Contacts of the helix formed by residues 263 - 273 (chain A) in PDB entry 3KAS
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 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A ILE* 1.3 76.7 - - - +
264A PHE* 1.3 65.4 + - - +
265A ALA* 3.7 11.0 + - - +
266A GLU* 2.6 46.8 + - - +
267A LYS* 3.1 19.9 + - - +
300A HIS 5.7 0.4 - - - -
303A LEU* 5.0 0.5 - - - +
536A THR* 5.6 2.7 - - - -
537A LEU* 4.9 12.2 - - + +
538A ASP* 4.0 38.6 - - + +
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Residues in contact with PHE 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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220A VAL* 4.0 17.3 - - + -
259A ALA* 4.2 14.8 - - + -
260A GLY 5.2 1.3 - - - -
262A ILE 4.8 1.1 - - - -
263A THR* 1.3 75.0 - - - +
265A ALA* 1.3 63.7 + - - +
267A LYS* 3.1 15.8 + - - +
268A VAL* 2.9 29.3 + - + +
281A ILE* 3.7 36.8 - - + -
297A PHE* 3.5 32.8 - + - -
298A PHE 4.3 2.9 - - - -
299A GLY* 3.9 36.1 - - - -
300A HIS 3.3 15.8 + - - +
301A ALA* 4.3 4.7 - - + -
336A THR* 5.2 0.7 - - - -
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Residues in contact with ALA 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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263A THR* 3.9 9.6 - - - +
264A PHE* 1.3 79.6 - - - +
266A GLU* 1.3 56.5 + - - +
268A VAL* 3.7 2.1 + - - +
269A ALA* 3.1 27.4 + - - +
300A HIS* 3.7 4.6 + - + +
301A ALA* 3.5 27.0 - - - +
302A HIS 3.3 29.8 - - - +
303A LEU* 3.6 16.4 - - + +
537A LEU* 5.3 3.6 - - + -
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Residues in contact with GLU 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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262A ILE* 3.1 23.8 - - + +
263A THR* 2.6 49.8 + - - +
264A PHE 3.2 1.0 - - - -
265A ALA* 1.3 74.2 - - - +
267A LYS* 1.3 56.3 + - - +
269A ALA* 3.1 4.1 + - - +
270A ASN* 2.7 45.2 + - - +
303A LEU* 3.9 18.8 - - + +
536A THR* 5.9 4.0 - - - +
537A LEU* 5.3 7.9 + - - +
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Residues in contact with LYS 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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237A PHE* 2.6 34.4 + - - +
238A GLY* 4.0 11.9 - - - +
243A PHE* 4.4 2.1 - - - -
257A VAL* 3.9 24.0 - - + -
258A ARG 2.8 23.7 + - - +
259A ALA* 4.1 4.5 - - - +
260A GLY 2.9 26.4 + - - +
262A ILE* 3.3 25.4 + - + +
263A THR 3.3 9.9 - - - +
264A PHE* 3.1 21.0 + - + +
266A GLU* 1.3 75.6 - - - +
268A VAL* 1.3 65.7 + - + +
270A ASN* 3.4 1.9 + - - +
271A ALA* 3.0 25.9 + - - +
279A VAL* 5.2 4.9 - - + -
281A ILE* 4.5 5.6 - - + -
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Residues in contact with VAL 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 PHE* 2.9 20.3 + - + +
265A ALA* 3.9 4.5 - - - +
267A LYS* 1.3 76.4 - - + +
269A ALA* 1.3 52.6 + - - +
271A ALA* 3.3 1.2 + - - +
272A GLU* 2.6 53.6 + - - +
279A VAL* 4.3 12.6 - - + -
281A ILE* 5.5 0.4 - - + -
301A ALA* 3.7 21.3 - - + +
330A PRO* 3.7 23.8 - - + -
332A ILE* 4.0 14.7 - - + +
334A VAL* 3.7 27.4 - - + -
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Residues in contact with ALA 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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265A ALA 3.1 19.0 + - - +
266A GLU* 3.5 5.4 - - - +
268A VAL* 1.3 77.6 - - - +
270A ASN* 1.3 56.5 + - - +
272A GLU* 3.6 8.2 - - - +
273A SER* 2.7 37.2 + - - -
303A LEU* 4.0 23.3 - - + -
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Residues in contact with ASN 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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238A GLY 2.8 19.7 + - - +
239A THR 3.6 0.2 - - - -
240A LYS* 3.3 45.1 - - + +
243A PHE* 3.5 22.1 - - + -
262A ILE* 3.8 12.3 - - - +
266A GLU* 2.7 27.5 + - - +
267A LYS 3.8 0.7 - - - +
269A ALA* 1.3 71.9 - - - +
271A ALA* 1.3 61.5 + - - +
273A SER* 3.2 19.7 - - - -
274A LEU* 3.4 14.4 + - - +
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Residues in contact with ALA 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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243A PHE* 3.6 24.1 - - + -
255A VAL* 4.6 4.3 - - + -
267A LYS 3.0 17.9 + - - +
268A VAL 3.6 2.9 - - - +
270A ASN* 1.3 72.4 - - - +
272A GLU* 1.3 66.3 + - - +
273A SER 3.0 1.3 - - - -
274A LEU* 2.9 14.6 + - - +
275A ASN 3.2 0.2 + - - -
276A ALA* 3.1 35.4 + - + +
279A VAL* 4.0 17.9 - - + -
332A ILE* 4.9 0.2 - - + -
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Residues in contact with GLU 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 VAL* 2.6 29.9 + - - +
269A ALA* 3.6 7.2 - - - +
271A ALA* 1.3 72.9 - - - +
273A SER* 1.3 58.6 + - - +
275A ASN* 3.0 24.2 + - - +
276A ALA 4.5 4.5 - - - +
329A LEU 4.7 1.2 - - - +
330A PRO* 3.6 10.4 - - - +
331A ASN* 2.7 58.5 + - - +
332A ILE* 4.2 23.7 - - + +
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Residues in contact with SER 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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269A ALA 2.7 18.0 + - - -
270A ASN* 3.2 13.2 - - - -
272A GLU* 1.3 78.7 - - - +
274A LEU* 1.3 64.2 + - - +
275A ASN* 3.4 5.1 + - - -
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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