Contacts of the helix formed by residues 67 - 79 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51H TYR 4.3 1.4 + - - -
53H SER* 3.3 22.5 + - - +
65H TYR* 3.7 22.8 + - + +
66H ILE* 1.3 77.5 - - - +
68H GLY* 1.3 68.2 + - - +
69H HIS* 3.4 31.3 + - + +
70H ARG* 3.0 40.0 + - + +
71H VAL* 3.4 3.6 + - - +
152H LYS* 4.8 0.4 - - - +
167I LEU 4.8 2.4 - - - +
169I LYS* 4.0 31.1 + - - +
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Residues in contact with GLY 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H ILE 3.5 2.0 + - - -
67H GLU* 1.3 66.5 - - - +
69H HIS* 1.3 63.8 + - - +
70H ARG 2.8 6.7 + - - -
71H VAL* 2.9 14.6 + - - +
72H ILE* 3.0 18.2 + - - +
148H THR* 4.1 25.7 - - - +
152H LYS* 4.3 11.5 - - - +
167I LEU* 5.3 1.3 - - - -
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Residues in contact with HIS 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H GLU* 3.4 42.3 + - + +
68H GLY* 1.3 70.1 + - - -
70H ARG* 1.3 80.9 + - + +
72H ILE* 3.8 1.8 - - - +
73H ASN* 3.1 21.2 + - - -
160I ASN* 5.9 0.2 - - - -
164I ASN* 2.8 60.2 + - - +
165I CYS* 5.6 0.2 - - - -
167I LEU* 4.0 21.1 - - + +
168I ASP* 3.5 49.4 + - + -
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Residues in contact with ARG 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195G ASP* 4.7 1.2 - - - +
50H GLU 3.9 15.5 + - - -
51H TYR* 3.5 44.3 + - + -
52H ILE 5.1 0.6 + - - -
53H SER* 4.2 2.8 + - - -
66H ILE* 3.5 15.5 - - + -
67H GLU* 3.0 42.3 + - + +
68H GLY 2.8 1.2 + - - -
69H HIS* 1.3 100.7 + - - +
71H VAL* 1.3 60.2 + - - +
72H ILE 3.2 0.2 + - - -
73H ASN* 3.2 7.2 + - - +
74H LEU* 2.8 33.5 + - - +
184H LEU* 5.7 3.2 - - - +
168I ASP* 4.5 6.3 + - - -
170I ASP* 3.7 21.4 + - - -
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Residues in contact with VAL 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H ILE* 3.8 21.5 - - + -
67H GLU 3.8 7.0 - - - +
68H GLY 2.9 5.7 + - - +
70H ARG* 1.3 76.2 - - - +
72H ILE* 1.3 66.2 + - + +
74H LEU* 3.7 10.6 - - + +
75H ALA* 3.1 19.9 + - - +
151H LEU* 5.6 0.9 - - + -
152H LYS* 3.7 39.7 - - + -
155H LEU* 3.4 34.7 - - + +
162H LEU* 4.4 15.0 - - + +
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Residues in contact with ILE 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68H GLY 3.0 17.2 + - - +
69H HIS* 3.6 2.9 - - - +
71H VAL* 1.3 77.6 - - + +
73H ASN* 1.3 60.3 + - - +
75H ALA* 3.0 8.7 + - - +
76H ASN* 2.9 47.7 + - - +
84H TRP* 4.4 8.0 - - + -
148H THR* 6.5 1.1 - - + -
151H LEU* 4.8 19.1 - - + -
155H LEU* 5.6 0.4 - - + -
156I ARG* 4.1 6.7 - - + +
157I SER* 3.5 33.4 - - - +
164I ASN* 3.2 38.6 - - + +
167I LEU* 5.4 3.8 - - + -
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Residues in contact with ASN 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195G ASP* 3.7 22.6 + - - +
69H HIS* 3.1 18.3 + - - +
70H ARG* 3.8 3.9 - - - +
72H ILE* 1.3 78.8 - - - +
74H LEU* 1.3 63.1 + - - +
76H ASN* 3.2 14.8 + - - +
77H GLU* 3.1 28.2 + - + +
46I ARG* 6.1 0.8 - - - +
159I GLY* 4.3 1.2 - - - -
160I ASN* 3.1 38.6 + - - +
164I ASN* 3.0 24.6 + - - +
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Residues in contact with LEU 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G LYS* 3.4 34.1 - - + -
195G ASP* 3.7 15.0 + - - +
47H LEU* 3.8 16.6 - - + -
51H TYR* 3.9 19.3 - - + +
66H ILE* 5.3 6.5 - - + -
70H ARG 2.8 19.8 + - - +
71H VAL* 3.7 12.3 - - + +
73H ASN* 1.3 77.7 - - - +
75H ALA* 1.3 57.9 + - - +
77H GLU* 3.4 4.2 + - - +
78H MET* 3.0 31.9 + - + +
161H ALA 3.1 23.8 - - - +
162H LEU* 3.7 18.8 - - + -
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Residues in contact with ALA 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H VAL 3.1 9.3 + - - +
72H ILE 3.0 9.5 + - - +
74H LEU* 1.3 76.0 - - - +
76H ASN* 1.3 62.1 + - - +
77H GLU 2.9 5.8 + - - -
78H MET* 4.4 0.7 - - - +
79H PHE* 3.0 39.6 + - + +
84H TRP* 3.8 28.6 - - + -
155H LEU* 4.3 10.3 - - + -
162H LEU* 3.8 13.4 - - + +
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Residues in contact with ASN 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H ILE* 2.9 45.0 + - - +
73H ASN* 3.2 11.9 + - - +
75H ALA* 1.3 75.3 - - - +
77H GLU* 1.3 62.2 + - - +
80H GLY* 3.1 14.5 + - - -
81H TYR* 3.6 15.0 + - + +
84H TRP* 3.2 18.9 + - - +
40I GLN* 3.0 25.0 + - - +
157I SER 3.2 11.3 + - - +
158I PHE* 3.3 25.1 + - - +
159I GLY* 3.9 5.2 - - - +
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Residues in contact with GLU 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G ASP* 3.7 41.7 - - + +
196G LEU* 3.5 16.8 - - - +
197G GLU* 5.0 8.6 - - + +
200G VAL* 4.5 3.1 - - - +
201G GLU* 4.5 3.1 + - - +
204G ARG* 3.1 20.4 + - - -
73H ASN* 3.1 17.9 + - + +
74H LEU 3.6 4.3 - - - +
75H ALA 2.9 0.6 - - - -
76H ASN* 1.3 85.2 - - - +
78H MET* 1.3 64.6 + - + +
79H PHE 3.2 1.6 - - - -
40I GLN* 3.9 6.6 + - - -
44I ARG* 2.6 50.6 + - - +
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Residues in contact with MET 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192G LYS* 5.9 5.2 - - - -
197G GLU* 4.3 14.4 - - + -
200G VAL* 3.7 4.0 - - - +
204G ARG* 2.6 20.7 + - - -
39H ILE* 3.1 69.2 - - + +
42H ALA* 3.6 23.8 - - - -
43H LEU* 3.2 32.8 - - + -
74H LEU* 3.0 20.6 + - + +
75H ALA* 3.3 3.8 + - - +
77H GLU* 1.3 71.2 - - + +
79H PHE* 1.3 68.8 + - + +
161H ALA* 5.1 7.2 - - + +
162H LEU* 4.8 6.1 - - + -
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Residues in contact with PHE 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G TYR* 4.5 2.9 - + - -
204G ARG* 3.2 17.1 + - - +
31H TYR* 3.6 17.7 - - - +
35H GLU* 4.8 2.6 - - - +
39H ILE* 4.2 24.0 - - + -
43H LEU* 4.7 2.9 - - + -
75H ALA* 3.0 21.3 + - + +
78H MET* 1.3 89.5 - - + +
80H GLY* 1.3 64.7 + - - +
82H ASN* 4.6 1.4 - - - +
83H GLY* 3.1 31.7 + - - +
84H TRP* 3.7 18.6 - + + -
115H LEU* 3.6 31.6 - - + -
116H LYS* 5.3 2.6 + - - -
155H LEU* 4.7 2.7 - - + -
158H PHE* 4.2 15.9 - + + -
162H LEU* 3.7 31.4 - - + -
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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