Contacts of the strand formed by residues 267 - 274 (chain A) in PDB entry 4P0S
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 TYR 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A LEU* 4.2 18.6 - - + -
263A ARG 3.2 25.8 - - - -
264A PRO* 3.5 16.0 - - + +
265A GLY* 3.2 10.4 + - - -
266A GLU* 1.3 80.3 - - - +
268A ARG* 1.3 70.0 + - - +
269A VAL* 4.5 12.1 - - + -
312A ALA* 4.5 4.5 - - + -
313A GLN 3.2 18.4 - - - +
314A GLU* 4.1 1.8 - - - -
315A THR* 3.8 8.8 - - - +
423A TYR* 2.7 39.1 + - + +
424A GLN* 4.2 5.3 - - + -
426A HIS 3.4 8.8 + - - -
428A LEU* 3.8 30.5 - - + -
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Residues in contact with ARG 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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267A TYR* 1.3 79.4 - - - +
269A VAL* 1.3 63.2 + - - +
270A LEU* 3.8 28.0 + - + +
297A THR* 5.7 7.2 - - - -
311A VAL 3.7 1.2 - - - +
312A ALA* 3.5 1.9 - - - -
313A GLN* 2.6 69.4 + - + +
315A THR* 4.4 27.2 + - + +
420A GLN* 6.1 1.3 - - - +
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Residues in contact with VAL 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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267A TYR* 4.9 14.6 - - + -
268A ARG* 1.3 75.1 - - - +
270A LEU* 1.3 65.8 + - - +
297A THR* 3.5 3.5 + - - +
310A TRP* 4.7 9.4 - - + -
311A VAL 3.7 6.3 - - - +
312A ALA* 4.7 3.8 - - + +
328A LEU* 4.4 16.4 - - + -
416A THR* 4.8 2.1 - - + +
419A LEU* 4.4 22.0 - - + +
420A GLN* 3.3 57.3 + - + +
423A TYR* 5.9 4.3 - - + -
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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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268A ARG* 4.0 35.2 - - + +
269A VAL* 1.3 76.0 - - - +
271A LEU* 1.3 62.3 + - - +
272A CYS 3.6 0.2 + - - -
297A THR* 3.7 20.9 - - - +
298A HIS* 4.3 10.8 - - - +
299A THR* 3.1 27.6 - - - +
310A TRP* 3.7 5.7 - - - -
311A VAL* 3.1 53.0 + - + +
313A GLN* 4.3 16.4 - - + +
416A THR* 5.1 1.3 - - - -
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Residues in contact with LEU 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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270A LEU* 1.3 74.7 - - - +
272A CYS* 1.3 63.5 + - - +
273A VAL* 3.8 24.9 - - + -
291A LEU* 4.5 8.3 - - + -
296A VAL* 4.2 15.9 - - + -
297A THR 3.3 13.5 + - - +
298A HIS* 3.6 2.6 - - + -
299A THR* 2.9 28.6 + - - +
308A PHE* 4.7 7.6 - - + -
309A VAL 4.1 4.3 - - - +
310A TRP* 3.3 46.6 - - + +
412A LEU* 4.1 33.0 - - + -
416A THR* 4.0 13.1 - - + +
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Residues in contact with CYS 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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270A LEU 3.6 0.8 + - - -
271A LEU* 1.3 75.0 - - - +
273A VAL* 1.3 63.7 + - - +
274A ASP 4.0 0.5 + - - -
299A THR* 3.8 9.0 - - - -
301A ARG* 4.4 26.7 - - - -
303A LEU* 4.4 6.4 - - - +
308A PHE* 3.7 3.1 - - - +
309A VAL* 2.5 58.8 + - + +
311A VAL* 4.4 18.4 - - + -
456A PHE* 4.1 24.7 - - - -
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Residues in contact with VAL 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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271A LEU* 3.8 25.6 - - + +
272A CYS* 1.3 72.9 - - - +
274A ASP* 1.3 76.7 + - - +
275A ILE 3.6 0.2 + - - -
277A GLU* 4.9 5.4 - - + +
278A THR* 6.1 2.0 - - - -
287A LEU* 4.3 17.5 - - + -
291A LEU* 4.7 6.1 - - + -
298A HIS* 5.5 2.5 - - + -
299A THR 3.1 13.3 + - - +
300A VAL* 3.8 9.0 - - + +
301A ARG 3.3 20.6 + - - -
307A ASP 4.2 0.4 - - - +
308A PHE* 3.2 42.4 - - + -
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Residues in contact with ASP 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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272A CYS 4.0 1.2 + - - -
273A VAL* 1.3 83.7 - - - +
275A ILE* 1.3 91.4 + - - +
276A GLY* 3.7 2.3 + - - -
277A GLU* 3.7 17.3 + - - +
278A THR* 4.4 2.4 - - - +
300A VAL* 5.5 0.4 - - - -
301A ARG 3.2 6.1 - - - -
302A LYS* 3.9 3.8 - - - +
303A LEU* 3.4 44.1 + - + +
306A GLY 3.5 14.2 - - - +
307A ASP* 2.9 36.1 + - - +
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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