Contacts of the helix formed by residues 67 - 80 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A LEU 5.1 1.4 - - - +
169A LYS* 3.9 31.9 + - - +
51K TYR 4.4 1.8 + - - -
53K SER* 3.3 23.5 + - - +
65K TYR* 3.6 24.1 + - + +
66K ILE* 1.3 75.2 - - - +
68K GLY* 1.3 68.6 + - - +
69K HIS* 3.4 30.9 + - + +
70K ARG* 3.0 40.6 + - + +
71K VAL* 3.4 4.3 + - - +
152K LYS* 4.7 0.4 - - - +
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Residues in contact with GLY 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A LEU* 5.4 0.7 - - - -
66K ILE 3.6 1.8 + - - -
67K GLU* 1.3 72.2 - - - +
69K HIS* 1.3 64.3 + - - +
70K ARG 2.8 1.7 + - - -
71K VAL* 2.9 14.9 + - - +
72K ILE* 3.1 18.0 + - - +
148K THR* 4.1 25.7 - - - +
152K LYS* 4.3 11.2 - - - +
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Residues in contact with HIS 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ASN* 3.1 46.2 + - - +
165A CYS* 5.8 0.4 - - - -
167A LEU* 3.8 26.8 - - + +
168A ASP* 3.6 46.0 - - + -
169A LYS 5.1 0.4 - - - -
67K GLU* 3.4 40.5 + - + +
68K GLY* 1.3 71.5 + - - +
70K ARG* 1.3 82.8 + - + +
72K ILE* 3.8 3.1 - - - -
73K ASN* 3.1 28.8 + - - -
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Residues in contact with ARG 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ASP* 4.3 7.5 + - - -
169A LYS 5.9 0.2 - - - +
170A ASP* 3.9 19.2 + - - -
195J ASP* 4.7 1.6 - - - +
50K GLU 4.0 15.9 + - - -
51K TYR* 3.8 41.9 + - + +
52K ILE 5.2 0.8 + - - -
53K SER* 4.2 3.2 + - - -
66K ILE* 3.8 14.4 - - + -
67K GLU* 3.0 44.5 + - + +
68K GLY 2.8 1.4 + - - -
69K HIS* 1.3 102.5 + - - +
71K VAL* 1.3 58.6 + - - +
73K ASN* 3.1 7.7 + - - +
74K LEU* 2.9 32.3 + - - +
184K LEU* 5.8 2.6 - - - +
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Residues in contact with VAL 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66K ILE* 3.9 21.8 - - + -
67K GLU 3.8 8.1 - - - +
68K GLY 2.9 5.5 + - - +
70K ARG* 1.3 74.5 - - - +
72K ILE* 1.3 64.2 + - + +
74K LEU* 3.6 9.6 - - + +
75K ALA* 3.0 22.0 + - - +
151K LEU* 5.7 1.6 - - + -
152K LYS* 3.7 39.3 - - + -
155K LEU* 3.3 34.5 - - + +
162K LEU* 4.4 16.6 - - + +
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Residues in contact with ILE 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ARG* 4.2 3.6 - - + +
157A SER* 3.5 37.2 - - - +
164A ASN* 3.6 28.9 - - - +
167A LEU* 5.6 3.4 - - + -
68K GLY 3.1 13.9 + - - +
69K HIS* 3.5 9.6 - - - +
70K ARG 3.1 0.6 - - - -
71K VAL* 1.3 77.4 - - + +
73K ASN* 1.3 60.0 + - - +
75K ALA* 3.1 8.4 + - - +
76K ASN* 2.9 46.6 + - - +
84K TRP* 4.3 7.8 - - + -
151K LEU* 4.6 20.6 - - + -
155K LEU* 5.5 0.4 - - - -
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Residues in contact with ASN 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ARG* 6.2 0.2 - - - +
159A GLY* 4.5 1.0 - - - -
160A ASN* 3.3 34.6 + - - +
164A ASN* 2.9 26.9 + - - +
195J ASP* 3.7 22.4 + - + +
69K HIS* 3.1 20.6 + - - -
70K ARG* 3.8 6.0 - - - +
72K ILE* 1.3 73.1 - - - +
74K LEU* 1.3 67.0 + - - +
76K ASN* 3.2 13.1 + - - +
77K GLU* 3.0 29.9 + - + +
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Residues in contact with LEU 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192J LYS* 3.4 34.7 - - + -
195J ASP* 3.8 17.7 + - - +
47K LEU* 3.9 14.1 - - + -
51K TYR* 3.9 17.9 - - + +
66K ILE* 5.3 7.2 - - + -
70K ARG 2.9 17.3 + - - +
71K VAL* 3.6 15.9 - - + +
72K ILE 3.2 0.2 - - - -
73K ASN* 1.3 74.5 - - - +
75K ALA* 1.3 58.0 + - - +
77K GLU* 3.1 6.7 + - - +
78K MET* 2.8 33.4 + - + +
161K ALA 3.3 22.4 - - - +
162K LEU* 3.8 18.8 - - + -
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Residues in contact with ALA 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71K VAL 3.0 14.3 + - - +
72K ILE 3.4 8.1 - - - +
74K LEU* 1.3 74.1 - - - +
76K ASN* 1.3 65.4 + - - +
78K MET* 4.4 0.2 - - - -
79K PHE* 2.9 35.0 + - + -
84K TRP* 3.6 33.0 - - + -
155K LEU* 4.3 13.7 - - + -
162K LEU* 3.8 10.7 - - + +
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Residues in contact with ASN 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLN* 3.1 12.0 + - - +
157A SER 3.2 24.2 + - - +
158A PHE 3.6 18.4 + - - +
159A GLY* 3.9 6.0 - - - +
72K ILE* 2.9 32.9 + - - +
73K ASN* 3.8 10.1 + - - +
75K ALA* 1.3 75.7 - - - +
77K GLU* 1.3 62.4 + - - +
80K GLY* 2.8 30.0 + - - -
81K TYR* 3.5 18.7 - - + +
84K TRP* 3.0 19.7 + - - +
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Residues in contact with GLU 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLN* 4.0 7.7 + - - +
44A ARG* 2.7 50.8 + - - +
195J ASP* 3.7 39.5 - - + +
196J LEU* 3.4 18.1 - - - +
197J GLU* 4.8 8.4 - - + +
200J VAL* 4.6 2.8 - - - +
201J GLU* 4.6 2.4 + - - +
204J ARG* 3.3 20.1 + - - -
73K ASN* 3.0 16.2 + - + +
74K LEU 3.5 7.4 - - - +
76K ASN* 1.3 82.9 - - - +
78K MET* 1.3 65.7 + - + +
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Residues in contact with MET 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192J LYS* 5.9 4.7 - - - -
197J GLU* 4.1 14.8 - - + +
200J VAL* 3.5 2.9 - - - +
204J ARG* 2.4 19.3 + - - +
39K ILE* 3.1 68.2 - - + +
42K ALA* 3.8 22.7 - - - -
43K LEU* 3.3 32.3 - - + -
74K LEU* 2.8 24.1 + - + +
75K ALA* 3.3 3.6 + - - +
77K GLU* 1.3 73.4 - - - +
79K PHE* 1.3 68.1 + - + +
161K ALA* 5.0 7.0 - - + +
162K LEU* 4.7 6.5 - - + -
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Residues in contact with PHE 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81J TYR* 4.5 3.6 - + - -
204J ARG* 3.3 20.1 + - - +
31K TYR* 3.6 12.5 + - - +
35K GLU* 4.6 1.9 - - - +
39K ILE* 4.2 24.5 - - + -
43K LEU* 4.6 3.6 - - + -
75K ALA* 2.9 26.2 + - + +
78K MET* 1.3 89.2 - - + +
80K GLY* 1.3 61.7 + - - +
82K ASN* 4.8 1.0 - - - +
83K GLY* 3.3 33.3 + - - -
84K TRP* 3.7 19.1 - + + +
115K LEU* 3.5 34.3 - - + -
116K LYS* 5.3 2.9 + - - -
155K LEU* 4.8 2.2 - - + -
158K PHE* 4.2 15.3 - + + -
162K LEU* 3.7 31.6 - - + -
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Residues in contact with GLY 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A TYR* 4.1 10.1 - - - -
40A GLN* 3.6 11.9 - - - -
204J ARG* 3.7 7.7 - - - -
76K ASN 2.8 25.7 + - - -
79K PHE* 1.3 73.6 - - - +
81K TYR* 1.3 66.2 + - - -
82K ASN* 2.7 9.0 + - - -
83K GLY 2.8 10.4 + - - -
84K TRP* 3.5 10.2 - - - -
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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