Contacts of the helix formed by residues 537 - 561 (chain A) in PDB entry 3VF1
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 ASN 537 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A ASP* 3.5 27.4 - - - +
502A VAL* 3.9 15.6 - - - +
535A PHE* 3.5 1.1 - - - +
536A GLU* 1.3 85.3 + - - +
538A ARG* 1.3 64.0 + - - +
539A GLU* 3.1 19.3 + - - +
540A GLU* 2.9 58.7 + - - +
541A LEU* 3.5 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 538 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ILE* 4.6 11.4 - - + +
493A GLN* 3.6 38.3 + - + +
496A TYR* 2.9 38.1 + - + -
497A ASN* 3.4 18.5 + - - +
498A ASP* 3.9 10.9 - - - +
499A ASP* 3.3 16.5 + - - +
502A VAL* 3.5 23.3 - - + -
537A ASN* 1.3 73.8 - - - +
539A GLU* 1.3 74.0 + - - +
541A LEU* 3.2 5.4 + - - +
542A VAL* 2.9 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A HIS* 5.6 0.7 + - - -
489A GLN* 5.7 6.7 + - - +
493A GLN* 5.2 5.9 + - - -
499A ASP* 3.9 7.1 - - - +
537A ASN* 3.1 17.5 + - - +
538A ARG* 1.3 96.5 + - - +
540A GLU* 1.3 65.6 + - + +
542A VAL* 3.3 6.7 + - - +
543A HIS* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 540 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A PRO* 4.7 9.5 - - + +
534A SER 3.6 13.0 - - - +
535A PHE* 3.9 11.9 - - + -
536A GLU* 3.5 24.7 + - - +
537A ASN* 2.9 40.6 + - - +
538A ARG 3.4 0.2 - - - -
539A GLU* 1.3 75.6 - - - +
541A LEU* 1.3 63.0 + - - +
543A HIS* 3.8 5.0 - - - +
544A PHE* 3.2 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A VAL* 5.0 0.4 - - + -
492A ILE* 3.9 26.2 - - + -
496A TYR* 4.0 25.8 - - + +
502A VAL* 4.3 15.9 - - + -
508A ILE* 4.1 14.8 - - + -
535A PHE* 3.6 39.0 - - + -
537A ASN 3.5 9.9 + - - +
538A ARG* 3.2 9.4 + - - +
539A GLU 3.2 0.6 - - - -
540A GLU* 1.3 80.9 - - - +
542A VAL* 1.3 62.3 + - - +
544A PHE* 4.0 1.0 - - - +
545A LEU* 3.2 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A HIS* 3.6 39.5 - - + +
488A VAL* 3.7 19.5 - - + +
489A GLN* 3.9 28.3 - - + +
492A ILE* 4.0 21.1 - - + -
493A GLN* 6.0 1.1 - - + -
538A ARG* 2.9 24.8 + - + +
539A GLU* 3.8 7.0 - - - +
541A LEU* 1.3 76.9 - - - +
543A HIS* 1.3 57.5 + - - +
545A LEU* 3.3 1.4 + - - -
546A THR* 2.8 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A PHE 5.4 3.4 + - - -
455A ASP* 3.6 38.4 + - + +
481A TRP* 4.1 20.2 - + - -
485A HIS* 4.8 10.0 + - - +
539A GLU 3.0 17.0 + - - +
540A GLU* 3.8 6.5 - - - +
542A VAL* 1.3 77.9 - - - +
544A PHE* 1.3 68.0 + + + +
546A THR* 3.0 8.5 + - - -
547A VAL* 3.0 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A THR* 4.7 3.1 - - + -
451A PHE* 4.1 36.1 - + + -
511A TRP* 3.7 36.3 - + - -
512A ILE* 4.0 5.2 - - + -
515A LEU* 3.9 20.4 - - + -
520A TYR* 5.0 3.6 - + - -
531A VAL* 4.0 22.2 - - + -
532A PRO* 4.2 17.3 - - + -
535A PHE* 4.0 13.2 - + + -
540A GLU 3.2 14.9 + - - +
541A LEU 4.0 3.6 - - - +
543A HIS* 1.3 85.3 - + + +
545A LEU* 1.3 61.8 + - + +
547A VAL* 3.4 8.0 + - + +
548A VAL* 3.3 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A VAL* 4.2 11.0 - - + -
401A LEU* 4.1 16.8 - - + -
402A LEU* 3.9 23.1 - - + -
488A VAL* 3.9 9.9 - - + -
492A ILE* 3.8 26.5 - - + -
511A TRP* 3.7 34.1 - - + -
541A LEU* 3.2 36.3 + - + +
542A VAL 3.8 2.7 - - - +
544A PHE* 1.3 73.9 - - + +
546A THR* 1.3 66.5 + - - +
548A VAL* 3.2 5.3 + - + +
549A VAL* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A TRP* 3.9 35.0 - - + +
484A ILE* 4.3 6.5 - - + +
485A HIS* 3.4 47.3 - - + +
488A VAL* 4.0 11.0 - - - +
542A VAL* 2.8 22.8 + - - +
543A HIS* 3.0 9.8 + - - -
545A LEU* 1.3 77.8 - - - +
547A VAL* 1.3 62.3 + - - +
549A VAL* 4.0 0.9 - - - +
550A PHE* 2.9 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A MET* 4.8 3.6 - - + -
451A PHE* 4.1 22.4 - - + +
454A TYR* 3.9 41.3 - - + +
481A TRP* 3.7 25.4 - - + -
543A HIS* 3.0 33.6 + - + +
544A PHE* 3.4 11.4 - - + +
546A THR* 1.3 76.7 - - - +
548A VAL* 1.3 59.7 + - + +
550A PHE* 3.9 1.0 - - - +
551A THR* 2.9 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A MET* 4.0 11.9 - - + -
384A THR* 4.0 39.3 - - + +
402A LEU* 4.2 18.4 - - + -
405A HIS* 5.7 1.1 - - + -
406A THR* 4.6 5.6 - - + -
451A PHE* 6.0 0.9 - - + -
511A TRP* 5.1 4.0 - - + -
544A PHE* 3.4 27.8 - - + +
545A LEU* 3.2 10.0 + - + +
547A VAL* 1.3 81.2 - - + +
549A VAL* 1.3 63.5 + - - +
551A THR* 3.9 0.5 - - - -
552A CYS* 3.0 42.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A LEU* 5.1 5.6 - - + -
402A LEU* 4.1 16.8 - - + -
405A HIS* 3.7 46.7 + - + +
484A ILE* 3.6 31.2 - - + -
487A PHE* 5.8 2.9 - - + -
488A VAL* 4.4 13.7 - - + -
545A LEU 3.0 16.4 + - - +
548A VAL* 1.3 76.5 - - - +
550A PHE* 1.3 54.6 + - - +
552A CYS* 4.1 1.0 - - - +
553A SER* 2.6 35.5 + - - +
623A LEU* 5.1 1.6 - - + -
626A TYR* 5.3 0.7 - - - +
643A PHE* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LEU* 3.7 26.2 - - + -
473A TYR* 5.7 0.2 - + - -
477A ALA* 3.5 33.4 - - + -
481A TRP* 3.5 46.4 - + + -
484A ILE* 4.0 13.4 - - + +
546A THR* 2.9 20.9 + - + +
547A VAL 3.9 2.0 - - - +
549A VAL* 1.3 78.0 - - - +
551A THR* 1.3 65.1 + - - +
553A SER* 3.9 3.8 - - - -
554A CYS* 2.9 47.8 + - + -
555A GLN* 3.0 35.8 + - + -
668A LEU* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ARG 3.8 19.5 - - - +
377A CYS* 4.2 11.0 - - - -
381A MET* 3.4 33.4 - - + -
454A TYR* 3.7 20.6 - - + -
481A TRP* 6.0 0.2 - - - -
547A VAL* 2.9 22.0 + - - +
550A PHE* 1.3 80.2 - - - +
552A CYS* 1.3 64.6 + - - +
555A GLN* 3.8 13.5 - - + +
556A HIS* 3.3 24.6 + - - +
677A ILE* 4.2 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A MET* 3.8 27.1 - - - -
384A THR* 5.3 0.4 - - - -
405A HIS* 3.2 31.2 - - + +
406A THR* 4.8 7.9 - - - -
409A ILE* 5.1 3.1 - - - -
548A VAL* 3.0 36.0 + - - +
549A VAL 4.2 2.5 - - - +
551A THR* 1.3 77.7 - - - +
553A SER* 1.3 59.9 + - - +
556A HIS* 4.1 2.7 - - - +
675A ASN 4.0 2.7 - - - +
676A SER 3.1 27.5 - - - +
677A ILE* 3.4 17.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A HIS* 4.6 0.4 - - - -
484A ILE* 4.2 1.2 - - - +
549A VAL 2.6 23.6 + - - -
550A PHE* 3.6 1.7 + - - -
552A CYS* 1.3 80.4 - - - +
554A CYS* 1.3 80.0 + - - +
556A HIS* 4.2 1.4 + - - +
557A ALA* 3.2 17.0 + - - +
623A LEU* 3.8 23.1 - - - +
673A VAL* 3.2 15.5 - - - +
674A PRO* 3.3 21.8 - - - +
675A ASN 3.6 10.3 - - - -
676A SER 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LEU* 3.7 35.2 - - + -
484A ILE* 4.0 14.6 - - - -
550A PHE* 2.9 27.0 + - + +
553A SER* 1.3 85.9 + - - +
555A GLN* 1.3 67.2 + - - +
557A ALA* 3.0 5.0 + - - +
558A ALA* 2.9 19.2 + - - +
623A LEU* 4.0 13.7 - - - -
668A LEU* 3.5 17.6 - - + +
673A VAL* 3.7 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PRO* 5.6 0.6 - - - +
249A GLU* 3.3 30.9 + - - +
372A THR* 4.9 1.2 + - - +
376A ARG 5.7 0.2 - - - +
377A CYS* 3.8 17.0 - - - -
454A TYR* 6.4 0.9 - - + -
456A LEU* 6.0 0.4 - - - -
473A TYR* 2.8 34.1 + - - -
550A PHE* 3.0 21.6 + - + +
551A THR* 3.8 24.9 - - + +
554A CYS* 1.3 78.2 - - - +
556A HIS* 1.3 63.9 + - - +
558A ALA* 3.1 12.6 + - - +
559A VAL* 3.2 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A HIS* 3.8 10.1 - + - -
377A CYS* 3.9 13.7 - - + -
378A HIS* 3.3 15.3 + + - -
551A THR 3.3 16.0 + - - +
552A CYS 4.1 5.4 + - - +
553A SER 4.2 1.0 + - - +
554A CYS 3.3 0.6 - - - -
555A GLN* 1.3 78.4 - - - +
557A ALA* 1.3 59.6 + - - +
559A VAL* 3.4 1.8 + - - +
560A ASN* 2.8 52.3 + - + +
561A PHE* 4.2 14.5 - + - -
674A PRO* 5.8 0.4 - - - +
676A SER 4.3 5.5 + - - -
677A ILE* 3.7 32.4 - - + +
678A ALA 4.9 0.2 - - - -
679A ILE* 3.0 17.0 + - + -
701A FE2 2.2 31.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A SER 3.2 17.7 + - - +
554A CYS 3.0 5.7 + - - +
556A HIS* 1.3 80.0 + - - +
558A ALA* 1.3 64.0 + - - +
561A PHE* 3.2 39.4 + - + +
562A SER 4.0 1.7 + - - -
667A TRP* 4.0 17.9 - - - +
672A HIS 4.9 0.9 - - - +
673A VAL* 3.7 18.4 - - + -
674A PRO* 4.1 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLY 4.1 7.1 - - - +
246A SER* 4.2 1.1 - - - -
248A PRO* 6.1 0.7 - - + -
473A TYR* 4.0 21.1 - - + -
554A CYS 2.9 11.5 + - - +
555A GLN* 3.1 9.2 + - - +
557A ALA* 1.3 77.6 - - - +
559A VAL* 1.3 55.9 + - + +
562A SER* 2.6 28.8 + - - -
665A TYR* 3.8 18.4 + - - +
667A TRP* 4.4 12.4 + - - +
668A LEU* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A SER 3.3 24.0 - - - +
248A PRO* 4.6 8.7 - - + -
368A HIS* 2.8 31.7 + - - +
372A THR* 3.7 31.0 - - + +
373A HIS* 4.1 21.5 - - + -
377A CYS* 4.2 7.9 - - - -
473A TYR* 5.7 0.2 - - + -
555A GLN* 3.2 31.6 + - - +
556A HIS 3.7 4.3 - - - +
558A ALA* 1.3 81.5 - - + +
560A ASN* 1.3 60.2 + - - +
562A SER* 4.0 4.0 - - - -
563A GLN* 3.8 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A HIS* 2.5 14.7 + - - +
556A HIS* 2.8 34.7 + - + +
558A ALA 3.4 0.4 - - - -
559A VAL* 1.3 80.2 - - - +
561A PHE* 1.3 75.3 + - + +
562A SER 3.1 3.8 - - - -
563A GLN* 3.0 38.5 + - - +
613A LEU* 2.9 29.4 + - - +
614A THR* 3.6 2.8 - - - +
679A ILE* 3.7 1.2 - - - +
701A FE2 2.3 31.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A HIS* 4.2 14.8 - + - -
557A ALA* 3.2 28.5 + - + +
560A ASN* 1.3 82.0 - - - +
562A SER* 1.3 56.9 + - - +
563A GLN 3.2 4.0 + - - -
564A MET* 4.6 2.9 + - - +
614A THR* 3.8 33.6 - - - +
615A THR 4.0 0.4 - - - -
616A ILE* 3.4 35.2 - - + -
620A GLU* 6.3 0.7 - - + -
667A TRP* 3.1 28.7 - - + -
672A HIS 5.0 3.6 - - - +
674A PRO* 3.4 35.9 - - + -
679A ILE* 3.6 31.4 - - + -
----------------------------------------------------------
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