Contacts of the helix formed by residues 507 - 525 (chain A) in PDB entry 5ULM
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 PRO 507 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ASP* 5.8 5.8 - - - +
475A TYR* 3.4 52.5 - - + +
505A LYS 3.5 5.8 - - - +
506A THR* 1.3 85.7 - - - +
508A ALA* 1.3 61.4 + - - +
509A TRP* 3.3 26.0 - - + +
510A TYR* 3.0 19.7 + - + +
511A LEU* 3.0 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ASP 5.7 5.0 + - - +
325A GLN* 3.7 28.0 - - + +
506A THR 3.6 3.1 + - - -
507A PRO* 1.3 69.1 - - - +
509A TRP* 1.4 67.7 + - - +
510A TYR 3.1 0.2 + - - -
511A LEU* 3.3 7.2 + - - +
512A LYS* 2.9 26.2 + - - +
549A ALA 5.5 6.7 - - - +
550A THR* 5.3 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ARG* 3.4 68.2 + - + +
323A ASP* 5.2 7.0 + - - -
325A GLN* 3.6 12.2 + - - +
327A TYR* 3.3 23.1 - - - +
357A PHE* 3.7 24.5 - + + -
395A ARG* 4.5 7.4 + - - -
475A TYR* 3.7 19.0 + + - -
507A PRO* 3.3 27.0 - - + +
508A ALA* 1.4 79.6 - - - +
510A TYR* 1.3 90.2 + + + +
512A LYS* 3.4 14.1 - - - +
513A SER* 3.8 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A TYR* 3.6 36.6 - + + -
476A TRP* 2.9 39.7 + - + -
479A GLY* 3.2 16.9 - - - -
480A PHE* 3.3 27.1 + + - -
501A LEU* 4.7 1.8 - - + -
506A THR* 3.7 17.3 - - + -
507A PRO* 3.0 9.5 + - + +
509A TRP* 1.3 107.3 - + + +
511A LEU* 1.3 68.3 + - - +
512A LYS 3.1 1.3 - - - -
513A SER* 2.9 25.6 + - - -
514A ILE* 3.4 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A LEU* 3.8 31.0 - - + -
506A THR* 4.2 13.5 - - + +
507A PRO 3.0 14.3 + - - +
508A ALA* 3.9 7.9 - - - +
510A TYR* 1.3 80.3 - - - +
512A LYS* 1.3 62.7 + - - +
514A ILE* 3.4 8.4 + - + -
515A VAL* 2.9 33.0 + - + +
546A LEU* 3.9 24.7 - - + +
549A ALA* 3.7 32.3 - - + +
550A THR* 4.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A GLN* 4.6 7.6 - - - +
361A ARG* 3.4 23.2 - - - +
395A ARG* 3.9 14.1 - - - +
402A LEU* 5.2 3.8 - - - +
403A ASP* 5.9 0.8 + - - -
508A ALA 2.9 18.1 + - - +
509A TRP* 3.4 10.8 - - - +
511A LEU* 1.3 77.1 - - - +
513A SER* 1.3 58.4 + - - +
515A VAL* 3.2 5.5 + - + +
516A GLU* 3.0 64.7 + - - +
519A LEU* 6.3 0.6 - - - +
550A THR* 3.9 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ARG* 3.6 32.0 + - - +
398A LYS* 3.3 8.7 + - - -
480A PHE* 5.7 2.4 - - - -
509A TRP* 3.8 7.2 + - - -
510A TYR* 2.9 22.8 + - - -
512A LYS* 1.3 75.0 - - - +
514A ILE* 1.3 70.0 + - - +
516A GLU* 3.3 10.5 + - - -
517A THR* 3.2 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ILE* 5.3 4.7 - - + -
479A GLY* 3.9 15.0 - - - +
480A PHE* 3.6 26.7 - - + -
482A LEU* 4.2 17.7 - - + -
483A GLY* 5.3 4.3 - - - +
501A LEU* 5.0 3.1 - - + -
510A TYR* 3.5 47.3 - - + +
511A LEU* 3.4 13.6 + - + +
513A SER* 1.3 80.6 + - - +
515A VAL* 1.3 63.1 + - + +
517A THR* 3.1 9.9 + - - +
518A ILE* 3.1 40.1 + - + +
546A LEU* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A LEU* 2.9 29.3 + - + +
512A LYS* 3.6 7.2 - - + +
514A ILE* 1.3 75.3 - - - +
516A GLU* 1.3 61.4 - - + +
518A ILE* 3.0 15.2 + - + +
519A LEU* 2.8 46.0 + - + +
546A LEU* 3.5 34.3 - - + +
547A VAL* 4.1 17.5 - - + +
550A THR* 3.8 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ARG* 3.1 15.4 + - - -
395A ARG* 3.1 22.0 + - - -
398A LYS* 2.8 35.4 + - - -
399A ASP* 2.9 23.8 - - - +
402A LEU* 3.9 20.1 - - + +
512A LYS* 3.0 45.0 + - - +
513A SER* 3.5 4.5 - - - +
514A ILE 3.3 0.2 - - - -
515A VAL* 1.3 77.3 - - + +
517A THR* 1.3 63.5 + - - +
519A LEU* 3.5 6.5 + - + +
520A ILE* 3.3 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LYS* 3.5 7.1 + - - +
433A ILE* 4.5 20.1 - - + +
434A ASN* 2.8 35.2 + - - +
437A VAL* 3.8 25.5 - - + +
483A GLY* 6.0 1.3 - - - -
487A LEU* 5.1 3.6 - - + -
513A SER 3.2 10.9 + - - -
514A ILE* 3.1 13.4 + - - -
516A GLU* 1.3 79.7 - - - +
518A ILE* 1.3 62.7 + - + +
520A ILE* 3.4 5.8 + - - +
521A TYR* 3.2 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LEU* 4.4 13.7 - - + -
483A GLY* 5.5 4.0 - - - -
486A VAL* 4.4 23.6 - - + -
514A ILE* 3.1 33.6 + - + +
515A VAL* 3.0 15.5 + - + +
517A THR* 1.3 77.0 - - + +
519A LEU* 1.3 61.7 + - + +
521A TYR* 3.5 6.5 - - - +
522A LYS* 2.9 40.1 + - + +
543A MET* 3.7 35.9 - - + -
546A LEU* 5.2 4.5 - - + -
547A VAL* 5.7 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LEU* 4.9 19.3 - - + -
406A PHE* 4.7 3.6 - - + -
512A LYS* 6.3 0.4 - - - +
515A VAL* 2.8 36.9 + - + +
516A GLU* 3.9 9.4 - - + +
517A THR 3.4 0.2 - - - -
518A ILE* 1.3 77.4 - - + +
520A ILE* 1.3 57.5 + - - +
522A LYS* 3.5 6.3 + - + +
523A HIS* 3.0 29.1 + - - +
547A VAL* 4.1 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LYS* 3.7 31.6 - - + -
401A PHE* 4.1 26.7 - - + -
402A LEU* 4.3 15.9 - - + -
406A PHE* 3.9 19.5 - - + -
437A VAL* 3.5 26.2 - - + +
438A LEU* 4.6 2.7 - - + -
441A ALA* 4.1 5.2 - - + -
516A GLU 3.3 17.6 + - - +
517A THR* 3.8 1.8 - - - +
518A ILE 3.2 0.4 - - - -
519A LEU* 1.3 74.3 - - - +
521A TYR* 1.3 65.5 + - - +
523A HIS* 3.3 1.0 + - - +
524A PHE* 3.2 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A VAL* 4.0 14.8 - - + +
440A LEU* 3.6 28.0 - - + +
486A VAL* 3.5 39.6 + - + -
487A LEU* 4.2 29.4 + - + -
489A ASN* 4.1 17.1 + - - +
517A THR 3.2 13.5 + - - +
518A ILE* 3.5 10.8 - - - +
520A ILE* 1.3 76.0 - - - +
522A LYS* 1.3 77.2 + - + +
524A PHE* 3.2 1.5 + - - -
525A VAL* 2.8 70.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A VAL* 5.9 2.1 - - - +
518A ILE* 2.9 28.8 + - + +
519A LEU* 3.9 7.6 - - + +
520A ILE 3.3 0.2 - - - -
521A TYR* 1.3 94.9 - - + +
523A HIS* 1.3 61.8 + - - +
524A PHE 3.4 0.5 + - - -
525A VAL* 4.1 15.3 + - + +
536A GLN* 4.6 9.9 - - - +
539A VAL* 4.2 14.5 - - - +
540A ASP* 4.9 4.1 + - - -
543A MET* 3.8 35.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A PHE* 3.4 41.8 - + + +
519A LEU 3.0 17.6 + - - +
520A ILE 3.7 5.8 - - - +
521A TYR 3.2 0.4 - - - -
522A LYS* 1.3 77.4 - - - +
524A PHE* 1.3 82.9 + + + +
525A VAL 4.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A PHE* 3.8 20.6 - + - -
406A PHE* 4.0 16.6 - + + -
412A ARG* 6.2 0.2 - - - -
440A LEU* 4.0 24.6 - - + +
441A ALA* 3.4 47.6 - - + +
520A ILE* 3.2 23.9 + - + +
521A TYR 3.2 2.5 + - - +
523A HIS* 1.3 105.1 - + - +
525A VAL* 1.3 68.1 + - - +
526A LYS* 3.4 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A LEU* 5.1 14.0 - - + +
521A TYR* 2.8 66.8 + - + +
522A LYS* 4.1 16.2 - - + +
523A HIS 4.9 0.9 - - - +
524A PHE* 1.3 75.3 - - - +
526A LYS* 1.3 72.2 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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