Contacts of the helix formed by residues 376 - 389 (chain A) in PDB entry 4TVJ
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 SER 376 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A LEU* 4.6 3.6 - - - +
373A ASP* 2.6 34.2 + - - -
374A HIS 3.2 1.5 - - - +
375A GLU* 1.3 82.0 - - - +
377A TYR* 1.3 58.9 + - - +
378A GLU* 3.6 17.2 + - - +
379A PHE* 3.0 18.9 + - - +
380A LYS* 3.1 25.3 + - - +
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Residues in contact with TYR 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLU 4.1 0.2 + - - -
376A SER* 1.3 72.7 - - - +
378A GLU* 1.3 82.5 + - - +
380A LYS* 3.2 26.6 + - + +
381A VAL* 2.9 57.4 + - + +
529A VAL* 3.8 22.3 - - - +
530A THR 4.8 3.5 + - - -
531A LEU* 4.1 16.4 - - + -
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Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LEU* 4.1 21.8 - - + -
376A SER* 3.8 16.7 - - - +
377A TYR* 1.3 91.2 + - - +
379A PHE* 1.3 63.2 + - - +
381A VAL* 3.4 3.3 + - - +
382A ILE* 3.1 31.2 + - - +
404A LEU* 4.6 0.2 - - - -
531A LEU* 4.6 15.2 - - + +
532A ASN* 4.7 7.6 + - - +
571A TYR* 3.9 23.8 - - + +
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Residues in contact with PHE 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LEU* 4.9 0.9 - - + -
373A ASP 3.5 7.9 - - - +
374A HIS* 3.3 68.0 - + + +
376A SER* 3.0 20.2 + - - +
378A GLU* 1.3 76.2 - - - +
380A LYS* 1.3 66.0 + - - +
382A ILE* 3.9 0.7 - - - +
383A SER* 2.9 42.0 + - - -
401A LEU* 3.5 34.0 - - + +
404A LEU* 3.8 35.5 - - + +
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Residues in contact with LYS 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A HIS 4.9 0.4 + - - +
376A SER 3.1 15.3 + - - +
377A TYR* 3.2 33.2 + - + +
379A PHE* 1.3 83.2 - - - +
381A VAL* 1.3 68.8 + - - +
383A SER* 3.3 5.9 + - - -
384A GLN* 3.0 52.2 + - + +
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Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR* 2.9 57.3 + - + +
378A GLU* 4.0 3.1 - - - +
380A LYS* 1.3 79.8 - - - +
382A ILE* 1.3 61.6 + - - +
384A GLN* 3.1 6.8 + - - +
385A TYR* 2.8 28.2 + - - +
529A VAL* 4.3 21.8 - - + -
531A LEU* 4.8 14.4 - - + -
536A VAL* 4.7 15.5 - - + -
538A LEU* 4.7 10.3 - - + -
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Residues in contact with ILE 382 (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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378A GLU 3.1 19.3 + - - +
379A PHE 4.1 2.7 - - - +
381A VAL* 1.3 75.0 - - - +
383A SER* 1.3 57.7 + - - +
385A TYR* 3.3 7.6 + - + +
386A LEU* 2.9 29.2 + - - +
401A LEU* 4.8 2.9 - - + -
404A LEU* 3.9 15.7 - - + -
425A LEU* 5.1 2.2 - - + -
427A TRP* 4.5 0.6 - - + -
487A LEU* 3.8 24.5 - - + -
531A LEU* 4.5 11.0 - - + -
571A TYR* 3.5 52.0 - - + -
573A LEU* 3.8 27.1 - - + -
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Residues in contact with SER 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A PHE* 2.9 33.0 + - - -
380A LYS* 3.6 7.4 - - - -
382A ILE* 1.3 76.8 - - - +
384A GLN* 1.3 57.8 + - - +
386A LEU* 3.5 6.3 + - - +
387A GLN* 3.1 35.0 + - - +
401A LEU* 3.3 24.7 - - - +
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Residues in contact with GLN 384 (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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380A LYS* 3.0 50.8 + - + +
381A VAL* 3.1 8.3 + - - +
383A SER* 1.3 75.0 - - - +
385A TYR* 1.3 54.8 + - - +
387A GLN* 4.5 3.6 - - - +
388A SER* 2.7 46.5 + - - +
538A LEU* 4.0 20.6 - - + +
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Residues in contact with TYR 385 (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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381A VAL 2.8 16.3 + - - +
382A ILE* 3.4 11.7 - - + +
384A GLN* 1.3 73.4 - - - +
386A LEU* 1.3 58.6 + - - +
388A SER* 3.9 0.4 - - - -
389A THR* 2.8 42.5 + - + -
425A LEU* 2.6 35.5 + - + -
426A LEU* 3.8 6.1 - - - +
427A TRP* 3.2 37.7 + + + -
465A ASP* 3.8 9.5 - - - -
487A LEU* 3.5 26.9 - - + -
536A VAL* 3.6 22.0 - - + -
537A PRO* 3.3 37.1 - - + +
538A LEU* 3.5 12.2 - - + +
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Residues in contact with LEU 386 (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 2.9 17.1 + - - +
383A SER* 3.5 5.2 - - - +
385A TYR* 1.3 76.1 - - - +
387A GLN* 1.3 83.2 + - - +
390A HIS* 3.6 6.4 + - - +
399A MET* 3.7 37.8 - - + +
401A LEU* 3.9 34.1 - - + +
427A TRP* 3.6 14.9 - - + -
467A SER* 2.7 26.3 + - - -
485A LEU* 3.7 23.8 - - + -
573A LEU* 4.3 11.7 - - + -
575A VAL* 4.9 3.8 - - + -
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Residues in contact with GLN 387 (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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383A SER* 3.1 18.3 + - - +
384A GLN* 4.2 3.4 - - - +
386A LEU* 1.3 98.1 - - - +
388A SER* 1.3 62.8 + - - +
390A HIS* 3.3 25.3 + - - +
398A THR* 5.7 2.4 - - - -
399A MET* 2.9 32.9 + - - +
400A THR* 4.8 2.2 - - - +
401A LEU* 5.0 1.6 - - - +
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Residues in contact with SER 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLN* 2.7 31.6 + - - -
385A TYR 3.6 2.6 + - - -
387A GLN* 1.3 72.8 - - - +
389A THR* 1.3 60.5 + - - +
390A HIS 3.5 3.1 + - - +
466A MET* 5.1 0.7 - - - +
538A LEU* 3.8 7.0 - - - +
539A GLY* 2.8 46.8 + - - -
540A PRO* 3.5 14.2 - - - +
541A ALA 4.5 0.7 + - - -
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Residues in contact with THR 389 (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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385A TYR* 2.8 25.1 + - + +
388A SER* 1.3 79.3 - - - +
390A HIS* 1.3 59.5 + - - +
391A ALA 3.4 1.4 + - - -
427A TRP* 3.6 8.1 + - - -
465A ASP 3.5 16.2 - - - +
466A MET* 3.1 23.9 - - - +
467A SER* 3.0 32.0 + - - -
523A PRO* 3.9 5.2 - - + -
537A PRO 3.5 16.6 - - - +
539A GLY* 3.3 29.2 - - - +
541A ALA 5.8 0.2 - - - +
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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