Contacts of the helix formed by residues 32 - 45 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A CYS* 4.3 2.0 - - - -
203B ALA 4.3 1.0 + - - -
207B SER* 3.4 33.7 + - - +
30C GLN 4.6 3.8 - - - +
31C TYR* 1.3 77.2 - - - +
33C ALA* 1.3 66.2 + - - +
34C GLU* 3.6 20.0 + - - +
35C GLU* 3.3 22.9 + - - +
36C TYR* 2.9 21.4 + - - +
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Residues in contact with ALA 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A TYR* 3.2 41.0 - - + +
208A CYS* 3.4 39.7 - - + +
32C THR* 1.3 72.8 - - - +
34C GLU* 1.3 70.3 + - - +
36C TYR* 3.8 0.6 - - - +
37C GLN* 3.0 19.4 + - - +
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Residues in contact with GLU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A TYR* 4.9 8.5 + - - +
203B ALA* 3.5 24.3 - - + +
206B ASN* 5.0 12.8 - - - +
32C THR* 3.1 19.0 + - - +
33C ALA* 1.3 89.4 + - + +
35C GLU* 1.3 62.0 + - - +
37C GLN* 3.8 5.3 + - - +
38C ALA* 3.1 22.7 + - - +
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Residues in contact with GLU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TYR* 4.6 0.2 - - - -
200B VAL* 4.7 3.6 - - + -
203B ALA* 3.4 15.0 - - + +
204B ARG* 3.1 45.0 + - + +
207B SER* 4.0 7.8 + - - -
31C TYR* 3.5 27.9 - - + -
32C THR* 3.2 16.4 + - - +
34C GLU* 1.3 75.7 - - - +
36C TYR* 1.3 67.4 + - - +
38C ALA* 3.3 2.1 + - - +
39C ILE* 3.0 40.2 + - + +
79C PHE 4.4 1.4 - - - +
116C LYS* 3.1 23.6 + - - -
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Residues in contact with TYR 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLU* 3.3 33.8 + - - -
204A ARG* 2.9 42.3 + - + -
205A TYR* 4.5 12.3 - + + -
208A CYS* 4.5 16.4 - - - -
80B GLY* 4.0 3.8 - - - -
81B TYR* 3.5 32.8 + + - -
82B ASN* 3.8 23.3 - - - -
31C TYR* 4.3 10.4 - - + +
32C THR 2.9 18.4 + - - +
33C ALA* 3.8 6.3 - - - +
35C GLU* 1.3 77.8 - - - +
37C GLN* 1.3 76.9 + - + +
40C GLN* 2.8 43.0 + - + +
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Residues in contact with GLN 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLU* 4.9 8.1 - - - +
205A TYR* 3.3 43.5 + - + -
33C ALA 3.0 12.5 + - - +
34C GLU* 3.8 5.8 + - - +
36C TYR* 1.3 89.4 - - - +
38C ALA* 1.3 61.7 + - - +
40C GLN* 3.5 2.6 + - + +
41C LYS* 3.2 55.4 + - + +
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Residues in contact with ALA 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B SER* 3.9 20.3 - - - +
200B VAL* 3.5 32.9 - - + +
203B ALA* 4.6 1.1 - - + -
34C GLU 3.1 16.6 + - - +
35C GLU* 3.7 5.4 - - - +
37C GLN* 1.3 78.4 - - - +
39C ILE* 1.3 56.9 + - - +
41C LYS* 3.4 6.2 + - - +
42C ALA* 2.9 30.1 + - - +
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Residues in contact with ILE 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B TYR* 3.5 26.0 - - + +
200B VAL* 3.4 21.3 - - + -
204B ARG* 4.1 0.2 - - - +
31C TYR* 3.8 15.9 - - + -
35C GLU* 3.0 42.5 + - + +
38C ALA* 1.3 72.9 - - - +
40C GLN* 1.3 60.5 + - - +
43C LEU* 2.8 40.2 + - + +
78C MET* 3.1 41.7 - - + +
79C PHE* 4.0 10.1 - - + -
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Residues in contact with GLN 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLU* 3.4 23.8 + - - +
204A ARG* 4.1 2.8 - - - +
76B ASN* 3.2 24.6 + - - +
77B GLU* 3.8 15.0 + - - -
80B GLY* 3.8 1.8 - - - -
81B TYR* 3.2 29.9 + - - +
36C TYR* 2.8 48.1 + - + +
37C GLN* 3.7 5.6 - - + +
39C ILE* 1.3 78.3 - - - +
41C LYS* 1.3 62.8 + - + +
43C LEU* 3.7 8.1 + - - +
44C ARG* 3.8 25.3 + - - +
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Residues in contact with LYS 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLU* 5.7 6.3 + - - +
37C GLN* 3.2 43.2 + - + +
38C ALA* 3.7 5.6 - - - +
40C GLN* 1.3 75.4 - - + +
42C ALA* 1.3 67.6 + - - +
44C ARG* 3.0 48.5 + - - +
45C GLN* 3.9 3.7 + - - +
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Residues in contact with ALA 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B GLU* 3.1 29.4 - - - +
200B VAL* 4.3 4.7 - - + -
38C ALA 2.9 17.9 + - - +
39C ILE 3.9 0.9 - - - +
41C LYS* 1.3 77.4 - - - +
43C LEU* 1.3 62.8 + - - +
44C ARG 3.1 1.0 + - - -
45C GLN* 3.0 32.9 + - - +
78C MET* 3.8 18.4 - - - -
161C ALA* 3.4 5.7 - - - +
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B TYR* 3.5 28.0 - - + -
39C ILE* 2.8 35.6 + - + +
40C GLN* 4.0 5.6 - - - +
41C LYS 3.2 0.4 + - - -
42C ALA* 1.3 72.7 - - - +
44C ARG* 1.3 58.1 + - - +
78C MET* 3.4 20.6 - - + -
79C PHE* 4.6 2.9 - - + -
158C PHE* 3.2 32.3 - - + +
159C GLY* 4.6 2.9 - - - -
160C ASN 3.1 10.6 + - - -
161C ALA* 2.8 32.4 + - + -
162C LEU* 3.8 32.3 - - + -
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Residues in contact with ARG 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU* 3.8 23.2 - - - +
201A GLU* 4.3 8.3 + - - +
77B GLU* 2.5 54.3 + - - +
40C GLN* 3.8 29.7 + - - +
41C LYS* 3.0 47.6 + - - +
43C LEU* 1.3 74.8 - - - +
45C GLN* 1.3 69.4 + - - +
46C ARG* 3.5 3.5 + - - +
160C ASN* 3.0 24.8 + - - +
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Residues in contact with GLN 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B LYS 4.5 13.0 + - - +
191B ALA 4.9 0.2 - - - -
192B LYS* 3.8 38.2 - - + +
194B GLN* 6.1 0.6 - - - +
197B GLU* 2.9 27.9 + - - +
41C LYS 4.7 1.3 - - - +
42C ALA* 3.0 28.6 + - - +
44C ARG* 1.3 83.3 - - - +
46C ARG* 1.3 59.8 + - - +
160C ASN* 3.2 1.7 - - - +
161C ALA* 3.0 27.2 + - + +
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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