Contacts of the helix formed by residues 266 - 277 (chain A) in PDB entry 6XAV
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 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A ILE* 3.3 46.2 + - - +
264A LEU* 3.2 29.0 - - - +
265A ASP* 1.3 77.7 - - - +
267A ILE* 1.3 57.0 + - - +
268A THR* 3.1 3.8 - - - -
269A ARG* 2.8 13.1 + - - -
270A LEU* 2.4 40.3 + - - +
318A THR* 4.5 0.6 + - - -
320A LEU* 6.1 0.9 - - - -
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Residues in contact with ILE 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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175A LEU* 3.7 23.3 - - + -
264A LEU* 4.0 13.9 + - + +
266A SER* 1.3 75.1 - - - +
268A THR* 1.3 60.7 + - - +
270A LEU* 4.2 5.2 - - + +
271A ALA* 3.1 27.5 + - - +
297A PRO* 5.3 6.5 - - + +
300A PHE* 6.4 1.3 - - + -
301A PHE* 4.4 19.7 - - + -
317A ALA* 3.7 22.4 - - + -
318A THR 3.3 25.5 + - - +
319A ALA* 4.1 8.5 - - + +
331A ILE* 5.5 0.4 - - - -
335A PHE* 3.6 33.8 - - + -
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Residues in contact with THR 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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266A SER 3.1 0.4 - - - -
267A ILE* 1.3 77.9 - - - +
269A ARG* 1.3 66.4 + - - +
271A ALA* 3.4 6.0 + - - +
272A ARG* 3.2 37.5 + - - +
318A THR 4.5 0.6 + - - -
319A ALA* 3.6 6.9 - - - +
320A LEU* 3.0 50.7 + - + +
328A ASP* 3.6 34.5 - - + +
331A ILE* 4.8 10.6 - - + +
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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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209A ILE* 3.8 25.1 - - + +
210A ASP* 3.9 32.4 + - + +
211A GLU* 5.1 5.5 + - - +
265A ASP 4.7 4.0 - - - +
266A SER* 2.8 14.7 + - - +
268A THR* 1.3 78.4 - - - +
270A LEU* 1.3 63.9 + - - +
272A ARG* 3.0 49.4 + - - +
273A ALA* 3.1 19.6 + - - +
320A LEU* 4.4 26.9 - - + +
323A THR* 5.9 2.8 - - - +
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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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209A ILE* 4.8 12.5 - - + +
239A HIS 4.2 11.9 - - - +
240A VAL* 4.9 0.7 - - - -
243A ALA* 4.1 27.1 - - + -
264A LEU* 4.5 18.6 - - + -
266A SER* 2.4 38.3 + - - +
267A ILE* 4.2 4.9 - - + +
269A ARG* 1.3 69.6 - - - +
271A ALA* 1.3 62.1 + - - +
273A ALA* 3.2 12.7 + - + +
274A TYR* 3.1 58.6 + - + +
297A PRO* 5.1 9.2 - - + -
300A PHE* 4.5 18.2 - - + -
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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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267A ILE 3.1 20.5 + - - +
268A THR 3.7 2.7 - - - +
269A ARG 3.2 0.2 - - - -
270A LEU* 1.3 77.9 - - - +
272A ARG* 1.3 56.2 + - - +
274A TYR* 3.5 2.4 + - - +
275A ASN* 3.0 30.0 + - - +
294A LEU* 4.4 12.9 - - + +
297A PRO* 4.6 12.7 - - + +
331A ILE* 3.7 37.0 - - + +
335A PHE* 4.7 4.3 - - + -
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Residues in contact with ARG 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 THR* 3.2 22.9 + - - +
269A ARG* 3.0 44.4 + - - +
271A ALA* 1.3 76.9 - - - +
273A ALA* 1.3 55.5 + - - +
275A ASN* 3.4 6.8 + - - +
276A THR* 2.6 39.0 + - - +
320A LEU* 5.3 0.2 - - - +
323A THR* 4.1 9.3 + - - +
325A SER* 5.6 1.9 - - - -
327A MET* 3.8 29.0 - - + +
328A ASP* 2.5 42.1 + - - +
331A ILE* 5.0 2.7 - - + -
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Residues in contact with ALA 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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209A ILE* 5.9 0.4 - - + -
236A ALA* 3.8 24.0 - - + -
239A HIS* 4.6 13.9 - - + -
240A VAL* 4.7 5.2 - - + -
269A ARG 3.1 11.7 + - - +
270A LEU* 3.2 21.7 + - + +
272A ARG* 1.3 77.1 - - - +
274A TYR* 1.3 63.1 + - - +
276A THR* 3.2 3.8 + - - -
277A VAL* 3.1 30.6 + - - +
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Residues in contact with TYR 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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240A VAL* 3.4 42.6 + - + +
243A ALA* 4.7 4.9 - - - +
244A GLU* 4.3 9.2 + - - +
270A LEU* 3.1 58.1 + - + +
271A ALA 4.1 3.1 - - - +
273A ALA* 1.3 77.2 - - - +
275A ASN* 1.3 61.8 + - - +
276A THR 3.3 0.9 + - - -
277A VAL* 3.4 25.2 + - + +
294A LEU 6.0 2.0 - - - +
296A ARG* 3.5 53.0 + - + +
297A PRO* 4.2 23.1 - - + -
300A PHE* 6.1 1.5 - - + +
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Residues in contact with ASN 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 ALA 3.0 20.3 + - - +
272A ARG* 3.8 7.0 - - - +
274A TYR* 1.3 76.7 - - - +
276A THR* 1.3 63.7 + - - +
277A VAL 5.1 0.7 - - - -
294A LEU* 6.3 2.0 - - + -
327A MET* 4.3 22.6 - - - -
331A ILE* 6.3 1.1 - - + -
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Residues in contact with THR 276 (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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236A ALA* 5.4 4.0 - - + -
272A ARG* 2.6 23.6 + - - +
273A ALA* 3.7 6.2 - - - -
274A TYR 3.1 0.2 - - - -
275A ASN* 1.3 83.7 + - - +
277A VAL* 1.3 64.9 + - + +
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ALA* 3.8 28.5 - - + +
237A SER* 4.7 7.4 - - - +
240A VAL* 4.4 13.2 - - + -
273A ALA 3.3 18.4 - - - +
274A TYR* 3.4 24.7 + - + +
275A ASN 5.1 0.4 - - - -
276A THR* 1.3 83.9 - - + +
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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