Contacts of the helix formed by residues 32 - 43 (chain J) 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 THR 32 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208H CYS* 4.4 0.9 - - - -
203I ALA 4.2 0.2 + - - -
207I SER* 3.1 34.7 + - - +
30J GLN 4.5 5.2 - - - +
31J TYR* 1.3 75.3 - - - +
33J ALA* 1.3 66.3 + - - +
34J GLU* 3.6 21.1 + - - +
35J GLU* 3.0 20.7 + - - +
36J TYR* 2.8 20.9 + - - +
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Residues in contact with ALA 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H TYR* 3.4 31.8 - - + +
208H CYS* 3.3 42.3 - - + +
32J THR* 1.3 71.3 - - - +
34J GLU* 1.3 70.7 + - - +
36J TYR* 3.8 0.8 - - - +
37J GLN* 2.9 27.9 + - - +
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Residues in contact with GLU 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H TYR* 5.0 7.6 - - - +
203I ALA* 3.3 30.8 - - + +
206I ASN* 4.6 15.8 - - + +
32J THR* 3.0 17.6 + - - +
33J ALA* 1.3 87.1 + - + +
35J GLU* 1.3 62.7 + - - +
37J GLN* 3.5 5.6 + - - +
38J ALA* 3.1 19.1 + - - +
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Residues in contact with GLU 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I TYR* 4.6 0.2 - - - -
200I VAL* 4.9 2.5 - - + -
203I ALA* 3.4 14.7 - - + +
204I ARG* 3.2 41.7 + - + +
207I SER* 3.8 13.9 + - - -
31J TYR* 3.5 27.9 - - + -
32J THR* 3.0 16.8 + - - +
34J GLU* 1.3 76.1 - - - +
36J TYR* 1.3 67.4 + - - +
38J ALA* 3.0 2.8 + - - +
39J ILE* 2.9 42.0 + - + +
79J PHE 4.7 1.4 - - - +
116J LYS* 3.1 22.9 + - - -
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Residues in contact with TYR 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201H GLU* 3.5 19.5 + - - -
204H ARG* 2.9 49.8 + - + -
205H TYR* 4.6 9.9 - + - -
208H CYS* 4.3 21.8 - - - -
80I GLY* 3.8 2.8 - - - -
81I TYR* 3.4 29.8 - + - -
82I ASN* 3.6 24.2 - - - +
31J TYR* 4.3 11.1 - - + +
32J THR 2.8 19.4 + - - +
33J ALA* 3.8 7.4 - - - +
35J GLU* 1.3 72.6 - - - +
37J GLN* 1.3 67.0 + - + +
40J GLN* 2.9 48.8 + - + +
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Residues in contact with GLN 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201H GLU* 4.6 12.3 - - - +
205H TYR* 2.7 52.0 + - + +
33J ALA 2.9 15.5 + - - +
34J GLU* 3.8 4.8 + - - +
36J TYR* 1.3 80.3 - - - +
38J ALA* 1.3 65.2 + - - +
40J GLN* 3.4 4.1 + - + +
41J LYS* 3.1 50.9 + - + +
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Residues in contact with ALA 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199I SER* 3.9 17.3 + - - +
200I VAL* 3.5 35.7 - - + +
203I ALA* 4.3 4.0 - - + -
34J GLU 3.1 16.8 + - - +
35J GLU* 3.0 4.8 + - - +
37J GLN* 1.3 77.4 - - - +
39J ILE* 1.3 58.4 - - - +
41J LYS* 3.8 5.2 - - - +
42J ALA* 2.9 29.6 + - - +
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Residues in contact with ILE 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81I TYR* 3.4 26.0 - - + +
200I VAL* 3.5 15.7 - - + -
204I ARG* 4.2 0.2 - - - +
31J TYR* 3.7 19.5 - - + -
35J GLU* 2.9 39.1 + - + +
38J ALA* 1.3 73.9 - - - +
40J GLN* 1.3 66.2 + - - +
43J LEU* 2.9 34.3 + - + +
78J MET* 3.1 46.4 - - + +
79J PHE* 4.1 10.5 - - + -
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Residues in contact with GLN 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201H GLU* 3.7 19.8 + - - +
204H ARG* 3.9 2.2 - - - +
76I ASN* 3.0 27.5 + - - +
77I GLU* 4.2 3.0 + - - -
80I GLY* 3.4 8.9 - - - -
81I TYR* 3.1 30.2 + - - +
36J TYR* 2.9 45.1 + - + +
37J GLN* 3.6 7.0 - - + +
38J ALA 3.3 0.2 - - - -
39J ILE* 1.3 78.4 - - - +
41J LYS* 1.3 66.8 + - + +
43J LEU* 3.6 7.9 + - - +
44J ARG* 3.8 31.7 + - - +
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Residues in contact with LYS 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201H GLU* 5.4 8.1 + - - +
37J GLN* 3.1 38.1 + - + +
38J ALA* 3.8 4.7 - - - +
40J GLN* 1.3 76.4 - - + +
42J ALA* 1.3 58.7 + - - +
44J ARG* 2.8 56.5 + - - +
45J GLN* 3.9 2.9 + - - +
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Residues in contact with ALA 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197I GLU* 3.1 25.8 - - - +
200I VAL* 3.9 7.6 - - + -
38J ALA 2.9 17.8 + - - +
39J ILE 3.7 1.3 - - - +
41J LYS* 1.3 76.6 - - - +
43J LEU* 1.3 61.1 + - - +
44J ARG 3.1 1.2 + - - -
45J GLN* 3.0 31.4 + - - +
78J MET* 3.6 19.3 - - - -
161J ALA* 3.4 8.8 - - - +
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Residues in contact with LEU 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I TYR* 3.4 32.8 - - + -
39J ILE* 2.9 24.4 + - + +
40J GLN* 3.9 5.4 - - - +
41J LYS 3.2 0.2 - - - -
42J ALA* 1.3 73.2 - - - +
44J ARG* 1.3 57.8 + - - +
45J GLN 3.4 0.4 - - - -
78J MET* 3.3 22.4 - - + -
79J PHE* 4.7 3.1 - - + -
158J PHE* 3.3 33.4 - - + +
159J GLY* 3.5 2.0 - - - +
160J ASN 3.0 11.8 + - - -
161J ALA* 2.8 33.6 + - + -
162J LEU* 3.9 33.9 - - + -
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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