Contacts of the helix formed by residues 67 - 80 (chain E) 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 GLU 67 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51E TYR 4.4 1.4 + - - -
53E SER* 3.2 24.8 + - - +
65E TYR* 3.7 19.9 + - + +
66E ILE* 1.3 76.9 - - - +
68E GLY* 1.3 68.3 + - - +
69E HIS* 3.4 31.5 - - + +
70E ARG* 3.0 41.9 + - + +
71E VAL* 3.4 3.3 + - - +
152E LYS* 4.5 0.7 - - - +
167F LEU 4.8 1.7 - - - +
169F LYS* 3.8 35.8 + - - +
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Residues in contact with GLY 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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66E ILE 3.5 2.0 + - - -
67E GLU* 1.3 71.9 - - - +
69E HIS* 1.3 64.0 + - - +
70E ARG 2.9 1.7 + - - -
71E VAL* 3.1 5.0 + - - +
72E ILE* 3.0 29.2 + - - +
148E THR* 4.1 25.9 - - - +
152E LYS* 4.3 12.2 - - - +
167F LEU* 5.7 0.9 - - - -
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Residues in contact with HIS 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E GLU* 3.4 42.1 - - + +
68E GLY* 1.3 73.0 + - - +
70E ARG* 1.3 80.4 + - + +
72E ILE* 3.8 2.0 - - - -
73E ASN* 3.1 19.6 + - - -
160F ASN* 5.9 0.4 - - - -
164F ASN* 2.8 59.0 + - - +
165F CYS* 5.5 0.2 - - - -
167F LEU* 3.7 25.1 - - + +
168F ASP* 3.5 46.6 + - + -
169F LYS 5.1 0.4 - - - -
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Residues in contact with ARG 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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195D ASP* 4.9 1.3 - - - +
50E GLU 3.9 14.8 + - - -
51E TYR* 3.4 44.4 + - + -
52E ILE 4.9 1.0 + - - -
53E SER* 4.2 2.2 + - - -
66E ILE* 3.5 15.7 - - + -
67E GLU* 3.0 46.1 + - + +
68E GLY 2.9 0.6 + - - -
69E HIS* 1.3 96.1 + - - +
71E VAL* 1.3 56.5 + - - +
73E ASN* 2.9 8.3 + - - +
74E LEU* 2.8 38.1 + - - +
184E LEU* 5.7 2.8 - - - +
168F ASP* 4.3 7.5 + - - -
170F ASP* 3.8 20.0 + - - -
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Residues in contact with VAL 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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66E ILE* 3.6 30.3 - - + -
67E GLU 3.8 4.9 - - - +
68E GLY 3.1 6.0 + - - +
70E ARG* 1.3 79.0 - - - +
72E ILE* 1.3 64.7 + - + +
74E LEU* 3.3 11.4 + - + +
75E ALA* 3.0 22.2 + - - +
151E LEU* 5.6 1.1 - - + -
152E LYS* 3.8 34.8 - - + -
155E LEU* 3.5 34.5 - - + -
162E LEU* 4.3 17.0 - - + +
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Residues in contact with ILE 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 GLY* 3.0 21.4 + - - +
69E HIS* 3.7 8.3 - - - +
71E VAL* 1.3 80.0 - - + +
73E ASN* 1.3 58.6 + - - +
75E ALA* 3.2 5.9 + - - +
76E ASN* 2.7 48.8 + - - +
84E TRP* 4.3 8.2 - - + -
148E THR* 6.4 1.1 - - + -
151E LEU* 4.9 18.4 - - + -
155E LEU* 5.6 0.7 - - - -
153F ARG 6.1 0.2 - - - +
156F ARG* 4.1 4.9 - - + +
157F SER* 3.2 37.9 - - - +
164F ASN* 3.4 26.9 - - - +
167F LEU* 5.3 4.3 - - + -
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Residues in contact with ASN 73 (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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195D ASP* 3.6 24.4 + - + +
69E HIS* 3.1 15.8 + - - +
70E ARG* 2.9 8.4 + - - +
72E ILE* 1.3 76.3 - - - +
74E LEU* 1.3 68.3 + - - +
76E ASN* 3.1 9.3 + - - +
77E GLU* 2.9 27.0 + - + +
46F ARG* 6.1 0.6 - - - +
159F GLY* 4.3 5.4 - - - -
160F ASN* 3.2 38.4 + - - +
164F ASN* 2.8 29.8 + - - +
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Residues in contact with LEU 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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192D LYS* 3.4 34.0 - - + -
195D ASP* 4.1 5.3 + - - +
47E LEU* 3.9 16.2 - - + -
51E TYR* 3.9 29.2 - - + +
66E ILE* 5.3 4.5 - - + -
70E ARG 2.8 13.6 + - - +
71E VAL* 3.5 19.7 - - + +
73E ASN* 1.3 77.7 - - - +
75E ALA* 1.3 57.7 + - - +
77E GLU* 3.1 4.9 + - - +
78E MET* 2.8 32.9 + - + +
161E ALA 3.3 24.2 - - - +
162E LEU* 3.7 18.2 - - + -
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Residues in contact with ALA 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 VAL 3.0 13.0 + - - +
72E ILE 3.5 7.9 - - - +
73E ASN 3.1 0.2 - - - -
74E LEU* 1.3 72.8 - - - +
76E ASN* 1.3 66.1 + - - +
77E GLU 2.8 3.2 + - - -
78E MET* 2.9 1.5 + - - +
79E PHE* 2.8 34.9 + - + +
80E GLY 3.8 0.9 + - - -
84E TRP* 3.7 35.9 - - + -
155E LEU* 4.5 7.0 - - + -
162E LEU* 3.8 14.3 - - + +
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Residues in contact with ASN 76 (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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72E ILE* 2.7 36.0 + - - +
73E ASN* 3.1 11.9 + - - +
75E ALA* 1.3 74.9 - - - +
77E GLU* 1.3 62.1 + - - +
80E GLY* 2.8 30.0 + - - -
81E TYR* 3.6 14.5 - - + +
84E TRP* 3.3 20.0 + - - +
40F GLN* 3.0 11.5 + - - +
121F HIS* 5.0 0.2 - - - -
157F SER 3.1 25.4 + - - +
158F PHE* 3.5 21.3 - - - +
159F GLY* 4.0 5.3 - - - +
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Residues in contact with GLU 77 (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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192D LYS* 6.0 0.4 - - - -
195D ASP* 3.5 44.4 - - + +
196D LEU* 3.2 20.5 - - - +
197D GLU* 4.4 8.5 + - + +
200D VAL* 4.5 3.3 - - - +
201D GLU* 4.7 1.7 - - - +
204D ARG* 3.3 20.1 + - - -
73E ASN* 2.9 11.1 + - + +
74E LEU* 3.5 8.5 - - - +
75E ALA 2.9 0.6 - - - -
76E ASN* 1.3 83.2 - - - +
78E MET* 1.3 65.2 + - - +
40F GLN* 4.1 5.6 + - - -
44F ARG* 2.6 51.8 + - - +
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Residues in contact with MET 78 (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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192D LYS* 5.8 3.1 - - - -
197D GLU* 4.3 14.8 - - + +
200D VAL* 3.6 4.1 - - - +
204D ARG* 2.5 18.6 + - - -
39E ILE* 3.1 66.9 - - + +
42E ALA* 3.6 22.4 - - - -
43E LEU* 3.3 32.1 - - + -
45E GLN* 5.7 0.2 - - - +
74E LEU* 2.8 21.5 + - + +
75E ALA* 2.9 4.0 + - - +
77E GLU* 1.3 76.5 - - - +
79E PHE* 1.3 68.1 + - + +
161E ALA* 5.0 7.9 - - + +
162E LEU* 4.8 6.3 - - + -
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Residues in contact with PHE 79 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D TYR* 4.4 3.1 - + - -
204D ARG* 3.2 19.8 + - - +
31E TYR* 3.6 19.7 - - - +
35E GLU* 4.5 2.9 - - - +
39E ILE* 4.1 25.4 - - + -
43E LEU* 4.5 3.4 - - + -
75E ALA* 2.8 23.5 + - + +
78E MET* 1.3 84.7 - - + +
80E GLY* 1.3 64.9 + - - +
82E ASN* 4.8 1.4 - - - +
83E GLY* 3.4 31.6 - - - +
84E TRP* 3.7 18.4 - + + +
115E LEU* 3.7 29.4 - - + -
116E LYS* 5.2 3.1 + - - -
155E LEU* 4.7 2.7 - - + -
158E PHE* 4.3 15.3 - + + -
162E LEU* 3.8 31.2 - - + -
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Residues in contact with GLY 80 (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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204D ARG* 3.7 9.1 - - - -
76E ASN 2.8 21.4 + - - -
79E PHE* 1.3 79.8 - - - +
81E TYR* 1.3 67.2 + - - -
82E ASN* 3.1 3.8 - - - -
83E GLY 2.9 12.3 + - - -
84E TRP* 3.4 11.1 - - - -
36F TYR* 4.1 7.0 - - - -
40F GLN* 3.5 13.5 - - - -
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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