Contacts of the helix formed by residues 509 - 531 (chain A) in PDB entry 3SV1
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 ASP 509 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A PHE* 4.2 21.3 - - + -
374A ALA 4.9 3.5 + - - +
507A SER* 2.7 11.9 + - - +
508A GLU* 1.3 88.5 - - - +
510A ALA* 1.3 69.0 + - - +
511A GLN 2.9 3.5 + - - +
512A LEU* 3.0 24.2 + - + +
513A ILE* 2.7 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ASP* 3.5 10.8 - - + +
465A GLY 3.2 27.4 - - - +
466A ASN* 3.3 7.4 - - - -
467A ILE 3.5 7.6 - - - +
468A VAL* 3.6 24.1 - - + +
507A SER* 2.5 24.3 + - - +
508A GLU 3.5 1.0 - - - -
509A ASP* 1.3 71.0 - - - +
511A GLN* 1.3 68.0 + - - +
513A ILE* 3.1 2.6 + - - +
514A ALA* 2.9 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ASP* 2.9 42.0 + - - +
465A GLY 4.9 0.2 + - - -
508A GLU 5.3 1.3 - - - +
509A ASP 2.9 0.8 + - - -
510A ALA* 1.3 81.6 - - - +
512A LEU* 1.3 78.8 + - + +
513A ILE 3.2 0.2 + - - -
514A ALA 3.2 3.5 + - - -
515A GLN* 3.0 41.9 + - - +
755D ASN* 5.3 6.7 - - - +
757D TYR* 4.9 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A PHE* 4.2 18.8 - - + -
508A GLU 4.7 2.2 - - - +
509A ASP* 3.0 33.4 + - + +
511A GLN* 1.3 89.7 - - + +
513A ILE* 1.3 62.5 + - - +
515A GLN* 3.2 24.3 + - - +
516A SER* 3.0 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A PHE* 3.6 39.0 - - + -
375A ALA* 4.5 2.5 - - + -
432A LEU* 4.1 25.8 - - + -
434A ILE* 4.3 6.8 - - + +
468A VAL* 4.0 19.1 - - + -
507A SER* 3.4 35.7 - - - +
509A ASP* 2.7 18.9 + - + +
510A ALA* 3.2 9.2 - - - +
512A LEU* 1.3 69.7 - - - +
514A ALA* 1.3 69.8 + - - +
516A SER* 3.4 7.6 + - - -
517A ILE* 3.4 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ILE* 4.1 15.4 - - + +
462A ALA 4.3 1.6 - - - -
463A ASP* 3.4 42.8 - - + +
468A VAL* 4.4 4.3 - - + -
510A ALA 2.9 9.3 + - - -
513A ILE* 1.3 74.4 - - - +
515A GLN* 1.3 65.8 + - - +
516A SER 3.1 0.3 + - - -
517A ILE* 3.1 6.2 + - - +
518A GLY* 2.9 19.2 + - - -
757D TYR* 3.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A GLN* 3.0 45.7 + - - +
512A LEU* 3.3 20.3 + - - +
514A ALA* 1.3 76.3 - - - +
516A SER* 1.3 63.0 + - - +
518A GLY* 3.0 11.7 + - - -
519A GLN* 3.0 18.5 + - + +
757D TYR* 4.2 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LEU* 4.0 5.5 - - - +
371A ILE* 3.9 21.9 - - - +
373A PHE* 3.6 16.3 - - - -
434A ILE* 4.3 10.8 - - - -
512A LEU 3.0 14.4 + - - -
513A ILE 3.6 5.6 - - - -
514A ALA 3.2 0.2 - - - -
515A GLN* 1.3 73.2 - - - +
517A ILE* 1.3 68.4 + - - +
518A GLY 2.9 1.3 - - - -
519A GLN* 2.8 20.9 + - - +
520A ALA* 2.9 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A LEU* 6.0 2.7 - - + -
434A ILE* 4.0 22.8 - - + +
439A ILE* 3.8 30.7 - - + -
461A ILE* 3.4 49.4 - - + -
468A VAL* 5.2 3.8 - - + -
470A LEU* 4.9 11.4 - - + -
513A ILE* 3.4 24.0 + - + +
514A ALA* 3.1 8.2 + - - +
516A SER* 1.3 77.6 - - - +
518A GLY* 1.3 54.1 + - - +
520A ALA* 3.1 4.5 + - - +
521A PHE* 2.8 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ALA 2.9 11.5 + - - -
515A GLN* 3.2 6.5 - - - -
516A SER 2.9 2.4 - - - -
517A ILE* 1.3 77.6 - - - +
519A GLN* 1.3 66.2 + - - +
521A PHE* 2.8 30.8 - - - +
522A SER* 3.3 5.4 + - - -
757D TYR* 4.7 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LEU* 3.8 12.1 - - + -
515A GLN 3.0 14.4 + - - +
516A SER* 2.8 15.5 + - - +
518A GLY* 1.3 72.5 - - - +
520A ALA* 1.3 50.9 + - - +
522A SER* 2.7 15.0 + - - -
523A VAL* 2.6 46.9 + - + +
526A GLN* 5.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LEU* 3.2 20.0 - - + +
434A ILE* 4.3 7.4 - - + -
435A SER 3.5 26.7 - - - +
436A THR* 4.9 1.6 - - - +
455A LEU* 3.9 5.8 - - + -
516A SER 2.9 9.9 + - - +
517A ILE* 3.2 14.6 - - - +
519A GLN* 1.3 73.9 - - - +
521A PHE* 1.3 57.3 + - - +
523A VAL* 4.2 2.9 - - - -
524A ALA* 2.4 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A LEU* 3.7 25.8 - - + -
458A ILE* 3.8 26.9 - - + -
459A SER 3.9 5.8 - - - -
460A TYR 4.0 1.3 - - - -
461A ILE* 4.0 12.8 - - + -
517A ILE* 2.8 25.2 + - + -
518A GLY* 2.8 14.8 - - - +
520A ALA* 1.3 74.9 - - - +
522A SER* 1.3 48.6 + - - +
524A ALA* 3.7 0.9 - - - +
525A TYR* 2.7 34.7 + - - +
757D TYR* 3.5 21.3 - - + -
758D GLU 3.2 22.2 - - - -
759D ASN* 3.3 53.0 - - + +
760D PRO* 4.1 6.3 - - + -
761D THR* 3.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A GLY 3.3 2.5 + - - -
519A GLN* 2.7 36.1 + - - -
521A PHE* 1.3 75.1 - - - +
523A VAL* 1.3 60.7 + - - +
524A ALA 3.0 1.1 - - - -
525A TYR* 2.7 12.6 + - - -
526A GLN* 2.3 57.1 + - - +
760D PRO* 4.8 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A SER* 3.9 22.7 - - - +
367A LEU* 3.9 19.5 - - + -
368A ILE* 4.2 9.0 - - + -
436A THR* 3.8 19.1 - - + -
519A GLN* 2.6 45.8 + - + +
520A ALA* 3.7 4.7 - - - +
522A SER* 1.3 78.2 + - - +
524A ALA* 1.3 62.6 + - - +
526A GLN* 3.4 13.2 + - - +
527A GLU* 3.0 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A THR* 3.3 24.4 - - - +
455A LEU* 3.1 28.3 - - + -
520A ALA 2.4 29.0 + - - +
521A PHE 3.7 2.5 - - - +
523A VAL* 1.3 73.3 - - - +
525A TYR* 1.3 50.9 + - - +
527A GLU* 3.1 5.5 + - - +
528A PHE* 2.6 49.0 + - + +
761D THR* 4.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A PHE 2.7 23.9 + - - +
522A SER* 2.7 17.7 + - - +
524A ALA* 1.3 70.3 - - - +
526A GLN* 1.3 62.4 + - + +
528A PHE* 2.8 39.6 - - - +
529A LEU* 2.9 36.9 + - + +
760D PRO* 3.3 39.5 - - + -
761D THR* 3.1 22.6 + - - +
764D PHE* 5.3 15.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A GLN* 5.8 0.4 + - - -
522A SER* 2.3 53.2 + - - +
523A VAL* 3.7 11.0 - - - +
525A TYR* 1.3 73.7 - - + +
527A GLU* 1.3 52.0 + - + +
529A LEU* 2.6 15.0 - - + +
530A ARG 2.6 33.3 + - - -
537A GLU* 3.0 35.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ILE* 5.7 7.3 - - + +
436A THR* 5.6 5.6 - - - +
523A VAL* 3.0 25.7 + - + +
524A ALA* 3.5 9.0 - - - +
526A GLN* 1.3 70.7 - - - +
528A PHE* 1.3 56.3 + - + +
529A LEU 2.3 18.2 + - - -
530A ARG* 2.7 47.5 + - - +
531A ALA* 3.2 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A THR 3.8 20.4 - - - -
437A GLN* 5.5 4.0 - - - -
455A LEU* 5.2 1.1 - - + -
456A ARG* 4.8 38.4 - - + -
524A ALA* 2.6 35.4 + - + +
525A TYR* 2.8 15.3 - - - +
527A GLU* 1.3 69.4 - - + +
529A LEU* 1.3 55.0 + - - +
531A ALA* 5.4 2.5 - - - -
532A ASN* 3.8 16.5 + - - +
761D THR* 3.6 33.8 - - + +
764D PHE* 5.8 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A TYR* 2.9 43.5 - - + +
526A GLN* 2.6 16.8 - - + +
527A GLU 2.3 19.8 + - - -
528A PHE* 1.3 68.0 - - - +
530A ARG* 1.3 61.0 + - - -
531A ALA 3.3 1.3 - - - +
532A ASN* 3.1 15.3 + - + +
534A ILE* 3.1 56.2 - - + +
537A GLU* 3.1 40.4 - - + -
540A SER* 5.4 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A GLN 2.6 10.5 + - - +
527A GLU* 2.7 50.2 + - - +
529A LEU* 1.3 68.1 - - - +
531A ALA* 1.3 58.2 + - - +
532A ASN 2.9 4.5 - - - -
533A GLY* 2.8 22.2 + - - -
534A ILE 3.5 12.2 + - - -
535A ASN* 3.6 35.5 + - - +
537A GLU* 2.7 58.3 + - - +
538A ASP* 3.8 16.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A GLU* 3.2 13.9 + - - +
528A PHE* 5.4 2.0 - - - -
529A LEU 5.1 0.4 - - - +
530A ARG* 1.3 80.0 - - - +
532A ASN* 1.3 61.4 - - - +
533A GLY 3.1 3.4 + - - -
----------------------------------------------------------
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