Contacts of the helix formed by residues 264 - 275 (chain A) in PDB entry 2A3K
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 ALA 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A SER* 1.3 74.5 - - - +
265A GLY* 1.3 67.1 + - - +
266A PRO* 3.4 2.5 - - - -
267A LEU* 3.1 15.9 + - - +
268A LEU* 3.1 15.1 + - - +
342A PHE* 3.8 13.9 - - + -
345A HIS* 3.7 19.7 - - + -
346A THR* 4.0 15.7 - - + +
349A LEU* 3.6 13.5 - - + -
503A PO4 3.1 16.6 + - - +
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Residues in contact with GLY 265 (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 ALA* 1.3 76.4 - - - +
266A PRO* 1.3 67.9 - - - +
268A LEU* 3.0 16.5 + - - +
269A ARG* 3.1 17.7 + - - +
349A LEU* 3.6 10.0 - - - +
503A PO4 2.8 9.6 + - - -
504A PO4 3.2 22.0 - - - -
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Residues in contact with PRO 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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229A PRO* 4.8 4.0 - - + +
230A GLU* 4.0 26.2 - - + -
231A TYR* 4.5 4.3 - - + -
252A PHE* 4.0 12.0 - - + -
261A PRO* 6.4 0.9 - - + -
263A SER* 3.4 23.1 - - - +
264A ALA 3.7 2.5 - - - +
265A GLY* 1.3 88.4 - - - +
267A LEU* 1.3 60.8 + - - +
269A ARG* 3.4 12.6 + - + +
270A LEU* 3.1 21.5 + - - +
504A PO4 4.4 3.4 - - - +
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Residues in contact with LEU 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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252A PHE* 4.2 12.4 - - + -
255A TRP* 3.7 35.9 - - + -
261A PRO* 4.9 3.4 - - + -
263A SER 5.0 3.3 + - - +
264A ALA* 3.1 15.5 + - - +
266A PRO* 1.3 79.2 - - - +
268A LEU* 1.3 57.6 + - - +
270A LEU* 3.3 22.6 - - + +
271A VAL* 3.1 26.8 + - + +
300A CYS* 6.1 0.2 - - + -
301A PHE* 4.3 13.5 - - + -
304A THR* 4.3 14.1 - - + +
342A PHE* 3.7 27.6 - - + -
346A THR* 3.8 18.6 - - + +
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Residues in contact with LEU 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 ALA 3.1 11.7 + - - +
265A GLY* 3.0 9.6 + - - +
267A LEU* 1.3 73.4 - - - +
269A ARG* 1.3 61.1 + - + +
271A VAL* 3.2 8.4 + - + +
272A ALA* 2.9 27.0 + - - +
304A THR* 4.3 4.9 - - + -
308A CYS* 4.0 24.9 - - - -
346A THR* 3.8 27.6 - - + +
349A LEU* 3.6 35.2 - - + +
350A TYR* 3.8 26.7 - - + +
353A GLN* 5.6 4.5 - - + -
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Residues in contact with ARG 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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231A TYR* 3.8 18.5 + - + +
265A GLY 3.1 16.2 + - - +
266A PRO* 3.5 13.9 - - + +
268A LEU* 1.3 78.5 - - + +
270A LEU* 1.3 56.0 + - - +
272A ALA* 3.3 8.1 + - - +
273A GLU* 3.0 26.3 + - - +
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Residues in contact with LEU 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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192A VAL* 4.6 7.2 - - + -
194A LEU* 4.0 12.8 - - + -
231A TYR* 4.1 17.4 - - + -
250A ILE* 3.4 37.0 - - + -
252A PHE* 3.4 36.1 - - + -
266A PRO 3.1 12.9 + - - +
267A LEU* 3.3 16.4 - - + +
268A LEU 3.2 0.2 - - - -
269A ARG* 1.3 73.1 - - - +
271A VAL* 1.3 66.9 + - - +
273A GLU* 3.2 6.4 + - + +
274A VAL* 3.0 23.1 + - + +
301A PHE* 3.9 24.5 - - + -
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Residues in contact with VAL 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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267A LEU* 3.1 16.0 + - + +
268A LEU* 3.2 11.4 + - + +
270A LEU* 1.3 77.4 - - - +
272A ALA* 1.3 57.2 + - - +
274A VAL* 3.0 26.3 + - - +
275A GLU* 3.4 13.0 - - + +
301A PHE* 3.8 23.6 - - + -
304A THR* 4.1 23.3 - - + -
305A ARG* 3.9 31.2 - - + -
308A CYS* 4.7 16.2 - - + -
350A TYR* 5.8 2.7 - - + -
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Residues in contact with ALA 272 (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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268A LEU 2.9 13.6 + - - +
269A ARG* 3.5 12.3 - - - +
270A LEU 3.3 0.2 - - - -
271A VAL* 1.3 76.2 - - - +
273A GLU* 1.3 61.9 + - - +
275A GLU* 3.3 22.8 + - - +
276A GLU* 3.9 9.9 - - - +
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Residues in contact with GLU 273 (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 CYS* 5.2 1.7 - - - -
231A TYR* 2.5 39.6 + - + +
233A VAL* 4.3 10.7 - - + +
248A LYS* 3.1 38.5 + - - +
250A ILE* 3.9 17.9 - - + -
269A ARG 3.0 11.9 + - - +
270A LEU* 3.3 13.0 - - + +
272A ALA* 1.3 77.5 - - - +
274A VAL* 1.3 59.6 + - - +
275A GLU 3.1 0.9 + - - -
276A GLU* 2.9 34.3 + - - +
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Residues in contact with VAL 274 (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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165A TYR* 5.7 0.2 - - + -
190A LEU* 3.5 22.7 - - + +
192A VAL* 3.6 20.4 - - + -
250A ILE* 4.2 9.4 - - + -
270A LEU* 3.0 17.2 + - + +
271A VAL* 3.0 11.2 + - - +
273A GLU* 1.3 76.5 - - - +
275A GLU* 1.3 54.1 + - - +
276A GLU 3.3 5.8 + - - -
287A ILE* 4.0 29.2 - - + +
301A PHE* 3.6 28.0 - - + -
305A ARG* 4.3 21.2 + - + +
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Residues in contact with GLU 275 (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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271A VAL* 3.4 18.4 - - + +
272A ALA* 3.6 12.6 - - - +
273A GLU 3.1 2.0 - - - -
274A VAL* 1.3 76.7 - - - +
276A GLU* 1.3 66.8 + - - +
305A ARG* 4.1 21.8 - - - +
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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