Contacts of the strand formed by residues 275 - 282 (chain A) in PDB entry 5A2E
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 GLU 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A LEU* 3.3 19.1 - - - +
270A GLY* 3.4 16.9 + - - -
271A ALA* 3.6 29.9 + - - +
272A ASP* 3.2 23.2 + - - +
273A ARG 3.5 1.4 - - - -
274A CYS* 1.3 77.9 - - - +
276A GLY* 1.3 59.7 + - - +
358A VAL 3.7 10.5 - - - +
359A LEU* 3.7 28.9 - - + +
363A SER* 4.1 4.5 - - - -
365A GLY* 3.8 18.8 + - - -
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Residues in contact with GLY 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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267A LEU* 3.5 8.0 - - - +
268A THR 3.5 8.5 - - - -
270A GLY* 3.8 9.2 - - - -
275A GLU* 1.3 77.7 - - - +
277A GLN* 1.3 64.1 + - - -
357A ARG* 3.5 18.2 - - - -
358A VAL 3.3 31.2 + - - -
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Residues in contact with GLN 277 (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* 3.5 5.0 - - - -
268A THR* 2.8 35.9 + - - +
276A GLY* 1.3 70.5 - - - -
278A VAL* 1.3 71.5 + - - +
279A GLU* 3.2 26.8 + - + +
288A THR* 4.0 14.0 - - + +
318A LEU* 4.4 19.9 - - - +
319A PRO 4.7 2.8 - - - +
321A SER* 4.7 10.0 + - - -
322A LEU* 4.3 4.0 - - - +
355A ALA* 3.2 30.9 - - + +
356A ALA 3.8 12.1 - - - +
357A ARG* 3.9 18.4 + - - +
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Residues in contact with VAL 278 (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 TRP* 5.1 1.8 - - + -
266A ARG 5.1 0.9 - - - +
267A LEU* 3.9 6.7 - - + -
277A GLN* 1.3 70.9 - - - +
279A GLU* 1.3 64.6 + - - +
288A THR* 3.9 4.2 - - - -
289A VAL* 3.5 45.3 + - + +
294A TRP* 3.7 37.0 - - + -
302A LEU* 4.5 15.9 - - + -
337A LEU* 5.0 4.7 - - + -
356A ALA 3.0 24.8 + - - +
357A ARG 4.1 1.1 - - - -
358A VAL* 3.7 21.8 - - + -
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Residues in contact with GLU 279 (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 TRP* 3.5 9.8 - - - +
266A ARG* 2.8 75.2 + - + +
268A THR* 2.9 27.2 + - - +
277A GLN* 3.7 21.5 + - - +
278A VAL* 1.3 77.9 - - - +
280A VAL* 1.3 61.4 + - - +
286A TRP* 3.8 14.9 - - + -
287A ASN 3.4 4.7 - - - +
322A LEU* 3.7 28.1 - - + +
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Residues in contact with VAL 280 (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 GLN* 4.1 15.5 - - + +
264A SER 3.5 6.7 - - - +
265A TRP* 3.2 33.0 - - + +
279A GLU* 1.3 75.0 - - - +
281A HIS* 1.3 63.3 + - - +
282A PHE* 3.4 6.6 + - + +
286A TRP* 3.5 4.9 - - - -
287A ASN* 2.8 51.6 + - + +
289A VAL* 4.5 7.9 - - + -
326A MET* 3.9 33.0 - - + -
328A TYR* 3.7 8.5 - - - +
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Residues in contact with HIS 281 (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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208A VAL* 4.3 11.4 - - + +
258A VAL* 4.8 16.4 - - + +
259A CYS 6.0 1.1 - - - -
262A HIS* 2.9 24.4 - + + +
263A GLN* 3.6 7.4 - - - -
264A SER* 2.9 22.2 + - - +
280A VAL* 1.3 70.3 - - - +
282A PHE* 1.3 57.4 - - - +
284A GLY* 3.5 38.0 - - - -
285A VAL* 3.6 13.3 - - - -
286A TRP* 3.5 40.8 + + + -
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Residues in contact with PHE 282 (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 SER 3.9 1.1 - - - -
261A GLU* 3.6 38.6 - - - -
262A HIS 3.7 7.4 - - - +
263A GLN* 3.5 27.4 - - + -
280A VAL* 3.4 8.8 + - + -
281A HIS* 1.3 73.6 - - - +
283A ARG* 1.3 114.5 + - + +
284A GLY 3.3 1.6 - - - -
285A VAL* 3.0 20.4 + - - +
287A ASN* 3.2 17.3 + - - +
326A MET* 4.2 9.2 - - + -
342A TRP* 3.7 23.6 - + - -
344A PHE* 3.7 33.9 - + + -
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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