Contacts of the helix formed by residues 222 - 232 (chain F) in PDB entry 1KQN
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 SER 222 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21F THR* 4.8 0.2 - - - -
23F MET* 4.3 8.5 - - - -
220F ASP* 2.6 16.6 + - - -
221F ILE* 1.3 73.4 - - - +
223F SER* 1.3 65.8 + - - +
224F THR* 3.5 9.7 + - - -
225F LYS* 3.2 32.1 + - - +
226F ILE* 3.0 22.7 + - - +
782F NAD 5.6 3.8 - - - -
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Residues in contact with SER 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ASN* 3.5 21.3 + - - -
19F PRO* 2.9 30.2 + - - +
21F THR* 4.6 2.3 - - - +
23F MET* 5.2 0.8 - - - +
24F HIS* 3.6 14.9 + - - -
57F LYS* 6.3 0.9 - - - -
221F ILE 3.9 1.2 + - - -
222F SER* 1.3 73.6 - - - +
224F THR* 1.3 58.2 + - - +
226F ILE* 3.0 8.5 + - - +
227F ARG* 2.9 38.9 + - - +
782F NAD 4.7 9.2 + - - -
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Residues in contact with THR 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F SER* 3.5 8.6 + - - -
223F SER* 1.3 78.8 - - - +
225F LYS* 1.3 59.8 + - + +
227F ARG* 3.2 28.0 + - - +
228F ARG* 2.9 51.7 + - - +
231F ARG* 5.1 0.3 + - - -
259F GLU* 5.8 1.1 - - - +
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Residues in contact with LYS 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B TYR* 3.6 21.0 + - - +
199B GLU* 6.1 0.9 - - - -
216E TRP* 2.6 26.0 + - - +
217E ILE* 3.4 38.0 - - + +
220F ASP* 3.0 27.1 + - - +
222F SER* 3.2 21.0 + - - +
224F THR* 1.3 78.7 - - - +
226F ILE* 1.3 61.8 + - - +
228F ARG* 3.8 20.3 - - - +
229F ALA* 3.1 22.9 + - - +
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Residues in contact with ILE 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E ILE* 4.6 3.1 - - + -
19F PRO* 3.8 24.7 - - + -
21F THR* 4.2 9.2 - - + -
221F ILE* 3.9 14.4 - - + -
222F SER 3.0 17.1 + - - +
223F SER* 3.0 8.3 + - - +
225F LYS* 1.3 79.3 - - - +
227F ARG* 1.3 62.8 + - - +
229F ALA* 3.2 5.0 + - - +
230F LEU* 3.1 33.1 + - + +
236F ILE* 3.9 25.1 - - + +
239F LEU* 3.3 44.4 - - + -
240F VAL* 4.7 5.6 - - + -
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Residues in contact with ARG 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ASN* 3.0 38.9 + - - +
19F PRO* 4.2 3.4 - - + -
57F LYS* 6.1 2.4 - - - +
58F LYS 4.7 7.3 + - - -
59F GLY 4.3 3.5 + - - -
223F SER* 2.9 28.3 + - - +
224F THR* 3.6 31.0 + - - +
226F ILE* 1.3 73.9 - - - +
228F ARG* 1.3 65.2 + - - +
230F LEU* 3.3 10.5 + - - +
231F ARG* 3.0 32.1 + - - +
254F TYR* 3.4 40.1 - - + +
259F GLU* 2.6 46.1 + - - +
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Residues in contact with ARG 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B TYR* 3.4 39.3 + - + +
199B GLU* 4.1 26.4 + - - +
201B ASP* 4.2 0.4 - - - -
224F THR* 2.9 35.3 + - - +
225F LYS* 3.8 23.0 - - - +
227F ARG* 1.3 76.6 - - - +
229F ALA* 1.3 64.8 + - - +
231F ARG* 3.3 28.4 + - - +
232F ARG* 3.0 70.3 + - - +
234F GLN* 5.6 0.4 - - - +
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Residues in contact with ALA 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ARG* 5.8 2.0 - - - +
217E ILE* 5.0 8.3 - - + -
225F LYS 3.1 12.2 + - - +
226F ILE* 3.4 9.2 - - - +
227F ARG 3.2 0.2 - - - -
228F ARG* 1.3 80.5 - - - +
230F LEU* 1.3 60.9 + - - +
232F ARG* 3.1 4.0 + - - -
233F GLY 3.0 4.7 + - - -
234F GLN* 2.8 53.0 + - + +
235F SER 4.8 1.8 - - - +
236F ILE* 3.8 18.6 - - + -
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Residues in contact with LEU 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226F ILE* 3.1 31.0 + - + +
227F ARG 3.7 3.8 - - - +
229F ALA* 1.3 74.3 - - - +
231F ARG* 1.3 56.2 + - - +
233F GLY* 2.7 24.5 + - - +
234F GLN 4.6 5.4 - - - +
236F ILE* 3.7 28.7 - - + -
248F ILE* 3.8 16.8 - - + -
249F GLU* 3.9 24.5 - - - +
254F TYR* 3.5 46.8 - - + +
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Residues in contact with ARG 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B ASP* 2.8 42.2 + - - +
224F THR 5.1 0.4 + - - -
227F ARG* 3.0 27.1 + - - +
228F ARG* 3.3 38.4 + - - +
230F LEU* 1.3 76.1 - - - +
232F ARG* 1.3 61.3 + - + +
233F GLY 3.2 0.4 + - - -
254F TYR* 4.5 4.9 + - + -
255F SER* 3.4 26.5 - - - +
256F SER* 3.4 32.3 - - - +
259F GLU* 3.4 33.5 + - - +
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Residues in contact with ARG 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B TYR* 2.8 45.4 + - - -
199B GLU 4.0 0.4 - - - -
200B SER 3.5 16.8 - - - +
201B ASP* 2.9 30.8 + - - +
204B TRP* 3.3 47.7 - - + +
228F ARG* 3.0 37.5 + - - +
229F ALA 3.1 7.7 + - - +
230F LEU 3.1 0.8 - - - -
231F ARG* 1.3 78.8 - - + +
233F GLY* 1.3 63.9 + - - +
234F GLN* 3.3 21.1 + - + +
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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