Contacts of the helix formed by residues 32 - 43 (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 THR 32 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208I CYS* 4.6 0.2 - - - -
203J ALA 4.3 0.2 + - - -
207J SER* 3.2 35.4 + - - +
30K GLN 4.5 4.0 - - - +
31K TYR* 1.3 76.7 - - - +
33K ALA* 1.3 66.1 + - - +
34K GLU* 3.6 21.2 + - - +
35K GLU* 3.4 20.8 + - - +
36K TYR* 2.8 21.6 + - - +
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Residues in contact with ALA 33 (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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205I TYR* 3.6 27.5 - - + +
208I CYS* 3.4 43.2 - - + +
32K THR* 1.3 71.7 - - - +
34K GLU* 1.3 71.6 + - - +
36K TYR* 3.8 1.1 - - - +
37K GLN* 3.0 26.7 + - - +
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Residues in contact with GLU 34 (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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205I TYR* 5.0 4.7 + - - +
203J ALA* 3.3 29.1 - - + +
206J ASN* 4.7 15.4 - - + +
32K THR* 3.2 18.5 + - - +
33K ALA* 1.3 88.4 + - - +
35K GLU* 1.3 63.8 + - - +
37K GLN* 3.5 7.8 + - - +
38K ALA* 3.0 19.8 + - - +
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Residues in contact with GLU 35 (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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200J VAL* 4.8 2.7 - - + -
203J ALA* 3.3 15.6 - - + +
204J ARG* 2.9 45.9 + - + +
207J SER* 3.7 16.3 + - - -
31K TYR* 3.6 23.2 - - + -
32K THR* 3.2 15.6 + - - +
34K GLU* 1.3 75.9 - - - +
36K TYR* 1.3 67.7 + - - +
38K ALA* 3.1 2.1 + - - +
39K ILE* 2.8 43.1 + - + +
79K PHE 4.6 1.2 - - - +
116K LYS* 3.1 25.1 + - - -
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Residues in contact with TYR 36 (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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201I GLU* 3.7 17.0 + - - -
204I ARG* 2.9 49.0 + - + -
205I TYR* 4.6 11.7 - + - -
208I CYS* 4.3 19.5 - - - -
80J GLY* 4.0 3.1 - - - -
81J TYR* 3.4 36.6 + + - -
82J ASN* 3.9 21.1 - - - -
31K TYR* 4.3 10.6 - - + +
32K THR 2.8 21.6 + - - +
33K ALA* 3.8 7.6 - - - +
35K GLU* 1.3 72.6 - - - +
37K GLN* 1.3 69.0 + - + +
40K GLN* 2.7 61.5 + - + +
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Residues in contact with GLN 37 (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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201I GLU* 5.0 8.3 - - - +
205I TYR* 3.1 48.5 + - + +
33K ALA 3.0 12.8 + - - +
34K GLU* 3.7 5.8 + - - +
36K TYR* 1.3 86.7 - - - +
38K ALA* 1.3 63.4 + - - +
40K GLN* 3.3 2.2 + - - +
41K LYS* 3.0 57.5 + - + +
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Residues in contact with ALA 38 (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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199J SER* 3.8 22.6 + - - +
200J VAL* 3.6 32.0 - - + +
203J ALA* 4.3 4.0 - - + -
34K GLU 3.0 17.0 + - - +
35K GLU 3.6 3.6 - - - +
37K GLN* 1.3 77.7 - - - +
39K ILE* 1.3 57.1 + - - +
41K LYS* 3.3 6.3 + - - +
42K ALA* 2.9 30.3 + - - +
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Residues in contact with ILE 39 (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* 3.4 28.3 - - + +
200J VAL* 3.4 22.2 - - + -
204J ARG* 4.1 0.2 - - - +
31K TYR* 3.7 29.6 - - + -
35K GLU* 2.8 32.6 + - + +
38K ALA* 1.3 71.6 - - - +
40K GLN* 1.3 57.7 + - - +
43K LEU* 2.9 41.2 + - + +
78K MET* 3.1 40.8 - - + +
79K PHE* 4.2 10.3 - - + -
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Residues in contact with GLN 40 (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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201I GLU* 3.7 20.5 + - - +
204I ARG* 4.1 2.2 - - - +
76J ASN* 3.3 25.8 + - - +
77J GLU* 4.1 5.1 + - - -
80J GLY* 3.6 2.8 - - - -
81J TYR* 3.4 27.9 + - - +
36K TYR* 2.7 55.1 + - + +
37K GLN* 3.6 6.3 - - - +
39K ILE* 1.3 74.2 - - - +
41K LYS* 1.3 60.2 + - + +
43K LEU* 4.2 6.0 + - - +
44K ARG* 3.6 33.6 + - - +
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Residues in contact with LYS 41 (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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201I GLU* 5.5 6.3 + - - +
37K GLN* 3.0 48.5 + - + +
38K ALA* 3.7 5.4 - - - +
40K GLN* 1.3 76.6 - - + +
42K ALA* 1.3 67.1 + - - +
44K ARG* 2.9 46.7 + - - +
45K GLN* 3.9 3.1 + - - +
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Residues in contact with ALA 42 (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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197J GLU* 2.9 33.7 - - - +
200J VAL* 3.9 5.8 - - + -
38K ALA 2.9 18.3 + - - +
39K ILE 3.9 0.7 - - - +
41K LYS* 1.3 77.1 - - - +
43K LEU* 1.3 60.9 + - - +
44K ARG 3.0 1.6 + - - -
45K GLN* 3.1 33.4 + - - +
78K MET* 3.8 13.7 - - - -
161K ALA* 3.4 6.4 - - - +
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Residues in contact with LEU 43 (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* 3.5 27.6 - - + -
39K ILE* 2.9 28.8 + - + +
40K GLN* 4.5 6.3 - - - +
41K LYS 3.2 0.2 + - - -
42K ALA* 1.3 75.2 - - - +
44K ARG* 1.3 57.3 + - + +
45K GLN 3.3 0.2 - - - -
78K MET* 3.3 23.6 - - + -
79K PHE* 4.6 3.4 - - + -
158K PHE* 3.4 31.0 - - + +
159K GLY* 4.6 1.8 - - - +
160K ASN 3.1 10.7 + - - -
161K ALA* 2.8 36.1 + - + -
162K LEU* 3.9 34.5 - - + -
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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