Contacts of the strand formed by residues 361 - 372 (chain A) in PDB entry 5L9X
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 ARG 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A LEU* 4.0 28.0 + - - +
316A PRO* 2.9 34.7 + - - +
317A LYS* 4.7 2.2 - - - +
319A ILE* 4.6 5.1 - - - +
355A ASP* 2.9 39.8 + - - +
356A ARG* 3.4 24.8 + - - +
359A ASN* 3.9 17.7 - - + +
360A ASP* 1.3 79.8 - - - +
362A VAL* 1.3 65.0 + - - +
390A TYR* 4.1 1.4 + - - -
429A PHE* 3.7 38.0 - - + +
430A SER 3.2 15.9 - - - +
431A ALA* 4.4 1.3 - - - -
432A SER* 3.2 7.8 + - - -
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Residues in contact with VAL 362 (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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356A ARG* 3.5 28.0 - - - +
361A ARG* 1.3 80.7 - - - +
363A ALA* 1.3 68.6 + - - +
364A THR* 3.6 6.6 - - + +
390A TYR* 3.2 9.9 - - + +
429A PHE* 3.3 4.6 - - - -
430A SER* 2.8 48.6 + - - +
431A ALA 4.7 1.1 - - - +
432A SER* 3.6 18.8 - - - +
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Residues in contact with ALA 363 (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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352A LEU* 4.1 2.0 - - + -
362A VAL* 1.3 79.8 - - - +
364A THR* 1.3 61.7 + - - +
365A GLN 3.8 0.2 - - - -
387A LEU* 3.6 19.5 - - + +
390A TYR* 2.7 23.3 + - - +
426A ALA* 3.7 28.0 - - + -
427A THR 3.7 13.2 - - - +
428A LYS 4.1 0.4 - - - -
429A PHE* 3.4 21.8 - - + -
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Residues in contact with THR 364 (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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362A VAL* 3.6 13.5 - - + +
363A ALA* 1.3 79.1 - - - +
365A GLN* 1.3 60.1 + - - +
386A ALA* 4.0 5.0 - - - +
387A LEU* 3.1 27.6 + - - +
427A THR 3.1 4.0 + - - -
428A LYS* 2.8 34.6 + - - +
430A SER* 3.8 17.5 - - - +
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Residues in contact with GLN 365 (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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364A THR* 1.3 82.6 - - - +
366A LEU* 1.3 64.3 + - - +
367A VAL* 4.1 7.7 - - + +
382A ARG* 5.4 2.3 + - - -
384A CYS* 3.6 35.4 - - + +
385A CYS 3.8 10.9 - - - +
386A ALA* 5.6 0.2 - - - -
387A LEU* 3.7 6.1 - - - +
425A CYS 3.7 0.2 - - - +
426A ALA* 3.4 4.3 - - - -
427A THR* 2.9 50.1 + - - +
428A LYS* 3.1 41.5 + - + +
1P A 4.8 6.3 + - - -
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Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 3.7 29.8 - - + -
365A GLN* 1.3 73.6 - - - +
367A VAL* 1.3 62.4 + - - +
368A VAL* 4.0 16.8 + - + +
383A ARG 4.1 0.2 - - - +
384A CYS* 3.3 2.6 - - - +
385A CYS* 2.9 60.4 + - - +
386A ALA 4.5 1.1 - - - +
387A LEU* 3.8 22.3 - - + +
395A MET* 3.7 42.0 - - + +
398A ASP* 4.8 1.6 - - + +
399A ALA* 4.7 2.0 - - + -
424A LEU* 4.5 8.1 - - + -
425A CYS 3.6 13.0 - - - +
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Residues in contact with VAL 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLN* 4.1 11.7 - - - +
366A LEU* 1.3 77.7 - - - +
368A VAL* 1.3 64.9 + - - +
369A SER* 5.0 2.2 - - - +
382A ARG* 3.6 48.5 - - + +
383A ARG 3.7 4.5 - - - +
384A CYS* 4.4 7.9 - - + -
423A PHE* 3.6 5.0 - - + +
424A LEU* 3.5 5.4 - - - +
425A CYS* 2.7 48.3 + - + +
427A THR* 4.1 24.5 - - + +
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Residues in contact with VAL 368 (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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341A LEU* 4.9 6.3 - - + -
366A LEU* 4.3 14.1 - - + +
367A VAL* 1.3 78.9 - - - +
369A SER* 1.3 64.9 + - - +
370A ILE* 4.9 3.1 - - + -
381A LEU* 3.9 2.8 - - - +
382A ARG* 3.4 2.4 - - - -
383A ARG* 2.7 40.7 + - - +
385A CYS* 5.1 2.5 - - - -
399A ALA* 3.6 38.6 - - + -
402A VAL* 3.9 14.6 - - + -
403A ILE* 3.6 25.8 - - + -
423A PHE 3.5 4.0 - - - +
424A LEU* 3.9 12.6 - - + -
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Residues in contact with SER 369 (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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367A VAL* 5.2 1.6 - - - -
368A VAL* 1.3 76.7 - - - +
370A ILE* 1.3 67.1 + - - +
379A SER* 3.1 30.5 + - - -
381A LEU* 3.2 6.6 + - - -
382A ARG* 4.0 13.3 - - - +
421A MET* 3.8 5.3 - - - +
422A LEU 3.6 0.5 - - - -
423A PHE* 2.9 60.5 + - - +
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Residues in contact with ILE 370 (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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368A VAL* 4.9 3.1 - - + -
369A SER* 1.3 80.1 + - - +
371A ARG* 1.3 64.3 + - - +
372A VAL* 4.6 7.2 - - + -
379A SER* 3.9 0.3 - - - -
380A SER* 2.9 21.9 + - - -
381A LEU* 3.1 28.8 + - + +
403A ILE* 4.2 27.1 - - + -
406A CYS* 4.1 31.9 - - + -
415A TRP* 5.1 0.4 - - + -
419A LEU* 3.8 25.4 - - + -
421A MET* 3.2 17.0 - - - +
422A LEU* 3.6 25.4 - - + -
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Residues in contact with ARG 371 (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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324A ASN* 5.8 5.7 + - - +
370A ILE* 1.3 75.7 - - - +
372A VAL* 1.3 70.3 + - - +
375A ASP* 3.1 22.3 + - + -
376A LYS* 3.3 16.4 + - - +
377A ARG 2.6 19.4 + - - +
378A LEU* 3.4 30.5 - - - +
380A SER* 3.4 12.1 - - - +
419A LEU* 3.4 11.1 - - - +
420A THR* 2.9 40.4 + - - +
421A MET* 3.1 23.6 + - + -
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Residues in contact with VAL 372 (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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370A ILE* 4.6 10.5 - - + -
371A ARG* 1.3 79.6 + - - +
373A GLN* 1.3 69.3 + - - +
374A GLY 3.2 0.5 + - - -
375A ASP* 3.1 27.1 + - + +
380A SER* 3.1 22.4 + - - +
406A CYS* 5.8 5.6 - - + +
415A TRP* 5.6 0.4 - - - +
417A PRO* 3.8 27.8 - - + +
418A PRO 3.7 3.1 - - - -
419A LEU* 3.8 19.5 - - + -
420A THR* 3.9 6.2 + - - -
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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