Contacts of the strand formed by residues 331 - 340 (chain A) in PDB entry 2EC8
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 VAL 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A ILE* 6.1 1.8 - - + -
323A VAL* 3.9 18.4 - - + -
324A PHE 5.1 1.6 - - - +
325A VAL* 3.5 34.3 - - + -
330A ASN* 1.3 82.5 - - - +
332A ASP* 1.3 71.2 + - - +
333A LEU* 4.0 6.7 - - + -
377A LEU 3.7 0.3 - - - +
379A LEU* 2.9 53.2 + - + +
382A LEU* 4.3 8.3 - - + -
407A VAL* 5.0 5.2 - - + -
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Residues in contact with ASP 332 (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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319A ILE* 3.6 15.1 - - - +
330A ASN* 6.0 1.2 - - - +
331A VAL* 1.3 80.6 - - - +
333A LEU* 1.3 65.0 + - - +
334A ILE* 3.3 18.3 + - + +
376A GLU* 2.8 29.3 - - - +
377A LEU 3.6 2.5 - - - -
378A HIS* 3.0 33.3 + - - +
380A THR* 6.1 0.2 - - - +
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Residues in contact with LEU 333 (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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319A ILE* 4.1 11.4 - - + -
323A VAL* 4.5 8.1 - - + -
331A VAL* 5.0 11.0 - - + +
332A ASP* 1.3 73.5 - - - +
334A ILE* 1.3 58.9 + - - +
348A TRP* 3.8 20.6 - - + -
375A SER 3.7 1.4 - - - +
376A GLU* 3.2 3.6 - - - -
377A LEU* 2.7 64.1 + - + +
379A LEU* 4.1 10.8 - - + -
390A TYR* 3.9 26.7 - - + -
405A PHE* 4.1 30.5 - - + -
407A VAL* 4.5 11.9 - - + -
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Residues in contact with ILE 334 (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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318A MET* 3.3 41.5 + - + +
319A ILE* 4.5 12.9 - - + +
332A ASP* 3.3 22.0 + - + +
333A LEU* 1.3 76.2 - - - +
335A VAL* 1.3 80.9 + - - +
336A GLU* 5.1 3.8 - - - +
362A TYR* 5.7 0.2 - - - +
374A VAL* 4.7 9.2 - - + -
375A SER 3.5 7.9 - - - +
376A GLU* 4.2 24.7 - - + +
405A PHE* 3.6 5.2 - - - -
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Residues in contact with VAL 335 (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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315A ILE* 4.5 5.4 - - + -
316A PHE 3.3 9.9 - - - +
317A PRO* 3.8 9.0 - - + -
318A MET 4.3 1.1 - - - +
334A ILE* 1.3 88.8 - - - +
336A GLU* 1.3 67.1 + - - +
337A TYR* 4.2 2.2 - - + -
348A TRP* 4.3 10.8 - - + -
374A VAL* 3.3 1.1 - - - -
375A SER* 2.9 34.3 + - - +
392A PHE* 4.0 30.7 - - + -
403A ILE* 4.4 7.0 - - + -
405A PHE* 3.2 32.3 - - + -
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Residues in contact with GLU 336 (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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315A ILE* 3.9 2.1 - - - +
316A PHE* 2.7 29.7 + - + +
318A MET* 3.6 27.8 - - - +
334A ILE* 5.1 4.6 - - + +
335A VAL* 1.3 76.6 - - - +
337A TYR* 1.3 68.0 + - - +
364A LYS* 3.0 29.4 + - - -
372A ARG* 2.8 33.2 + - - +
373A TYR 3.1 9.2 - - - +
374A VAL* 3.5 25.4 - - + +
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Residues in contact with TYR 337 (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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313A ILE* 4.2 8.1 - - + -
314A ASN 3.3 13.9 - - - +
315A ILE* 3.7 15.5 - - + -
316A PHE* 4.1 7.2 - - - -
335A VAL* 4.2 7.6 - - + -
336A GLU* 1.3 80.9 - - - +
338A GLU* 1.3 68.0 + - - +
339A ALA* 4.0 13.0 - - + -
343A PRO* 3.7 8.2 - - + +
346A GLN* 3.0 28.3 + - - -
372A ARG* 3.3 8.1 - - - +
373A TYR* 2.7 74.7 + + + +
374A VAL* 4.3 7.9 - - - -
375A SER* 5.1 0.9 - - - -
392A PHE* 4.0 27.6 - + - -
394A VAL* 3.4 18.4 - - + +
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Residues in contact with GLU 338 (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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312A PHE* 3.7 14.1 - - + -
313A ILE* 3.1 5.4 - - - +
314A ASN* 2.9 55.4 + - - +
316A PHE* 4.7 8.4 - - + -
337A TYR* 1.3 73.6 - - - +
339A ALA* 1.3 59.6 + - - +
371A ILE* 3.2 40.7 - - + +
372A ARG* 4.3 11.7 + - - +
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Residues in contact with ALA 339 (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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312A PHE 3.6 2.7 - - - -
313A ILE* 3.8 20.6 - - + -
337A TYR* 4.0 21.6 + - + -
338A GLU* 1.3 75.1 - - - +
340A PHE* 1.3 59.3 + - - +
341A PRO 3.4 13.2 - - - +
342A LYS 4.6 0.2 + - - -
343A PRO* 4.3 7.6 - - + -
371A ILE* 2.6 38.4 + - - +
373A TYR* 3.9 14.5 + - + -
394A VAL* 6.0 0.2 - - + -
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Residues in contact with PHE 340 (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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222A LEU* 4.0 31.0 - - + -
223A LEU 3.7 24.7 - - - -
224A ARG* 4.6 17.9 - - + -
308A VAL* 4.7 12.6 - - + -
310A LYS 5.4 1.6 - - - -
311A GLY* 3.3 3.5 - - - -
312A PHE* 2.7 68.0 + + + -
339A ALA* 1.3 75.6 - - - +
341A PRO* 1.4 86.5 + - + +
342A LYS* 4.2 17.0 - - - -
371A ILE* 3.6 12.3 - - + +
396A ASN* 3.5 2.2 - - - -
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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