Contacts of the helix formed by residues 67 - 80 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B TYR 4.4 1.2 + - - -
53B SER* 3.3 23.1 + - - +
65B TYR* 3.7 22.9 + - + +
66B ILE* 1.3 76.5 - - - +
68B GLY* 1.3 68.5 + - - +
69B HIS* 3.4 29.0 - - + +
70B ARG* 2.9 41.8 + - + +
71B VAL* 3.3 4.2 + - - +
152B LYS* 4.6 0.9 - - - +
167C LEU 5.0 1.6 - - - +
169C LYS* 4.0 31.1 + - - +
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Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ILE 3.6 2.0 + - - -
67B GLU* 1.3 70.8 - - - +
69B HIS* 1.3 62.0 + - - +
70B ARG 2.9 1.4 + - - -
71B VAL* 3.1 6.6 + - - +
72B ILE* 3.0 27.8 + - - +
148B THR* 4.1 24.3 - - - +
152B LYS* 4.4 11.9 - - - +
167C LEU* 5.2 2.0 - - - -
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Residues in contact with HIS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLU* 3.5 40.5 + - + +
68B GLY* 1.3 74.8 + - - +
70B ARG* 1.3 81.4 + - + +
72B ILE* 3.9 1.8 - - - -
73B ASN* 3.1 20.2 + - - -
160C ASN* 5.9 0.2 - - - -
164C ASN* 3.0 57.1 + - - +
165C CYS* 5.6 0.2 - - - -
167C LEU* 3.8 23.6 - - + +
168C ASP* 3.5 46.7 - - + -
169C LYS 5.1 0.2 - - - -
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ASP* 4.6 1.5 - - - +
50B GLU 4.0 15.2 + - - -
51B TYR* 3.8 41.3 + - + -
52B ILE 5.2 0.6 + - - -
53B SER* 4.1 3.6 + - - -
66B ILE* 3.7 15.3 - - + -
67B GLU* 2.9 48.7 + - + +
69B HIS* 1.3 97.0 + - - +
71B VAL* 1.3 56.4 + - - +
73B ASN* 3.0 7.0 + - - +
74B LEU* 2.8 38.4 + - - +
184B LEU* 5.8 3.4 - - - +
168C ASP* 4.2 7.5 + - - -
170C ASP* 3.8 19.6 + - - -
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 4.0 21.3 - - + +
67B GLU 3.9 5.6 - - - +
68B GLY 3.1 6.4 + - - +
70B ARG* 1.3 75.0 - - - +
72B ILE* 1.3 64.4 + - + +
74B LEU* 3.3 11.3 + - + +
75B ALA* 3.0 22.7 + - - +
151B LEU* 5.5 1.8 - - + -
152B LYS* 3.9 38.6 - - + -
155B LEU* 3.4 35.2 - - + -
162B LEU* 4.5 17.4 - - + +
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B GLY 3.0 19.1 + - - +
69B HIS* 3.8 5.8 - - - +
70B ARG 3.1 0.2 - - - -
71B VAL* 1.3 76.8 - - + +
73B ASN* 1.3 59.1 + - - +
75B ALA* 3.1 8.0 + - - +
76B ASN* 2.9 46.7 + - - +
84B TRP* 4.4 8.5 - - + -
151B LEU* 4.7 18.6 - - + -
155B LEU* 5.6 0.2 - - - -
153C ARG 6.0 0.2 - - - +
156C ARG* 4.1 4.0 - - + +
157C SER* 3.4 37.9 - - - +
164C ASN* 3.5 29.4 - - - +
167C LEU* 5.6 3.1 - - + -
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Residues in contact with ASN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ASP* 3.4 24.9 + - + +
69B HIS* 3.1 16.6 + - - +
70B ARG* 3.0 5.7 + - - +
72B ILE* 1.3 78.4 - - - +
74B LEU* 1.3 64.0 + - - +
76B ASN* 3.2 13.1 + - - +
77B GLU* 3.0 28.6 + - + +
46C ARG* 6.2 0.2 - - - +
159C GLY* 4.3 1.0 - - - -
160C ASN* 3.0 36.3 + - - +
164C ASN* 3.0 26.1 + - - +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LYS* 3.2 37.1 - - + -
195A ASP* 3.9 5.1 + - - +
47B LEU* 3.8 15.7 - - + -
51B TYR* 3.9 28.7 - - + +
66B ILE* 5.2 6.7 - - + -
70B ARG 2.8 19.2 + - - +
71B VAL* 3.4 18.2 - - + +
73B ASN* 1.3 72.5 - - - +
75B ALA* 1.3 57.5 + - - +
77B GLU* 3.3 4.5 + - - +
78B MET* 2.9 32.3 + - + +
161B ALA 3.3 23.6 - - - +
162B LEU* 3.9 17.5 - - + -
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B VAL 3.0 12.2 + - - +
72B ILE 3.4 8.1 - - - +
74B LEU* 1.3 72.9 - - - +
76B ASN* 1.3 65.9 + - - +
77B GLU 3.0 1.6 - - - -
78B MET* 4.5 0.2 - - - -
79B PHE* 2.8 40.3 + - + +
84B TRP* 3.7 29.3 - - + -
155B LEU* 4.4 10.5 - - + -
162B LEU* 3.8 15.2 - - + +
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Residues in contact with ASN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ILE* 2.9 33.7 + - - +
73B ASN* 3.2 9.8 + - - +
75B ALA* 1.3 75.6 - - - +
77B GLU* 1.3 62.3 + - - +
80B GLY* 2.8 30.0 + - - -
81B TYR* 3.6 19.4 - - + +
84B TRP* 3.1 20.2 + - - +
40C GLN* 3.2 10.9 + - - +
157C SER 3.2 25.0 + - - +
158C PHE* 3.8 19.1 + - - +
159C GLY* 3.8 5.8 - - - +
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ASP* 3.4 41.7 - - + +
196A LEU* 3.3 20.8 - - - +
197A GLU* 4.5 8.6 + - + +
200A VAL* 4.4 3.6 - - - +
201A GLU* 4.4 2.1 + - - +
204A ARG* 3.4 17.2 + - - -
73B ASN* 3.0 19.5 + - + +
74B LEU 3.7 3.1 - - - +
76B ASN* 1.3 80.4 - - - +
78B MET* 1.3 65.1 + - - +
40C GLN* 3.8 9.2 + - - -
44C ARG* 2.5 49.5 + - - +
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Residues in contact with MET 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LYS* 5.8 4.5 - - - -
197A GLU* 4.2 14.8 - - + +
200A VAL* 3.4 11.5 - - + +
204A ARG* 2.3 26.4 + - - -
39B ILE* 3.2 58.4 - - + +
42B ALA* 3.7 24.5 - - - +
43B LEU* 3.3 32.5 - - + -
74B LEU* 2.9 19.3 + - + +
75B ALA* 3.2 2.9 + - - +
77B GLU* 1.3 70.9 - - + +
79B PHE* 1.3 69.4 + - + +
161B ALA* 5.0 7.0 - - + +
162B LEU* 4.7 6.7 - - + -
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A TYR* 4.4 2.7 - + - -
204A ARG* 3.2 16.5 + - - +
31B TYR* 3.7 12.9 + - - +
35B GLU* 4.6 2.1 - - - +
39B ILE* 4.2 24.7 - - + -
43B LEU* 4.6 2.9 - - + -
75B ALA* 2.8 27.2 + - + +
78B MET* 1.3 90.7 - - + +
80B GLY* 1.3 56.9 + - - +
82B ASN* 4.7 0.7 - - - +
83B GLY* 3.1 34.3 - - - -
84B TRP* 3.8 17.9 - + + -
115B LEU* 3.6 35.9 - - + -
116B LYS* 5.4 2.3 - - - -
155B LEU* 4.8 2.9 - - + -
158B PHE* 4.2 15.0 - + + -
162B LEU* 3.5 33.9 - - + -
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Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ARG* 3.6 10.8 - - - -
76B ASN 2.8 23.5 + - - -
79B PHE* 1.3 73.2 - - - +
81B TYR* 1.3 64.2 + - - -
82B ASN* 2.9 8.4 + - - -
83B GLY 2.9 9.9 + - - -
84B TRP* 3.5 11.1 - - - -
36C TYR* 4.0 11.2 - - - -
40C GLN* 3.8 11.2 - - - -
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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