Contacts of the helix formed by residues 506 - 524 (chain A) in PDB entry 4OSI
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 506 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A GLY 4.3 3.8 + - - -
504A ASN 3.5 0.6 + - - -
505A ILE* 1.3 79.7 - - - +
507A GLY* 1.3 60.1 + - - +
508A LYS 3.2 2.7 - - - -
509A GLN* 3.0 23.5 + - - +
510A ALA* 3.1 11.5 + - - +
541A GLY 5.3 1.6 + - - -
9I T 3.7 42.8 + - - +
10I A 3.8 5.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A GLY 5.4 0.4 + - - -
476A ALA* 4.3 9.9 - - - +
501A ILE 4.0 6.7 - - - -
502A ALA* 4.0 12.6 - - - -
504A ASN* 3.2 17.2 + - - -
505A ILE 3.2 0.4 - - - -
506A GLY* 1.3 74.2 - - - +
508A LYS* 1.3 66.1 + - - +
510A ALA* 3.6 9.8 - - - +
511A LEU* 2.9 30.1 + - - +
9I T 4.8 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A GLN* 3.8 38.6 - - + +
476A ALA* 4.1 6.5 - - - +
479A THR* 3.0 36.7 - - + +
482A ARG* 5.6 0.6 - - - +
506A GLY* 3.2 1.2 - - - -
507A GLY* 1.3 75.3 - - - +
509A GLN* 1.3 71.3 + - - +
512A GLU* 3.0 51.8 + - - +
8I T 5.2 0.4 - - - -
9I T 3.5 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A GLY 3.0 10.7 + - - +
508A LYS* 1.3 96.1 + - - +
510A ALA* 1.3 60.7 + - - +
512A GLU* 4.4 11.5 + - - +
513A THR* 2.8 37.2 + - - -
542A LYS* 3.6 37.4 - - + +
9I T 3.4 38.6 + - - +
10I A 3.6 24.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
501A ILE* 3.3 24.5 - - + +
504A ASN* 6.2 0.9 - - + -
506A GLY 3.1 11.0 + - - +
507A GLY* 3.2 9.8 + - - +
509A GLN* 1.3 76.5 - - - +
511A LEU* 1.3 56.8 + - - +
514A VAL* 2.9 35.3 + - - +
536A ALA* 3.9 15.9 - - + +
538A ASN 5.6 0.4 - - - +
541A GLY* 4.3 12.6 - - - +
542A LYS* 4.3 9.3 - - - +
545A LEU* 4.0 2.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
476A ALA 4.2 2.2 - - - +
479A THR* 3.7 26.7 - - + +
480A VAL* 3.4 34.3 - - + +
483A LEU* 3.9 9.0 - - + -
487A LEU* 3.6 14.9 - - + +
498A VAL* 3.7 29.8 - - + +
501A ILE* 3.5 26.9 - - + -
502A ALA* 3.5 12.3 - - + -
507A GLY 2.9 17.2 + - - +
510A ALA* 1.3 72.6 - - - +
512A GLU* 1.3 65.9 + - - +
514A VAL* 3.3 2.4 + - - -
515A GLN* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A THR* 4.4 2.2 - - + -
482A ARG* 3.0 32.0 + - - +
483A LEU* 3.8 13.9 - - + +
508A LYS* 3.0 46.6 + - - +
509A GLN* 3.9 15.0 + - - +
511A LEU* 1.3 75.6 - - - +
513A THR* 1.3 59.8 + - - +
515A GLN* 2.8 24.4 + - - +
516A ARG* 2.9 16.8 + - + +
542A LYS* 5.9 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A GLN 2.8 23.0 + - - -
512A GLU* 1.3 73.3 - - - +
514A VAL* 1.3 61.0 + - - +
516A ARG* 3.3 14.5 + - - +
517A LEU* 2.9 49.5 + - + +
542A LYS* 2.9 30.8 + - + +
545A LEU* 3.7 24.9 - - + -
546A GLU* 4.1 10.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A LEU* 4.0 6.0 - - + +
493A LEU* 4.1 23.3 - - + -
501A ILE* 4.0 13.0 - - + -
510A ALA 2.9 26.7 + - - +
511A LEU* 3.8 4.7 - - - +
513A THR* 1.3 76.0 - - - +
515A GLN* 1.3 57.7 + - - +
517A LEU* 5.0 0.7 - - - -
518A LEU* 2.9 42.6 + - + +
532A VAL* 4.3 10.5 - - + -
533A VAL* 6.1 0.2 - - + -
536A ALA* 3.4 30.5 - - + -
545A LEU* 3.6 14.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
482A ARG* 5.9 0.3 + - - -
483A LEU* 4.2 26.8 - - + +
486A VAL* 4.6 13.8 - - + +
487A LEU* 3.3 30.7 - - + -
491A HIS* 3.3 27.2 + - + -
511A LEU 3.0 12.4 + - - +
512A GLU* 2.8 16.6 + - - +
514A VAL* 1.3 77.4 - - - +
516A ARG* 1.3 64.0 + - - +
519A PRO* 4.2 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A GLU 2.9 16.0 + - - +
513A THR* 3.3 13.2 + - - +
515A GLN* 1.3 83.6 - - - +
517A LEU* 1.3 94.9 + - + +
518A LEU 3.7 0.4 - - - -
519A PRO* 3.6 13.3 - - - +
520A VAL* 4.5 7.4 - - - +
546A GLU* 3.8 23.4 + - - +
549A GLN* 4.6 2.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A THR* 2.9 31.7 + - + +
514A VAL* 5.0 0.2 - - - -
516A ARG* 1.3 119.9 - - + +
518A LEU* 1.3 67.4 + - - +
519A PRO* 3.1 3.8 - - - -
520A VAL* 4.7 11.4 - - + -
521A LEU* 2.9 41.1 + - + +
545A LEU* 4.4 5.4 - - + -
546A GLU* 4.2 15.0 - - + +
549A GLN* 3.0 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A HIS* 3.0 52.7 - - + +
493A LEU* 4.2 15.7 - - + -
514A VAL* 2.9 28.0 + - + +
517A LEU* 1.3 75.3 - - - +
519A PRO* 1.3 74.7 - - + +
521A LEU* 3.7 0.9 - - - +
522A CYS* 3.0 43.1 + - - -
529A PRO* 4.2 14.1 - - + +
532A VAL* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A HIS* 4.1 21.1 - - + +
515A GLN 4.6 0.7 - - - +
516A ARG 3.6 14.8 - - - +
517A LEU 3.1 4.5 - - - +
518A LEU* 1.3 94.0 - - + +
520A VAL* 1.3 60.9 + - + +
521A LEU 2.4 18.9 + - - -
522A CYS* 2.4 20.5 + - + -
523A GLN* 3.1 24.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A ARG 4.5 12.6 - - - +
517A LEU* 4.3 15.0 - - + +
519A PRO* 1.3 83.7 - - + +
521A LEU* 1.3 64.2 + - + +
523A GLN* 2.9 10.0 + - - +
524A ALA* 2.9 36.9 + - + -
525A HIS* 3.6 11.9 + - + +
549A GLN* 5.3 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A VAL* 6.1 0.2 - - - -
517A LEU* 2.9 38.7 + - + +
518A LEU 3.7 4.0 - - - +
519A PRO 2.4 11.1 + - - -
520A VAL* 1.3 74.5 - - + +
522A CYS* 1.3 57.6 + - - +
525A HIS* 2.9 44.3 - - + +
527A LEU* 3.3 17.7 + - + +
532A VAL* 3.7 27.1 - - + -
535A ILE* 5.8 1.8 - - + -
545A LEU* 3.9 28.3 - - + +
548A VAL* 4.2 17.5 - - + -
549A GLN* 4.2 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A LEU* 3.0 40.6 - - - -
519A PRO* 2.4 22.3 + - + +
521A LEU* 1.3 68.1 - - - +
523A GLN* 1.3 63.7 + - + +
526A GLY* 3.8 10.2 - - - +
527A LEU 3.0 25.6 - - - +
528A THR* 3.9 11.0 - - - -
529A PRO* 3.9 7.6 - - + -
532A VAL* 3.8 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A PRO* 3.4 31.1 - - + +
520A VAL* 2.9 9.4 + - - +
522A CYS* 1.3 84.1 + - + +
524A ALA* 1.3 63.8 + - + +
525A HIS 3.4 0.2 - - - -
526A GLY* 4.0 4.3 + - - -
232B TRP* 3.5 35.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
520A VAL* 2.9 19.3 + - + +
523A GLN* 1.3 77.2 - - + +
525A HIS* 1.3 74.8 + - + +
526A GLY 3.5 0.2 - - - -
----------------------------------------------------------
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