Contacts of the strand formed by residues 394 - 402 (chain A) in PDB entry 6PAU
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 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A ARG* 4.0 20.9 - - - +
345A ASP* 3.6 35.9 - - + +
348A SER* 3.7 28.9 + - - +
349A VAL* 4.2 5.8 - - + +
352A LEU* 3.9 26.2 - - + +
386A VAL* 4.0 24.0 - - + -
387A VAL 3.4 3.8 - - - +
388A GLU* 4.0 12.1 - - + -
392A GLY 4.0 10.3 - - - +
393A LYS* 1.3 93.2 - - - +
395A THR* 1.3 59.3 + - - +
396A ASP 5.0 1.1 - - - +
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Residues in contact with THR 395 (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 7.2 - - - +
387A VAL* 2.9 18.0 + - - +
389A SER* 4.0 22.7 - - - -
393A LYS* 3.6 22.2 - - - +
394A LEU* 1.3 77.7 - - - +
396A ASP* 1.3 82.8 + - - +
426A HIS* 4.5 0.2 - - - -
427A THR* 2.5 32.9 + - - +
428A GLU* 3.3 34.1 - - + +
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Residues in contact with ASP 396 (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* 4.2 5.6 - - - +
386A VAL* 3.4 2.6 - - - +
387A VAL* 2.8 38.6 + - + +
394A LEU* 3.8 0.5 - - - +
395A THR* 1.3 97.0 + - - +
397A PHE* 1.3 69.0 + - - +
425A ILE* 3.3 12.6 - - - +
426A HIS* 3.0 6.7 - - - +
427A THR 2.6 28.9 + - - -
428A GLU 3.1 0.4 + - - -
429A THR* 2.7 40.6 + - - -
434A LEU* 4.2 9.9 - - + -
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Residues in contact with PHE 397 (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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349A VAL* 3.9 29.4 - - + -
352A LEU* 4.0 27.4 - - + -
353A ILE* 4.2 13.5 - - + -
375A PHE* 3.9 20.0 - + - -
384A THR* 4.1 15.5 - - + -
385A PHE 3.0 16.6 - - - +
386A VAL* 3.7 15.5 - - + +
387A VAL* 5.1 0.4 - - - -
396A ASP* 1.3 76.5 - - - +
398A LEU* 1.3 60.9 + - - +
423A TYR 3.6 19.3 - - - -
424A ASN* 3.4 1.7 - - - -
425A ILE* 2.9 68.7 + - + +
434A LEU* 3.5 7.9 - - - +
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Residues in contact with LEU 398 (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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338A LEU* 4.3 15.7 - - + -
384A THR* 3.3 2.9 - - - +
385A PHE* 2.8 54.5 + - + +
397A PHE* 1.3 75.6 - - - +
399A SER* 1.3 66.9 + - - +
400A PHE* 4.0 26.5 - - + -
423A TYR 3.9 1.6 - - - -
424A ASN* 3.1 15.7 - - - +
434A LEU* 3.6 42.8 - - + +
435A MET* 5.2 0.2 - - - -
437A ASP* 4.5 5.6 - - + -
438A ALA* 3.9 22.7 - - + +
441A LEU* 4.3 4.3 - - + -
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Residues in contact with SER 399 (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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375A PHE* 3.7 13.1 - - - -
382A ILE* 4.4 0.4 - - - -
383A ASP 3.1 14.1 - - - -
384A THR* 3.6 13.7 - - - -
397A PHE* 4.8 0.4 - - - -
398A LEU* 1.3 79.1 - - - +
400A PHE* 1.3 65.2 + - - +
421A SER* 3.9 1.7 - - - -
422A PHE* 2.9 32.2 + - - +
423A TYR* 2.6 36.6 + - - -
424A ASN* 3.0 12.9 + - - +
450A PHE* 5.3 0.9 - - - -
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Residues in contact with PHE 400 (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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382A ILE* 4.0 4.0 - - - -
383A ASP* 2.9 60.6 + - + +
385A PHE* 4.8 2.2 - + - -
398A LEU* 4.0 24.0 - - + -
399A SER* 1.3 77.8 - - - +
401A TYR* 1.3 59.3 + - - +
419A ALA* 3.8 16.2 - - + -
420A TYR 3.0 24.9 - - - +
421A SER 4.2 0.2 - - - +
422A PHE* 4.0 2.7 - - - -
438A ALA* 4.1 14.4 - - + -
441A LEU* 4.4 7.9 - - + -
442A ALA* 4.1 17.0 - - + -
445A LYS* 4.3 8.3 - - + -
447A PHE* 3.9 22.7 - + - -
450A PHE* 3.9 21.8 - + + -
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Residues in contact with TYR 401 (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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196A PHE* 3.7 26.2 - + + -
199A TRP* 4.1 16.2 - + + -
296A TYR* 4.9 0.3 + - - -
381A ILE 3.1 14.4 - - - +
382A ILE* 4.3 3.1 - - + -
400A PHE* 1.3 76.5 - - - +
402A THR* 1.3 61.3 + - - +
403A LEU* 3.9 7.7 + - + -
419A ALA* 3.5 5.7 - - - -
420A TYR* 2.9 65.6 + + + +
421A SER 4.2 5.7 + - - -
422A PHE* 3.7 35.2 - + - -
494A VAL* 4.3 8.7 - - + +
495A LEU 3.6 10.6 + - - -
496A GLN* 4.3 11.7 - - + -
503A GOL 2.5 33.0 + - - -
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Residues in contact with THR 402 (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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196A PHE* 3.0 26.2 - - - -
380A HIS* 3.3 40.7 - - + +
381A ILE 2.7 11.5 + - - -
383A ASP* 4.4 7.8 + - - -
400A PHE* 5.4 0.2 - - - -
401A TYR* 1.3 70.0 - - - +
403A LEU* 1.3 62.2 + - - +
404A PRO* 4.2 16.7 - - + +
417A LYS* 4.4 11.2 - - + -
418A ALA 3.9 3.8 - - - +
447A PHE* 3.2 31.6 - - + -
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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