Contacts of the helix formed by residues 62 - 75 (chain E) in PDB entry 1KQO
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 PRO 62 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E ASP* 3.5 12.6 - - - +
61E ILE* 1.3 91.3 - - + +
63E ALA* 1.3 67.4 + - - +
64E TYR* 3.6 31.6 - - + -
65E HIS* 3.1 25.0 + - + +
66E ARG* 3.3 8.8 + - - +
261E ARG* 3.4 31.2 - - - +
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Residues in contact with ALA 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E VAL 4.1 2.0 - - - +
52E GLY* 4.7 0.2 - - - -
53E ASP* 2.6 32.6 + - - +
62E PRO* 1.3 71.4 - - - +
64E TYR* 1.3 58.5 + - - +
66E ARG* 3.0 22.7 + - - +
67E VAL* 2.7 35.6 + - + +
87E SER* 4.0 28.3 - - - +
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Residues in contact with TYR 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E ASP* 5.0 0.6 + - - -
62E PRO* 3.2 29.2 + - + -
63E ALA* 1.3 77.8 - - - +
65E HIS* 1.3 93.0 + + - +
67E VAL* 3.4 8.5 + - - +
68E ILE* 3.0 47.6 + - + +
247E TYR* 5.0 0.4 - - - -
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Residues in contact with HIS 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E ILE* 3.7 17.2 - - + +
62E PRO* 3.1 21.0 + - + +
64E TYR* 1.3 118.5 + + - +
66E ARG* 1.3 66.2 + - - +
68E ILE* 3.3 2.4 + - - +
69E MET* 3.0 31.0 + - - +
247E TYR* 2.6 37.0 + + - -
251E HIS* 4.5 11.5 + - - +
253E LEU* 3.5 30.0 - - + +
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Residues in contact with ARG 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E SER 3.0 27.2 + - - +
17E PHE* 3.6 19.6 - - + +
18E ASN* 3.7 11.0 - - - +
20E ILE* 5.5 0.7 - - - +
50E PRO* 3.9 11.1 - - + +
51E VAL* 2.9 38.4 + - - +
53E ASP* 2.8 28.1 + - - +
60E LEU* 3.1 30.2 - - - +
61E ILE* 2.8 36.0 + - + -
62E PRO 3.3 0.9 + - - +
63E ALA* 3.0 16.3 + - - +
65E HIS* 1.3 77.0 - - - +
67E VAL* 1.3 63.4 + - - +
69E MET* 3.4 11.7 + - + +
70E ALA* 3.1 22.9 + - - +
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Residues in contact with VAL 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E PRO* 4.2 23.1 - - + -
63E ALA 2.7 28.2 + - - +
64E TYR* 3.5 8.3 - - - +
66E ARG* 1.3 73.2 - - - +
68E ILE* 1.3 59.7 + - + +
70E ALA* 3.1 5.2 + - - +
71E GLU* 2.8 47.7 + - + +
82E VAL* 4.1 6.9 - - + +
84E THR* 3.4 28.0 - - + -
87E SER* 3.9 21.8 - - - +
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Residues in contact with ILE 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E TYR* 3.0 35.4 + - + +
65E HIS 3.8 3.4 - - - +
67E VAL* 1.3 78.0 - - + +
69E MET* 1.3 52.9 + - - +
71E GLU* 3.0 20.8 + - + +
72E LEU* 2.8 43.7 + - + +
247E TYR* 3.6 38.1 - - + +
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Residues in contact with MET 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E PRO* 3.7 17.7 - - + -
20E ILE* 3.9 8.1 - - + -
61E ILE* 3.9 12.6 - - + -
65E HIS 3.0 22.1 + - - +
66E ARG* 3.8 16.8 - - + +
68E ILE* 1.3 72.1 - - - +
70E ALA* 1.3 61.8 + - - +
72E LEU* 3.4 7.5 + - - -
73E ALA* 2.8 30.3 + - - +
244E VAL* 3.5 19.2 - - + +
247E TYR* 3.7 18.6 - - + -
248E ILE* 3.6 29.6 - - - -
253E LEU* 4.0 8.1 - - + -
254E TYR* 3.4 25.8 - - + +
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Residues in contact with ALA 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E PHE* 5.7 2.0 - - + -
20E ILE* 4.1 13.8 - - + +
48E ILE* 4.0 18.2 - - + -
50E PRO* 4.6 2.9 - - + -
66E ARG 3.1 13.6 + - - +
67E VAL* 3.4 9.9 - - - +
69E MET* 1.3 75.9 - - - +
71E GLU* 1.3 61.1 + - - +
73E ALA* 3.4 8.2 + - - +
74E THR* 2.7 29.1 + - - +
82E VAL* 3.5 23.1 - - + +
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Residues in contact with GLU 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E VAL* 2.8 42.0 + - + +
68E ILE* 3.0 22.8 + - + +
70E ALA* 1.3 74.5 - - - +
72E LEU* 1.3 62.6 + - + +
74E THR* 3.0 8.0 + - - -
75E LYS* 2.7 31.0 + - - +
82E VAL* 3.9 18.3 - - + +
84E THR* 4.9 4.3 - - - +
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Residues in contact with LEU 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E ILE* 2.8 31.2 + - + +
69E MET* 3.8 7.0 - - - +
71E GLU* 1.3 71.6 - - + +
73E ALA* 1.3 61.8 + - - +
75E LYS* 3.1 27.0 + - + +
76E ASN* 4.7 1.2 + - - +
241E PRO* 5.5 0.9 - - - +
243E LEU* 3.8 49.1 - - + +
244E VAL* 4.5 1.6 - - + -
247E TYR* 3.6 44.2 - - + -
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Residues in contact with ALA 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ILE* 3.9 24.5 - - + -
25E LEU* 3.8 24.8 - - + +
69E MET 2.8 18.7 + - - +
70E ALA 3.5 5.6 - - - +
72E LEU* 1.3 76.3 - - - +
74E THR* 1.3 62.1 + - - +
75E LYS 3.5 0.2 - - - -
76E ASN* 5.1 1.6 + - - +
77E SER 5.3 0.3 + - - -
241E PRO* 4.2 10.2 - - - +
244E VAL* 3.8 17.2 - - + +
238F TYR* 4.3 9.2 + - - -
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Residues in contact with THR 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LEU* 3.8 14.4 - - + -
48E ILE* 3.6 29.2 - - + -
70E ALA 2.7 18.4 + - - +
71E GLU* 3.0 4.7 + - - -
73E ALA* 1.3 79.8 - - - +
75E LYS* 1.3 66.2 + - - +
76E ASN 3.1 3.6 - - - -
77E SER* 2.8 26.9 + - - +
80E VAL* 3.5 31.6 + - + +
81E GLU* 4.5 1.4 - - - -
82E VAL* 3.4 13.7 - - - +
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Residues in contact with LYS 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E GLU 2.7 12.0 + - - +
72E LEU* 3.1 22.2 + - + +
74E THR* 1.3 77.0 - - - +
76E ASN* 1.3 77.3 + - - +
77E SER 4.6 2.4 - - - +
243E LEU* 3.8 29.3 - - + +
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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