Contacts of the helix formed by residues 32 - 43 (chain G) in PDB entry 1KN0
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 32 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208E CYS* 5.3 0.2 - - - -
203F ALA 4.3 0.3 + - - -
207F SER* 3.2 36.1 + - - +
30G GLN 3.5 4.9 + - - +
31G TYR* 1.3 76.3 - - - +
33G ALA* 1.3 66.7 + - - +
34G GLU* 3.5 19.8 + - - +
35G GLU* 3.5 21.4 + - - +
36G TYR* 2.9 20.7 + - - +
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Residues in contact with ALA 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E TYR* 3.5 26.7 - - + +
208E CYS* 3.3 44.5 - - + +
32G THR* 1.3 73.1 - - - +
34G GLU* 1.3 72.6 + - - +
36G TYR* 3.7 0.9 - - - +
37G GLN* 3.0 26.3 + - - +
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Residues in contact with GLU 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E TYR* 5.1 6.7 - - - +
203F ALA* 3.4 30.6 - - + +
206F ASN* 4.7 14.4 - - + +
32G THR* 3.2 18.0 + - - +
33G ALA* 1.3 90.0 + - + +
35G GLU* 1.3 64.3 + - - +
37G GLN* 3.3 6.7 + - - +
38G ALA* 3.0 19.4 + - - +
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Residues in contact with GLU 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200F VAL* 5.0 2.7 - - + -
203F ALA* 3.3 15.4 - - + +
204F ARG* 3.1 42.4 + - + +
207F SER* 3.6 17.2 + - - -
31G TYR* 3.6 24.6 - - + -
32G THR* 3.3 14.9 + - - +
34G GLU* 1.3 77.9 - - - +
36G TYR* 1.3 66.9 + - - +
38G ALA* 4.4 1.3 - - - -
39G ILE* 3.0 41.7 + - + +
79G PHE 4.7 1.4 - - - +
116G LYS* 3.3 22.6 + - - -
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Residues in contact with TYR 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E GLU* 3.7 15.3 + - - -
204E ARG* 2.6 49.9 + - + -
205E TYR* 4.6 11.4 - + - -
208E CYS* 4.2 22.0 - - - -
80F GLY* 4.1 2.1 - - - -
81F TYR* 3.5 32.8 - + - -
82F ASN* 3.7 24.5 - - - -
31G TYR* 4.2 11.8 - - + +
32G THR 2.9 17.4 + - - +
33G ALA 3.7 4.9 - - - +
35G GLU* 1.3 77.9 - - - +
37G GLN* 1.3 66.6 + - + +
40G GLN* 2.8 53.6 + - + +
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Residues in contact with GLN 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E GLU* 4.8 9.0 - - - +
205E TYR* 2.9 51.2 + - + +
33G ALA 3.0 12.4 + - - +
34G GLU* 3.6 5.4 + - - +
36G TYR* 1.3 84.8 - - - +
38G ALA* 1.3 65.4 + - - +
40G GLN* 3.3 2.8 + - - +
41G LYS* 3.0 56.8 + - + +
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Residues in contact with ALA 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199F SER* 4.0 16.7 - - - +
200F VAL* 3.5 36.8 - - + +
203F ALA* 4.4 3.8 - - + -
34G GLU 3.0 12.8 + - - +
35G GLU* 3.7 7.9 - - - +
36G TYR 3.3 0.2 - - - -
37G GLN* 1.3 75.6 - - - +
39G ILE* 1.3 55.1 + - - +
41G LYS* 3.0 8.6 + - - +
42G ALA* 2.7 34.5 + - - +
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Residues in contact with ILE 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F TYR* 3.2 38.1 - - + +
200F VAL* 3.4 14.8 - - + -
204F ARG* 4.2 0.2 - - - +
31G TYR* 3.7 11.7 - - + -
35G GLU* 3.0 37.2 + - + +
38G ALA* 1.3 78.6 - - - +
40G GLN* 1.3 63.3 + - - +
43G LEU* 2.9 31.7 + - + +
78G MET* 3.1 48.9 - - + +
79G PHE* 4.1 9.6 - - + -
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Residues in contact with GLN 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E GLU* 3.4 25.0 + - - +
204E ARG* 3.8 3.0 - - - +
76F ASN* 3.1 24.7 + - - +
77F GLU* 4.2 2.9 + - - -
80F GLY* 3.4 9.3 - - - -
81F TYR* 3.2 31.8 + - + +
36G TYR* 2.8 47.4 + - + +
37G GLN* 3.7 4.9 - - - +
38G ALA 3.2 0.2 - - - -
39G ILE* 1.3 73.5 - - - +
41G LYS* 1.3 62.5 + - + +
43G LEU* 4.0 6.5 + - - +
44G ARG* 3.9 30.3 + - - +
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Residues in contact with LYS 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E GLU* 5.1 9.6 + - - +
37G GLN* 3.0 49.5 + - + +
38G ALA* 3.5 7.0 - - - +
40G GLN* 1.3 75.5 - - + +
42G ALA* 1.3 67.0 + - - +
44G ARG* 2.9 48.5 + - - +
45G GLN* 3.9 3.0 + - - +
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Residues in contact with ALA 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197F GLU* 3.3 26.0 - - - +
199F SER* 6.4 0.2 - - - -
200F VAL* 3.8 7.9 - - + -
38G ALA 2.7 19.5 + - - +
39G ILE 3.8 1.1 - - - +
41G LYS* 1.3 71.5 - - - +
43G LEU* 1.3 59.5 + - - +
44G ARG 2.8 6.8 + - - -
45G GLN* 2.9 33.7 + - - +
78G MET* 3.6 20.2 - - - -
161G ALA* 3.7 4.3 - - - +
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Residues in contact with LEU 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F TYR* 3.4 34.1 - - + -
39G ILE* 2.9 25.3 + - + +
40G GLN* 4.2 5.4 - - - +
41G LYS 3.2 0.2 + - - -
42G ALA* 1.3 71.9 - - - +
44G ARG* 1.3 56.3 + - - +
45G GLN 3.3 0.2 - - - -
78G MET* 3.2 24.5 - - + -
79G PHE* 4.6 3.4 - - + -
158G PHE* 3.3 31.4 - - + +
159G GLY* 3.7 1.5 - - - -
160G ASN 3.1 11.3 + - - -
161G ALA* 3.0 29.4 + - + -
162G LEU* 3.8 34.3 - - + -
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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