Contacts of the helix formed by residues 508 - 531 (chain A) in PDB entry 4BC4
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 GLY 508 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A MSE 3.8 6.7 - - - -
506A SER 3.3 0.4 + - - -
507A PRO* 1.3 72.1 - - - +
509A ALA* 1.4 64.6 + - - +
510A SER* 3.3 2.7 - - - -
511A GLN* 3.2 21.2 + - - +
512A VAL* 3.1 24.6 + - - +
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Residues in contact with ALA 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A MSE 3.7 24.1 - - - +
454A ASP* 3.6 31.9 - - + +
457A ASP* 4.7 1.8 - - - +
505A PRO* 4.3 8.5 - - + -
506A SER 3.1 18.0 + - - +
507A PRO 3.4 1.4 + - - -
508A GLY* 1.4 73.9 - - - +
510A SER* 1.3 63.6 + - - +
512A VAL* 3.1 2.4 + - - -
513A TYR* 3.0 30.4 + - - -
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Residues in contact with SER 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A ASP* 3.7 32.1 + - - -
508A GLY 3.3 0.8 - - - +
509A ALA* 1.3 77.2 - - - +
511A GLN* 1.4 72.4 + - - +
513A TYR* 4.9 1.1 - - - +
514A GLU* 3.1 32.7 + - - +
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Residues in contact with GLN 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A GLY* 3.2 25.4 + - - +
510A SER* 1.4 87.0 + - - +
512A VAL* 1.3 67.3 + - + +
514A GLU* 4.3 4.4 - - - +
515A ALA* 3.9 16.5 + - - +
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Residues in contact with VAL 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A MSE 3.7 23.8 - - + +
368A GLY* 3.7 34.5 - - - +
508A GLY* 3.1 13.3 + - - +
509A ALA 3.1 7.7 + - - +
511A GLN* 1.3 81.2 - - + +
513A TYR* 1.3 74.7 + - + +
515A ALA* 3.5 4.4 + - - +
516A LEU* 3.2 23.1 + - + +
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Residues in contact with TYR 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A MSE 3.6 15.9 - - + +
368A GLY 3.5 3.6 + - - -
409A ARG* 3.9 3.6 + - - -
413A GLU* 2.6 38.9 + - + +
417A MSE 4.0 18.2 - - + -
420A ARG* 5.4 0.4 - - - +
451A VAL* 4.7 1.6 - - - +
454A ASP* 3.5 36.5 + - + +
455A VAL* 3.7 32.4 - - + +
509A ALA 3.0 27.5 + - - +
510A SER* 4.9 0.7 - - - +
512A VAL* 1.3 89.3 - - + +
514A GLU* 1.3 60.1 + - - +
515A ALA 3.2 1.6 - - - -
516A LEU* 4.1 10.3 - - + +
517A LEU* 2.9 49.0 + - + +
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Residues in contact with GLU 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A SER* 3.1 21.2 + - - +
511A GLN* 4.3 5.6 - - - +
512A VAL 3.4 0.4 - - - -
513A TYR* 1.3 75.8 - - - +
515A ALA* 1.3 57.0 + - - +
517A LEU* 5.0 3.4 - - - -
518A PRO* 3.1 23.6 - - - +
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Residues in contact with ALA 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A GLN 3.9 8.6 + - - +
512A VAL 3.5 9.3 + - - +
513A TYR 3.2 0.2 - - - -
514A GLU* 1.3 79.9 - - - +
516A LEU* 1.3 61.6 + - - +
517A LEU 3.6 0.2 - - - -
518A PRO* 3.5 10.3 - - - +
519A GLN* 3.9 10.7 + - - +
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Residues in contact with LEU 516 (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 GLY* 3.7 37.0 - - - +
371A GLY* 4.6 10.8 - - - -
373A LEU* 3.7 35.4 - - + -
413A GLU* 4.2 3.4 - - - +
417A MSE 3.8 22.0 - - + -
512A VAL* 3.2 14.5 + - + +
513A TYR* 3.3 9.8 + - + -
515A ALA* 1.3 79.8 - - - +
517A LEU* 1.3 60.3 + - - +
519A GLN* 3.1 9.1 + - + +
520A TYR* 2.9 26.7 + - - +
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Residues in contact with LEU 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A MSE 3.7 48.7 - - + +
420A ARG* 3.8 45.5 - - + +
421A ILE* 3.6 17.2 - - + +
424A GLU* 5.5 2.7 - - - +
455A VAL* 4.2 2.2 - - + +
513A TYR* 2.9 39.1 + - + +
514A GLU* 4.7 2.7 - - - +
516A LEU* 1.3 74.3 - - - +
518A PRO* 1.4 66.7 - - + +
520A TYR* 3.2 4.7 + - - +
521A ALA* 2.9 23.1 + - - +
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Residues in contact with PRO 518 (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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514A GLU 3.1 28.5 - - - +
515A ALA* 3.5 9.9 - - - +
517A LEU* 1.4 89.4 - - + +
519A GLN* 1.4 55.3 + - - +
521A ALA* 3.4 8.0 + - + +
522A LYS* 3.0 27.9 + - - +
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Residues in contact with GLN 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LEU* 4.2 13.5 - - + -
396A ASN* 3.0 41.7 + - - +
515A ALA 3.9 10.0 + - - +
516A LEU* 3.1 15.2 + - + +
518A PRO* 1.4 75.5 - - - +
520A TYR* 1.3 66.1 + - - +
522A LYS* 3.4 11.8 + - - +
523A LEU* 3.0 32.8 + - - +
526A ARG* 5.9 0.2 - - - +
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Residues in contact with TYR 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LEU* 4.0 18.3 - - + +
374A GLY 2.8 35.8 + - - -
375A PHE* 3.4 46.2 - + - -
377A PHE* 5.6 0.5 - - - -
414A GLY* 3.2 37.7 + - - -
417A MSE 3.7 28.0 - - + -
418A ALA* 4.1 13.3 - - + +
421A ILE* 3.9 18.4 - - + -
516A LEU 2.9 12.3 + - - +
517A LEU 3.6 7.6 - - - +
519A GLN* 1.3 76.5 - - - +
521A ALA* 1.4 56.6 + - - +
523A LEU* 3.3 3.2 + - - -
524A GLU* 3.0 28.6 + - + +
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Residues in contact with ALA 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ILE* 3.8 28.4 - - + +
517A LEU 2.9 16.5 + - - +
518A PRO* 3.6 9.4 - - + +
520A TYR* 1.4 75.3 - - - +
522A LYS* 1.3 56.7 + - - +
524A GLU* 3.3 9.9 + - - +
525A GLN* 3.0 32.0 + - + +
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Residues in contact with LYS 522 (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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518A PRO 3.0 18.1 + - - +
519A GLN* 3.8 16.2 - - - +
520A TYR 3.3 0.2 - - - -
521A ALA* 1.3 71.7 - - - +
523A LEU* 1.3 61.5 + - - +
525A GLN* 3.2 9.5 + - - +
526A ARG* 2.9 27.8 + - - +
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Residues in contact with LEU 523 (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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373A LEU* 3.6 32.5 - - + -
375A PHE* 3.9 13.9 - - + -
392A PHE* 3.9 35.9 - - + -
396A ASN* 3.7 17.3 - - - +
519A GLN* 3.0 23.4 + - - +
520A TYR* 3.3 4.5 + - - +
522A LYS* 1.3 72.8 - - - +
524A GLU* 1.3 65.6 + - - +
526A ARG* 3.2 41.7 + - - +
527A ILE* 3.0 26.9 + - - +
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Residues in contact with GLU 524 (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* 3.6 22.1 - - + -
377A PHE* 5.7 0.5 - - - -
384A PRO* 3.6 16.6 - - + +
386A ILE* 3.9 17.4 - - + +
418A ALA* 4.9 6.8 - - - +
421A ILE* 4.8 10.1 - - - +
422A HIS* 2.7 40.4 + - - -
520A TYR* 3.0 16.6 + - + +
521A ALA* 3.5 11.2 - - - +
523A LEU* 1.3 76.5 - - - +
525A GLN* 1.4 70.7 + - - +
527A ILE* 3.3 6.9 + - - +
528A LEU* 3.0 30.7 + - + +
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Residues in contact with GLN 525 (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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521A ALA* 3.0 17.6 + - + +
522A LYS* 3.2 11.4 + - - +
524A GLU* 1.4 82.3 + - - +
526A ARG* 1.4 60.4 + - - +
528A LEU* 3.4 27.0 + - - +
529A SER* 2.9 30.8 + - - -
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Residues in contact with ARG 526 (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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392A PHE* 4.0 17.8 - - + -
396A ASN* 3.1 31.9 + - - +
398A LYS* 5.4 7.1 - - - +
522A LYS 2.9 14.6 + - - +
523A LEU* 3.2 35.7 + - + +
525A GLN* 1.4 74.9 - - - +
527A ILE* 1.3 62.4 + - + +
529A SER* 3.0 23.8 + - - +
530A GLN* 3.3 21.3 + - - +
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Residues in contact with ILE 527 (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* 3.6 38.8 - - + -
386A ILE* 3.4 33.4 - - + -
390A HIS* 3.7 37.9 - - + +
392A PHE* 4.0 13.5 - - + -
398A LYS* 4.5 3.8 - - - +
523A LEU 3.0 20.9 + - - +
524A GLU* 3.3 6.5 + - - +
526A ARG* 1.3 75.6 - - + +
528A LEU* 1.3 62.7 + - - +
530A GLN* 3.3 13.7 + - - +
531A THR 3.1 25.7 + - - +
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Residues in contact with LEU 528 (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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384A PRO* 4.0 26.2 - - + -
385A GLU* 3.7 26.0 - - + +
386A ILE* 3.7 15.7 - - + -
524A GLU* 3.0 20.3 + - + +
525A GLN* 3.6 35.9 - - - +
527A ILE* 1.3 75.0 - - - +
529A SER* 1.4 56.9 + - - +
531A THR* 3.1 21.6 + - - +
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Residues in contact with SER 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A GLN 2.9 14.9 + - - -
526A ARG* 3.0 20.1 + - - +
527A ILE 3.3 0.2 - - - -
528A LEU* 1.4 75.8 - - - +
530A GLN* 1.3 58.0 + - - +
531A THR* 3.9 4.0 + - - -
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Residues in contact with GLN 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A HIS* 4.3 12.5 + - - -
398A LYS* 3.5 26.3 + - - +
526A ARG* 3.3 23.4 + - - +
527A ILE* 3.4 21.1 + - - +
528A LEU 3.3 0.8 - - - -
529A SER* 1.3 76.8 + - - +
531A THR* 1.4 74.6 + - - +
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Residues in contact with THR 531 (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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386A ILE* 5.5 4.3 - - - +
387A ILE* 5.6 3.4 + - - +
390A HIS* 5.7 1.6 - - - -
527A ILE* 3.1 21.9 + - - +
528A LEU* 3.1 16.8 + - - +
529A SER 4.2 4.2 + - - -
530A GLN* 1.4 91.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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