Contacts of the helix formed by residues 259 - 271 (chain A) in PDB entry 2KXH
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 LYS 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A ASN* 3.6 4.0 - - - +
257A TYR* 3.3 10.2 - - - +
258A GLU* 1.3 105.7 + - + +
260A ALA* 1.3 64.6 + - - +
261A GLN* 3.4 15.7 + - + +
262A SER* 3.4 19.6 + - - +
263A SER 3.3 16.1 + - - -
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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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206A ARG* 6.3 0.4 - - - +
209A ASN* 3.6 19.4 + - + +
259A LYS* 1.3 71.3 - - - +
261A GLN* 1.3 77.9 - - - +
263A SER* 3.6 7.1 + - - -
264A GLN* 3.3 27.9 + - - +
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Residues in contact with GLN 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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259A LYS* 3.2 15.2 - - + -
260A ALA* 1.3 89.6 - - - +
262A SER* 1.3 63.8 + - - +
264A GLN* 3.1 31.8 + - - +
265A ASP* 2.9 21.6 + - - +
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Residues in contact with SER 262 (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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232A PHE* 5.4 2.3 - - - +
233A GLY* 4.2 14.9 - - - -
234A LYS 4.7 2.2 + - - -
257A TYR* 3.5 26.3 - - - -
259A LYS* 3.4 22.4 + - - +
260A ALA 3.4 0.2 - - - -
261A GLN* 1.3 75.7 - - - +
263A SER* 1.3 65.9 + - - +
265A ASP* 3.2 12.9 + - - +
266A ALA* 3.0 24.1 + - - +
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Residues in contact with SER 263 (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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209A ASN* 4.3 11.6 + - - -
210A ARG 5.1 0.5 - - - -
211A ILE* 3.9 20.4 - - - +
257A TYR* 3.9 23.2 - - - -
259A LYS 3.3 10.6 + - - -
260A ALA* 3.6 13.5 - - - -
261A GLN 3.2 0.6 - - - -
262A SER* 1.3 79.1 - - - +
264A GLN* 1.3 62.9 + - - +
266A ALA* 3.2 4.9 + - - +
267A VAL* 3.1 29.8 + - - +
284A LYS* 5.4 5.5 - - - +
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Residues in contact with GLN 264 (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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260A ALA* 3.3 19.1 + - - +
261A GLN* 3.1 29.3 + - - +
263A SER* 1.3 74.1 - - - +
265A ASP* 1.3 64.3 + - - +
267A VAL* 3.5 10.3 + - + +
268A SER* 3.0 25.6 + - - -
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Residues in contact with ASP 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A PHE* 4.8 11.9 - - + -
261A GLN* 2.9 30.1 + - - +
262A SER* 3.2 11.7 + - - +
264A GLN* 1.3 77.4 - - - +
266A ALA* 1.3 63.4 + - - +
268A SER* 3.3 16.6 + - - -
269A SER* 3.7 9.4 + - - -
24B MET* 3.3 20.1 - - - +
25B GLY* 2.9 36.6 + - - +
27B VAL* 5.3 8.9 - - + +
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Residues in contact with ALA 266 (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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211A ILE* 4.3 1.3 - - + -
229A PHE* 4.0 14.6 - - + -
232A PHE* 3.6 19.0 - - + -
257A TYR* 3.2 31.9 - - + +
262A SER 3.0 9.4 + - - +
263A SER 3.2 8.5 + - - +
265A ASP* 1.3 78.2 - - - +
267A VAL* 1.3 54.9 + - - +
269A SER* 2.9 3.3 + - - -
270A MET* 2.7 37.7 + - + +
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Residues in contact with VAL 267 (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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211A ILE* 3.5 19.7 - - + +
263A SER* 3.1 22.1 + - - +
264A GLN* 3.8 9.9 - - - +
265A ASP 3.4 0.2 - - - -
266A ALA* 1.3 74.7 - - - +
268A SER* 1.3 62.3 + - - +
269A SER 3.3 0.9 + - - -
270A MET 3.8 1.6 + - - -
271A ASN* 4.1 6.2 + - - +
282A VAL* 3.5 34.5 - - + +
283A GLY* 4.1 13.9 - - - +
284A LYS* 6.1 2.0 - - + -
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Residues in contact with SER 268 (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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264A GLN 3.0 13.9 + - - -
265A ASP 3.3 5.8 + - - -
266A ALA 3.1 0.8 + - - -
267A VAL* 1.3 78.9 - - - +
269A SER* 1.3 58.8 + - - +
271A ASN* 5.1 1.1 - - - +
272A LEU* 4.4 10.6 - - - +
25B GLY* 3.4 30.0 - - - +
26B TYR* 5.9 6.1 - - - -
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Residues in contact with SER 269 (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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232A PHE* 4.4 7.9 - - - -
265A ASP 3.7 4.6 + - - -
266A ALA 2.9 4.7 + - - -
268A SER* 1.3 77.1 + - - +
270A MET* 1.3 59.1 + - - +
271A ASN 3.1 4.7 - - - -
272A LEU* 3.0 23.9 + - - +
25B GLY 3.3 19.8 + - - -
26B TYR* 5.0 0.7 - - - -
27B VAL* 3.8 15.3 + - - +
31B PHE* 3.3 46.5 - - - -
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Residues in contact with MET 270 (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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228A VAL* 3.4 33.9 - - + -
229A PHE* 3.4 42.4 - - + -
232A PHE* 3.4 26.7 - - + -
266A ALA 2.7 24.0 + - - +
267A VAL 3.8 0.4 + - - -
269A SER* 1.3 70.0 - - - +
271A ASN* 1.3 64.9 + - - +
272A LEU 3.2 0.4 - - - -
273A PHE* 3.3 38.9 - - + +
280A LEU* 3.4 15.7 - - + +
282A VAL* 3.4 22.3 - - + +
31B PHE* 5.1 1.1 - - - -
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Residues in contact with ASN 271 (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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172A GLN* 4.6 12.9 - - - +
267A VAL 4.1 10.0 + - - +
268A SER 5.3 0.7 - - - +
269A SER 3.0 0.6 + - - -
270A MET* 1.3 78.4 - - - +
272A LEU* 1.3 71.6 + - + +
273A PHE 3.2 0.4 - - - -
279A TYR* 3.5 4.9 - - - +
280A LEU 2.7 36.4 + - - +
281A ARG* 2.7 44.5 + - - +
282A VAL* 3.8 11.7 + - + +
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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