Contacts of the helix formed by residues 61 - 72 (chain A) in PDB entry 3KOV
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 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A THR* 1.3 80.4 + - - +
62A MET* 1.3 66.4 + - - +
63A ASP* 4.0 8.0 + - - +
64A LYS* 2.9 46.0 + - + +
65A VAL* 3.0 14.4 + - - +
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Residues in contact with MET 62 (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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44A ALA* 3.9 17.9 - - - -
45A LEU 3.9 4.3 - - - +
46A ILE* 4.4 11.9 - - - -
56A GLN* 3.3 40.8 - - + +
57A TYR 2.9 30.5 - - - +
58A ALA* 3.5 14.8 - - + +
60A THR 3.6 5.5 + - - -
61A ASP* 1.3 72.8 + - - +
63A ASP* 1.3 65.1 + - - +
65A VAL* 3.0 9.5 + - - +
66A LEU* 2.9 39.4 + - + +
69B TYR* 3.3 24.9 - - + +
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Residues in contact with ASP 63 (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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61A ASP* 3.4 8.4 + - - +
62A MET* 1.3 75.5 - - - +
64A LYS* 1.3 64.6 + - - +
66A LEU* 3.8 6.3 - - - +
67A LEU* 2.9 27.3 + - - +
69B TYR* 2.7 36.9 + - - -
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Residues in contact with LYS 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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42A GLU* 3.8 24.5 + - - +
60A THR* 5.1 4.0 + - - +
61A ASP* 2.9 42.5 + - + +
63A ASP* 1.3 77.8 - - - +
65A VAL* 1.3 57.7 + - + +
67A LEU* 3.4 9.8 - - - +
68A LYS* 3.0 44.7 + - + +
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Residues in contact with VAL 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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42A GLU* 4.4 23.1 - - + +
43A ILE 4.8 7.0 - - - +
44A ALA* 3.7 28.7 - - + +
58A ALA* 5.7 0.7 - - + -
60A THR* 4.3 13.9 - - - +
61A ASP 3.0 13.6 + - - +
62A MET* 3.0 10.1 + - - +
64A LYS* 1.3 76.6 - - + +
66A LEU* 1.3 67.9 + - - +
68A LYS* 3.1 9.1 + - - +
69A TYR* 2.9 20.4 + - - +
46B ILE* 3.8 21.5 - - + +
48B PHE* 4.0 11.8 - - + -
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Residues in contact with LEU 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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44A ALA* 4.3 15.0 - - + -
46A ILE* 4.2 13.5 - - + -
62A MET* 2.9 24.5 + - + +
63A ASP* 3.8 7.9 - - - +
65A VAL* 1.3 73.5 - - - +
67A LEU* 1.3 63.8 + - - +
69A TYR* 3.1 8.1 + - - +
70A THR* 2.9 29.9 + - + +
46B ILE* 3.8 24.0 - - + -
66B LEU* 4.5 11.4 - - + -
69B TYR* 3.3 43.7 - - + -
70B THR* 5.8 2.0 - - + -
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Residues in contact with LEU 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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63A ASP 2.9 18.0 + - - +
64A LYS* 3.4 9.4 - - - +
66A LEU* 1.3 73.4 - - - +
68A LYS* 1.3 67.0 + - - +
70A THR* 2.6 31.0 + - + +
71A GLU* 3.2 22.4 + - + +
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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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42A GLU* 2.9 29.6 + - - +
64A LYS* 3.0 33.1 + - + +
65A VAL* 3.4 9.9 - - - +
67A LEU* 1.3 73.4 - - - +
69A TYR* 1.3 66.2 + - - +
71A GLU* 2.9 20.6 + - - +
72A TYR* 3.1 10.7 + - - +
48B PHE* 3.6 33.0 - - + +
52B ASN* 2.9 32.5 + - + +
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Residues in contact with TYR 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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65A VAL 2.9 12.2 + - - +
66A LEU 3.1 9.6 + - - +
68A LYS* 1.3 74.9 - - - +
70A THR* 1.3 88.3 + - + +
72A TYR* 2.9 22.6 + - - +
76A HIS* 5.1 1.8 - + - -
46B ILE* 3.7 33.7 - - + -
48B PHE* 3.8 8.9 - - - -
54B LEU* 3.9 24.2 - - + -
56B GLN* 3.2 24.2 + - + -
62B MET* 3.1 24.5 - - + +
63B ASP* 3.2 18.9 + - - -
66B LEU* 3.3 27.4 - - + -
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Residues in contact with THR 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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66A LEU* 2.9 14.8 + - + +
67A LEU* 2.6 32.6 + - + +
69A TYR* 1.3 90.5 - - + +
71A GLU* 1.3 64.4 + - - +
72A TYR 3.6 4.7 + - - +
66B LEU* 5.6 2.9 - - + -
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Residues in contact with GLU 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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67A LEU* 3.8 26.1 - - + +
68A LYS* 2.9 12.6 + - - +
70A THR* 1.3 82.5 + - - +
72A TYR* 1.3 67.7 + - - +
73A ASN* 3.4 7.3 + - - +
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Residues in contact with TYR 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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68A LYS 3.1 5.2 + - - +
69A TYR* 2.9 16.6 + - - +
70A THR 4.1 5.4 - - - +
71A GLU* 1.3 79.1 - - - +
73A ASN* 1.3 64.6 + - - +
74A GLU* 3.3 54.5 + - + +
75A PRO 4.1 3.2 + - - -
76A HIS* 3.7 11.7 - + + +
48B PHE* 3.8 11.4 - + - -
52B ASN 3.7 15.9 - - - -
53B LYS* 3.3 17.0 - - - +
54B LEU* 3.2 59.7 + - + -
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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