Contacts of the helix formed by residues 246 - 261 (chain A) in PDB entry 1KPI
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 ASN 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A CYS* 3.7 2.2 - - - -
44A ALA 3.2 21.8 - - - +
45A TYR* 3.8 14.1 - - - -
46A PHE* 2.9 40.4 + - + +
243A ILE* 3.0 36.8 + - - +
244A GLY 3.0 0.2 - - - -
245A ALA* 1.3 79.7 - - - +
247A TYR* 1.3 55.8 + - - +
248A VAL 3.2 0.2 - - - -
249A PRO* 3.0 19.9 - - - +
250A THR* 3.0 17.7 + - - -
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Residues in contact with TYR 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A SER* 3.6 2.4 - - - -
43A CYS* 3.3 35.8 + - + -
184A ILE* 4.1 2.2 - - + -
244A GLY 2.9 15.2 + - - +
246A ASN* 1.3 77.2 - - - +
248A VAL* 1.3 58.7 + - - +
250A THR* 3.8 9.2 - - + -
251A LEU* 2.9 48.3 + - + +
254A TRP* 3.9 21.2 - + - -
288A PHE* 3.6 28.9 - + + -
295A VAL* 3.3 23.6 - - + -
901A 10A 3.2 27.4 - - + +
902A CO3 2.6 32.4 + - - -
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Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ALA* 3.4 13.7 - - - +
247A TYR* 1.3 75.4 - - - +
249A PRO* 1.3 73.9 - - + +
252A ASN* 2.9 42.3 + - - +
285A SER* 3.4 25.8 + - - +
288A PHE* 4.1 7.0 - - + -
289A ARG* 3.7 47.1 - - + +
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Residues in contact with PRO 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 3.5 33.0 - - + -
245A ALA 3.4 9.6 - - - +
246A ASN* 3.0 13.9 - - - +
248A VAL* 1.3 95.5 - - + +
250A THR* 1.3 51.2 + - - +
252A ASN* 3.2 8.2 + - + +
253A ALA* 2.7 37.0 + - - +
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Residues in contact with THR 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A SER 4.1 0.2 - - - +
44A ALA* 3.1 41.9 + - + +
46A PHE* 4.0 1.3 - - - -
53A LEU* 4.3 12.8 - - + -
246A ASN 3.0 14.4 + - - -
247A TYR* 3.7 17.3 - - + -
248A VAL 3.2 0.4 - - - -
249A PRO* 1.3 76.9 - - - +
251A LEU* 1.3 64.4 + - - +
253A ALA* 3.0 5.5 + - - +
254A TRP* 2.9 61.8 + - + -
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Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A TYR* 2.9 45.0 + - + +
250A THR* 1.3 72.7 - - - +
252A ASN* 1.3 57.1 + - - +
254A TRP* 3.8 17.0 - - + +
255A ALA* 3.0 28.8 + - - +
280A TYR* 5.0 1.3 - - + -
281A LEU* 3.7 46.7 - - + +
284A CYS* 3.8 19.1 - - + -
285A SER* 3.7 29.6 - - - +
288A PHE* 3.9 12.6 - - + -
901A 10A 4.4 9.9 - - + -
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Residues in contact with ASN 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A VAL* 2.9 44.5 + - - +
249A PRO* 3.6 6.7 - - + +
251A LEU* 1.3 73.2 - - - +
253A ALA* 1.3 62.5 + - - +
255A ALA* 3.3 1.1 + - - +
256A ASP* 2.8 43.9 + - - +
282A ARG* 4.2 17.2 + - - +
285A SER* 3.0 19.2 + - - -
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Residues in contact with ALA 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 6.0 1.6 - - + -
53A LEU* 3.9 31.4 - - + -
249A PRO 2.7 21.9 + - - +
250A THR 3.4 5.2 - - - +
252A ASN* 1.3 74.1 - - - +
254A TRP* 1.3 57.3 + - - +
256A ASP* 3.7 6.1 - - - +
257A ALA* 2.9 32.0 + - - +
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Residues in contact with TRP 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TRP* 3.5 43.6 - + + +
35A LEU* 3.4 18.4 - - + +
36A ASP 4.5 0.4 - - - +
40A THR 3.7 21.5 + - - -
41A TYR* 3.6 27.1 - + - -
42A SER* 3.8 13.5 - - - -
53A LEU* 3.6 26.2 - - + +
57A GLN* 3.9 6.2 - - - +
247A TYR* 3.9 21.8 - + - -
250A THR* 2.9 32.1 + - + +
251A LEU* 3.8 24.2 - - + +
253A ALA* 1.3 77.2 - - - +
255A ALA* 1.3 61.9 + - - +
257A ALA 3.4 0.2 + - - -
258A LEU* 3.0 22.9 + - - +
281A LEU* 3.8 15.2 - - + +
901A 10A 4.0 10.1 - - + -
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Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A LEU 3.0 18.7 + - - +
252A ASN 3.9 0.2 - - - +
254A TRP* 1.3 75.8 - - - +
256A ASP* 1.3 63.6 + - - +
258A LEU 3.2 1.2 + - - -
259A GLN* 3.0 19.6 + - - +
278A MET* 3.3 14.2 - - + +
281A LEU* 3.7 24.4 - - + +
282A ARG* 3.4 40.8 - - - +
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Residues in contact with ASP 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ASN* 2.8 29.7 + - - +
253A ALA* 3.7 6.6 + - - +
255A ALA* 1.3 76.8 - - - +
257A ALA* 1.3 57.5 + - - +
259A GLN* 2.9 7.3 + - - +
260A ALA* 2.8 29.3 + - - +
282A ARG* 3.0 26.0 + - - +
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Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU 4.3 2.9 - - - +
34A TRP* 3.5 30.1 - - - +
253A ALA 2.9 17.0 + - - +
254A TRP 3.7 1.1 - - - +
256A ASP* 1.3 75.9 - - - +
258A LEU* 1.3 60.8 + - - +
260A ALA* 3.3 6.8 - - - +
261A HIS* 2.9 36.1 + - + +
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Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PHE* 4.7 4.9 - - + -
33A LEU* 5.7 1.6 - - + -
34A TRP* 3.7 30.7 - - + +
254A TRP 3.0 13.4 + - - +
255A ALA* 3.5 9.2 - - - +
257A ALA* 1.3 76.3 - - - +
259A GLN* 1.3 64.4 + - - +
261A HIS* 3.4 2.8 + - - +
262A LYS* 3.0 23.1 + - + +
265A ALA* 3.9 25.6 - - + -
274A CYS* 4.3 9.9 - - + +
277A TYR* 4.0 15.9 - - + -
278A MET* 3.6 40.8 - - + +
281A LEU* 4.1 9.4 - - + -
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Residues in contact with GLN 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ALA 3.0 12.0 + - - +
256A ASP* 2.9 12.7 + - - +
258A LEU* 1.3 76.2 - - - +
260A ALA* 1.3 66.3 + - - +
262A LYS* 3.1 46.3 + - - +
278A MET* 4.0 18.9 - - + +
282A ARG* 4.7 9.0 - - - +
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Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ASP 2.8 11.1 + - - +
257A ALA* 3.3 14.8 - - - +
259A GLN* 1.3 80.3 - - - +
261A HIS* 1.3 70.4 + - + +
262A LYS* 3.4 2.4 + - - +
263A ASP* 5.0 1.0 + - - +
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Residues in contact with HIS 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.2 40.0 + - + +
257A ALA* 2.9 31.8 + - - +
258A LEU* 3.5 4.5 - - + +
260A ALA* 1.3 84.0 - - + +
262A LYS* 1.3 53.4 + - - +
263A ASP* 3.3 2.9 - - - -
264A GLU* 3.0 31.0 + - + +
265A ALA* 2.8 33.5 + - + +
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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