Contacts of the strand formed by residues 344 - 351 (chain A) in PDB entry 2YA6
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 LEU 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336A LEU* 4.4 13.9 - - + -
337A LEU 3.4 4.0 - - - +
338A LYS* 3.8 27.4 - - + +
342A GLY 3.7 0.6 + - - +
343A THR* 1.3 75.1 - - - +
345A ILE* 1.3 61.3 + - - +
346A ALA 4.0 0.2 - - - -
367A ARG* 3.3 5.5 - - - -
368A SER* 2.8 39.1 + - - +
371A ASN* 3.6 43.1 - - - +
372A GLY* 3.7 4.0 - - - +
375A TRP* 3.5 17.4 - - + -
741A GLN* 4.9 0.4 - - + -
743A LEU* 3.7 23.3 - - + -
766A PHE* 3.8 25.4 - - + -
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Residues in contact with ILE 345 (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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335A ALA 3.5 1.0 - - - +
336A LEU* 3.4 7.3 - - - +
337A LEU* 2.7 50.5 + - + +
339A THR* 3.7 15.9 - - + -
343A THR* 4.6 1.6 - - + -
344A LEU* 1.3 75.0 - - - +
346A ALA* 1.3 61.0 + - - +
347A GLY 3.9 0.2 + - - -
365A ILE* 3.7 33.7 - - + -
366A ARG 3.6 2.7 - - - +
367A ARG* 4.2 14.1 - - + -
405A LEU* 3.7 16.3 - - + +
414A ILE* 3.7 34.1 - - + -
529A ASP 3.8 3.4 - - - +
530A GLY* 3.8 19.5 - - - -
533A TRP* 4.9 2.5 - - + -
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Residues in contact with ALA 346 (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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314A ILE* 3.9 17.3 - - + -
315A PHE* 3.2 7.3 - - + -
335A ALA 3.4 4.3 - - - -
336A LEU* 4.4 2.5 - - + -
345A ILE* 1.3 70.5 - - - +
347A GLY* 1.3 60.0 + - - +
365A ILE* 3.1 5.7 - - - -
366A ARG 2.9 31.9 + - - +
375A TRP* 3.5 26.6 - - + -
751A LEU* 3.7 21.8 - - + -
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Residues in contact with GLY 347 (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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333A ILE 4.2 0.9 - - - -
334A PRO* 3.3 5.5 - - - +
335A ALA* 2.7 38.0 + - - +
345A ILE 3.9 1.4 + - - -
346A ALA* 1.3 74.0 - - - +
348A ALA* 1.3 63.6 + - - +
364A VAL 3.3 9.4 - - - -
365A ILE* 3.8 9.4 - - - +
403A MET* 4.0 14.8 - - - -
405A LEU* 4.3 3.1 - - - +
751A LEU* 4.1 3.8 - - - +
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Residues in contact with ALA 348 (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 PHE* 3.8 22.0 - - + -
331A TYR* 4.3 4.5 - - + -
332A ARG 3.8 1.3 - - - +
333A ILE 3.6 9.2 - - - -
347A GLY* 1.3 75.9 - - - +
349A ASP* 1.3 70.0 + - - +
350A GLU 3.9 0.2 - - - -
362A GLY 3.6 0.9 - - - +
363A MET* 3.9 0.5 - - - -
364A VAL* 3.0 32.4 + - + +
403A MET* 3.5 12.4 - - - +
764A LEU* 3.5 24.5 - - + -
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Residues in contact with ASP 349 (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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331A TYR* 3.4 10.4 - - - -
332A ARG 2.8 32.6 + - - +
333A ILE* 3.7 11.8 + - - +
348A ALA* 1.3 71.5 - - - +
350A GLU* 1.3 61.0 + - - +
351A ARG* 2.9 42.0 + - - +
361A ILE* 3.7 13.4 - - + +
362A GLY 3.6 5.2 - - - -
363A MET* 4.1 9.7 - - - +
401A ILE* 3.3 15.0 - - - +
402A ASP* 3.0 25.2 + - - -
403A MET 4.4 0.5 + - - -
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Residues in contact with GLU 350 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A ILE* 3.7 26.2 - - + +
331A TYR* 2.6 41.2 + - + +
348A ALA 3.8 0.8 + - - -
349A ASP* 1.3 68.6 - - - +
351A ARG* 1.3 58.4 + - - +
352A ARG* 3.3 11.1 + - - +
360A ASP 3.7 0.5 - - - +
361A ILE* 3.2 5.0 - - - -
362A GLY 2.8 38.8 + - - +
364A VAL* 3.9 21.2 - - + +
378A ARG* 2.8 33.4 + - - -
380A THR* 4.9 3.3 + - - +
383A ASN* 4.8 10.0 + - - -
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Residues in contact with ARG 351 (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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328A ILE* 4.3 0.4 - - - -
330A SER* 2.8 39.8 + - - +
332A ARG* 3.5 29.4 - - + +
333A ILE* 3.4 7.1 - - - +
349A ASP* 2.9 42.2 + - + +
350A GLU* 1.3 69.1 - - - +
352A ARG* 1.3 65.0 + - - +
353A LEU 3.4 2.8 + - - -
354A HIS 3.3 17.2 + - - +
355A SER 3.1 21.5 + - - -
356A SER 3.2 18.0 + - - +
357A ASP* 2.9 22.2 + - - -
358A TRP 5.7 0.4 - - - +
360A ASP 4.1 4.5 - - - -
361A ILE* 3.9 15.2 - - + +
401A ILE* 3.3 12.1 - - - +
1777A DAN 2.7 26.9 + - - -
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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