Contacts of the helix formed by residues 63 - 75 (chain A) in PDB entry 5B6Q
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 THR 63 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASP 4.7 4.3 - - - +
62A CYS* 1.3 76.7 - - - +
64A ASP* 1.3 67.1 + - - +
65A GLU* 3.4 18.0 + - - +
66A ASP* 2.9 36.2 + - - +
67A TYR* 3.0 22.4 + - - -
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Residues in contact with ASP 64 (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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43A VAL* 3.8 20.7 - - + +
47A LYS* 2.8 39.7 + - - +
62A CYS 5.4 0.2 - - - +
63A THR* 1.3 73.9 - - - +
65A GLU* 1.3 67.5 + - - +
67A TYR* 3.3 3.8 + - - +
68A LYS* 2.9 30.2 + - - +
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Residues in contact with GLU 65 (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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63A THR* 3.6 18.0 + - - +
64A ASP* 1.3 84.6 + - - +
66A ASP* 1.3 58.1 + - - +
68A LYS* 3.4 11.3 + - + +
69A SER* 2.9 34.9 + - - +
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Residues in contact with ASP 66 (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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1A GLN* 2.9 56.7 + - - +
6A VAL* 4.1 10.6 - - + +
61A ASP 3.6 2.6 - - - +
62A CYS* 3.5 15.0 - - - -
63A THR* 2.9 40.9 + - - +
65A GLU* 1.3 78.6 - - - +
67A TYR* 1.3 56.9 + - - +
69A SER* 3.3 7.2 + - - -
70A ALA* 3.0 29.7 + - - +
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Residues in contact with TYR 67 (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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43A VAL* 4.1 15.7 - - + -
46A VAL* 3.7 22.0 - - + -
47A LYS* 3.5 33.8 - - + +
56A GLY* 2.9 42.7 + - - -
59A CYS 3.7 9.9 + - - -
62A CYS* 3.5 34.5 + - + +
63A THR 3.0 22.1 + - - -
64A ASP* 3.6 6.1 - - - +
66A ASP* 1.3 76.7 - - - +
68A LYS* 1.3 63.9 + - - +
70A ALA* 3.3 5.6 + - - +
71A ILE* 3.0 31.2 + - + +
101A HEC 3.9 19.4 - - + +
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Residues in contact with LYS 68 (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 LEU* 3.6 37.9 - - + +
43A VAL* 4.0 14.0 - - + +
64A ASP 2.9 17.9 + - - +
65A GLU* 3.7 11.2 - - + +
67A TYR* 1.3 76.5 - - - +
69A SER* 1.3 62.6 + - - +
71A ILE* 3.3 8.0 + - - +
72A GLU* 3.0 38.9 + - - +
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Residues in contact with SER 69 (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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1A GLN 4.1 10.8 + - - -
3A GLY* 3.5 29.1 - - - -
65A GLU* 2.9 21.6 + - - +
66A ASP 3.3 4.7 + - - -
68A LYS* 1.3 75.3 - - - +
70A ALA* 1.3 57.7 + - - +
72A GLU* 3.3 15.8 + - - +
73A TYR* 3.0 23.9 + - - +
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Residues in contact with ALA 70 (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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3A GLY* 3.6 13.6 - - - +
6A VAL* 3.8 28.0 - - + -
7A TYR* 4.7 1.3 - - - +
11A CYS* 4.1 6.1 - - - -
66A ASP 3.0 16.1 + - - +
67A TYR 3.5 5.8 - - - +
69A SER* 1.3 76.0 - - - +
71A ILE* 1.3 62.3 + - - +
73A TYR* 3.2 4.7 + - - +
74A MET* 3.0 29.4 + - - +
101A HEC 3.8 15.0 - - + -
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Residues in contact with ILE 71 (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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31A TRP* 4.1 13.8 - - + -
35A ILE* 3.7 27.4 - - + -
39A LEU* 4.9 8.5 - - + +
42A LEU* 3.7 37.9 - - + -
43A VAL* 4.3 8.1 - - + +
46A VAL* 4.4 6.5 - - + -
67A TYR* 3.0 19.0 + - + +
68A LYS* 3.6 7.6 - - - +
70A ALA* 1.3 73.3 - - - +
72A GLU* 1.3 61.0 + - - +
74A MET* 3.1 9.7 + - - +
75A SER* 2.9 28.2 + - - -
101A HEC 3.7 29.4 - - + -
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Residues in contact with GLU 72 (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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35A ILE* 5.7 1.6 - - + -
39A LEU* 3.7 16.4 - - + +
68A LYS* 3.0 45.1 + - - +
69A SER* 3.5 16.7 + - - +
71A ILE* 1.3 76.5 - - + +
73A TYR* 1.3 61.7 + - - +
75A SER* 2.9 22.9 + - - +
76A LYS* 3.6 19.5 + - - +
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Residues in contact with TYR 73 (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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3A GLY* 4.0 10.5 - - - -
4A LYS* 3.6 48.9 - - + +
7A TYR* 3.5 48.0 - + + -
8A ASP* 4.9 0.9 + - - -
26A HIS* 3.4 37.2 + + - -
69A SER 3.0 13.5 + - - +
70A ALA 3.5 7.4 - - - +
71A ILE 3.2 0.2 - - - -
72A GLU* 1.3 78.1 - - - +
74A MET* 1.3 61.9 + - - +
76A LYS* 3.2 20.5 + - - +
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Residues in contact with MET 74 (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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7A TYR* 3.5 31.4 - - + -
11A CYS* 3.9 4.7 - - + -
15A HIS* 3.6 32.8 - - + -
25A ALA* 4.1 4.5 - - + +
26A HIS* 2.7 29.6 + - - +
31A TRP* 3.5 42.9 - - + +
70A ALA 3.0 16.5 + - - +
71A ILE* 3.1 6.5 + - - +
73A TYR* 1.3 80.4 - - - +
75A SER* 1.3 62.5 + - - +
101A HEC 3.6 39.9 - - + -
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Residues in contact with SER 75 (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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28A ALA* 3.6 24.2 - - - +
31A TRP* 3.8 16.6 - - - +
35A ILE* 3.8 31.9 - - - +
71A ILE 2.9 13.6 + - - -
72A GLU* 2.9 22.7 + - - +
73A TYR 3.3 0.2 - - - -
74A MET* 1.3 78.2 - - - +
76A LYS* 1.3 64.8 + - - +
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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