +
72V GLU* 3.3 21.8 + - + +
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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