Contacts of the helix formed by residues 67 - 80 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51I TYR 4.4 1.2 + - - -
53I SER* 3.2 23.5 + - - +
65I TYR* 3.7 23.4 + - + +
66I ILE* 1.3 79.7 - - - +
68I GLY* 1.3 65.9 + - - +
69I HIS* 3.5 31.5 - - + +
70I ARG* 3.1 37.7 + - + +
71I VAL* 3.4 5.0 + - - +
152I LYS* 4.8 0.7 - - - +
167J LEU 5.1 1.4 - - - +
169J LYS* 3.9 30.9 + - - +
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Residues in contact with GLY 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I ILE 3.6 1.0 + - - -
67I GLU* 1.3 68.0 - - - +
69I HIS* 1.3 65.9 + - - +
70I ARG 2.9 3.3 + - - -
71I VAL* 3.0 5.1 + - - +
72I ILE* 3.0 27.8 + - - +
148I THR* 4.2 25.3 - - - +
152I LYS* 4.2 11.5 - - - +
167J LEU* 5.5 0.7 - - - -
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Residues in contact with HIS 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I GLU* 3.5 40.5 + - + +
68I GLY* 1.3 73.8 + - - +
70I ARG* 1.3 83.6 + - + +
72I ILE* 3.8 1.3 - - - -
73I ASN* 3.1 22.3 + - - -
164J ASN* 3.1 55.0 + - - +
165J CYS* 5.8 0.2 - - - -
167J LEU* 3.9 26.4 + - + +
168J ASP* 3.6 45.9 - - + -
169J LYS 5.1 0.4 - - - -
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Residues in contact with ARG 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195H ASP* 4.7 1.6 - - - +
50I GLU 4.0 14.7 + - - -
51I TYR* 3.6 40.7 + - + -
52I ILE 5.0 1.0 + - - -
53I SER* 4.1 4.6 + - - -
66I ILE* 3.5 14.8 - - + -
67I GLU* 3.1 45.5 + - + +
68I GLY 2.9 0.2 - - - -
69I HIS* 1.3 97.8 + - - +
71I VAL* 1.3 61.2 + - - +
73I ASN* 3.2 7.2 + - - +
74I LEU* 2.9 33.0 + - - +
184I LEU* 5.8 3.2 - - - +
168J ASP* 4.5 6.3 + - - -
170J ASP* 3.9 20.0 + - - -
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Residues in contact with VAL 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I ILE* 3.7 30.5 - - + -
67I GLU 3.8 5.6 - - - +
68I GLY 3.0 6.1 + - - +
70I ARG* 1.3 72.5 - - - +
72I ILE* 1.3 66.6 + - + +
74I LEU* 3.4 10.8 + - + +
75I ALA* 3.0 22.7 + - - +
151I LEU* 5.7 0.7 - - + -
152I LYS* 3.9 33.2 - - + -
155I LEU* 3.3 34.9 - - + +
162I LEU* 4.4 17.0 - - + +
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Residues in contact with ILE 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I GLY 3.0 17.4 + - - +
69I HIS* 3.7 9.0 - - - +
71I VAL* 1.3 79.1 - - + +
73I ASN* 1.3 63.5 + - - +
75I ALA* 3.1 5.6 + - - +
76I ASN* 3.0 43.3 + - - +
84I TRP* 4.4 7.4 - - + -
151I LEU* 4.8 18.2 - - + -
155I LEU* 5.5 1.1 - - + -
156J ARG* 4.1 4.0 - - + +
157J SER* 3.4 37.5 - - - +
164J ASN* 3.3 30.3 - - + +
167J LEU* 5.6 3.1 - - + -
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Residues in contact with ASN 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195H ASP* 3.7 24.8 + - + +
69I HIS* 3.1 19.7 + - - +
70I ARG* 3.8 4.8 - - - +
72I ILE* 1.3 77.7 - - - +
74I LEU* 1.3 62.4 + - - +
76I ASN* 3.2 14.9 + - - +
77I GLU* 3.1 28.0 + - + +
46J ARG* 6.0 1.4 - - - +
159J GLY* 4.5 1.0 - - - -
160J ASN* 3.1 36.1 + - - +
164J ASN* 3.0 26.3 + - - +
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Residues in contact with LEU 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192H LYS* 3.4 34.2 - - + -
195H ASP* 3.8 6.4 + - - +
47I LEU* 3.8 15.9 - - + -
51I TYR* 3.8 30.3 - - + +
66I ILE* 5.4 4.5 - - + -
70I ARG 2.9 20.2 + - - +
71I VAL* 3.6 15.3 - - + +
73I ASN* 1.3 76.2 - - - +
75I ALA* 1.3 58.4 + - - +
77I GLU* 3.3 4.9 + - - +
78I MET* 3.0 32.2 + - + +
161I ALA 3.1 24.5 - - - +
162I LEU* 3.8 17.5 - - + -
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Residues in contact with ALA 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71I VAL 3.0 16.6 + - - +
72I ILE 3.5 2.9 - - - +
74I LEU* 1.3 74.9 - - - +
76I ASN* 1.3 57.4 + - - +
77I GLU 3.0 5.2 - - - -
78I MET 4.4 0.2 - - - +
79I PHE* 2.9 43.8 + - + +
84I TRP* 3.7 27.7 - - + -
155I LEU* 4.2 12.6 - - + -
162I LEU* 4.0 15.0 - - + -
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Residues in contact with ASN 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I ILE* 3.0 44.7 + - - +
73I ASN* 3.8 10.9 + - - +
75I ALA* 1.3 74.2 - - - +
77I GLU* 1.3 62.8 + - - +
80I GLY* 2.9 21.5 + - - -
81I TYR* 3.7 13.7 - - + +
84I TRP* 2.9 24.2 + - - +
40J GLN* 3.0 19.5 + - - +
121J HIS* 4.9 0.2 - - - -
157J SER 3.3 13.4 + - - +
158J PHE 3.6 20.6 + - - +
159J GLY* 4.1 5.8 - - - +
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Residues in contact with GLU 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195H ASP* 3.6 39.9 - - + +
196H LEU* 3.3 22.2 - - - +
197H GLU* 4.5 7.2 + - + +
200H VAL* 4.6 2.6 - - - +
201H GLU* 4.6 2.4 + - - +
204H ARG* 3.2 19.9 + - - -
73I ASN* 3.1 15.3 + - + +
74I LEU 3.6 7.6 - - - +
75I ALA 3.0 0.6 - - - -
76I ASN* 1.3 84.0 - - - +
78I MET* 1.3 66.3 + - + +
79I PHE 3.1 2.3 + - - -
40J GLN* 4.2 4.2 + - - +
44J ARG* 2.7 50.4 + - - +
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Residues in contact with MET 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192H LYS* 5.8 5.4 - - - -
197H GLU* 4.4 13.9 - - + +
200H VAL* 3.7 3.4 - - - +
204H ARG* 2.7 15.7 + - - +
39I ILE* 3.1 68.3 - - + +
42I ALA* 3.7 24.2 - - - +
43I LEU* 3.2 32.8 - - + -
74I LEU* 3.0 20.3 + - + +
75I ALA* 3.4 0.4 + - - -
77I GLU* 1.3 76.6 - - + +
79I PHE* 1.3 73.4 + - + +
161I ALA* 5.1 7.0 - - + +
162I LEU* 4.8 6.3 - - + -
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Residues in contact with PHE 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81H TYR* 4.5 2.9 - + - -
204H ARG* 3.3 17.9 + - - +
31I TYR* 3.7 13.2 - - - +
35I GLU* 4.8 2.2 - - - +
39I ILE* 4.1 24.7 - - + -
43I LEU* 4.7 2.9 - - + -
75I ALA* 2.9 28.6 + - + +
78I MET* 1.3 90.7 - - + +
80I GLY* 1.3 66.5 + - - +
82I ASN* 4.8 1.0 - - - +
83I GLY* 3.2 30.8 + - - -
84I TRP* 3.8 16.4 - + + +
115I LEU* 3.5 34.1 - - + -
116I LYS* 5.4 2.4 - - - -
155I LEU* 4.7 2.5 - - + -
158I PHE* 4.3 14.6 - + + -
162I LEU* 3.8 31.2 - - + -
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Residues in contact with GLY 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204H ARG* 3.5 10.3 - - - -
76I ASN 2.9 20.1 + - - -
79I PHE* 1.3 77.1 - - - +
81I TYR* 1.3 60.1 + - - -
82I ASN* 2.8 13.9 + - - -
83I GLY 2.8 11.4 + - - -
84I TRP* 3.6 9.2 - - - -
36J TYR* 3.8 10.1 - - - -
40J GLN* 3.4 12.8 - - - -
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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