Contacts of the helix formed by residues 568 - 593 (chain B) in PDB entry 3U1K
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 ILE 568 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B SER* 3.7 21.0 + - - +
226B ILE* 4.1 22.9 - - + -
245B ILE* 5.3 1.1 - - + -
246B LYS* 4.3 30.5 - - + +
249B VAL* 3.7 29.6 - - + -
566B ILE 3.7 1.0 + - - -
567B PRO* 1.3 72.4 - - - +
569B LYS* 1.3 64.5 + - - +
571B VAL* 3.1 3.5 + - - +
572B MET* 3.0 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 569 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B TYR* 3.4 30.9 + - - +
567B PRO* 3.1 14.6 - - + +
568B ILE* 1.3 78.6 - - - +
570B ILE* 1.3 64.4 + - - +
572B MET* 3.4 9.0 + - - +
573B GLU* 3.0 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 570 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B LEU* 4.0 15.5 - - + -
524B ILE* 3.9 15.3 - - + -
527B TYR* 3.9 43.1 - - + -
529B LEU* 3.8 25.7 - - + +
543B MET* 5.2 1.6 - - + -
566B ILE* 4.2 17.3 - - + -
567B PRO* 3.2 31.9 + - + +
568B ILE 3.2 0.6 - - - -
569B LYS* 1.3 84.7 - - - +
571B VAL* 1.3 57.5 + - - +
573B GLU* 3.5 4.9 + - - -
574B ALA* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 571 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ILE* 3.6 31.0 - - + -
229B LEU* 4.1 15.7 - - + -
245B ILE* 4.4 1.1 - - + -
543B MET* 6.1 0.2 - - - -
545B PHE* 4.0 15.7 - - + -
561B ILE* 5.3 0.7 - - + -
566B ILE* 3.8 22.9 - - + -
567B PRO 3.6 15.0 - - - +
568B ILE 3.1 3.2 + - - +
570B ILE* 1.3 74.6 - - - +
572B MET* 1.3 85.0 + - + +
574B ALA* 3.4 6.1 + - - +
575B ILE* 3.0 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 572 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLN* 5.5 0.5 + - - -
242B CYS* 3.6 32.6 - - - +
245B ILE* 3.9 29.6 - - + -
246B LYS* 4.0 22.9 - - - +
568B ILE* 3.0 30.9 + - + +
569B LYS* 3.7 9.0 - - - +
571B VAL* 1.3 107.4 - - + +
573B GLU* 1.3 63.1 + - + +
575B ILE* 3.3 11.2 + - + +
576B GLN* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 573 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B TYR* 2.5 40.8 + - - -
529B LEU* 3.6 14.1 - - + +
569B LYS* 3.0 35.9 + - + +
570B ILE* 3.9 1.1 - - - +
572B MET* 1.3 74.1 - - + +
574B ALA* 1.3 59.9 + - - +
576B GLN* 3.3 6.3 + - - +
577B GLN* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 574 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B ILE* 3.9 12.9 - - + +
529B LEU* 3.6 11.8 - - + +
543B MET* 4.0 26.7 - - + -
545B PHE* 4.2 12.8 - - + -
570B ILE 3.0 18.5 + - - +
571B VAL* 3.6 8.5 - - - +
572B MET 3.3 0.2 - - - -
573B GLU* 1.3 76.6 - - - +
575B ILE* 1.3 57.3 + - - +
577B GLN* 3.4 1.7 + - - -
578B ALA* 2.8 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 575 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLN* 3.9 28.0 - - + +
241B PHE* 4.2 10.3 - - + -
242B CYS* 3.7 18.8 - - - -
245B ILE* 3.6 30.7 - - + -
545B PHE* 3.6 21.3 - - + -
547B ILE* 4.3 9.1 - - + +
554B ILE* 4.2 14.6 - - + -
571B VAL* 3.0 21.3 + - + +
572B MET* 3.5 9.4 - - + +
573B GLU 3.3 0.2 - - - -
574B ALA* 1.3 75.4 - - - +
576B GLN* 1.3 57.4 + - - +
578B ALA* 3.3 7.2 + - - +
579B SER* 2.9 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 576 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLN* 2.8 37.7 + - - +
572B MET 3.1 12.9 + - - +
573B GLU* 3.8 8.7 - - - +
575B ILE* 1.3 75.6 - - - +
577B GLN* 1.3 60.0 + - - +
579B SER* 2.9 28.2 + - - -
580B VAL* 3.1 24.7 + - + +
583B LYS* 6.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 577 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B LEU* 3.6 2.4 + - - +
365B THR* 4.1 18.0 - - + +
511B ILE* 4.5 4.8 - - + +
529B LEU* 3.1 47.4 + - - +
530B LEU 3.7 1.2 - - - -
531B THR* 2.8 40.7 - - + +
573B GLU 2.9 17.0 + - - +
574B ALA* 3.9 4.7 - - - +
576B GLN* 1.3 77.1 - - - +
578B ALA* 1.3 62.0 + - - +
580B VAL* 3.4 12.2 + - + +
581B ALA* 3.3 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 578 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B VAL* 3.9 8.5 - - + +
511B ILE* 3.7 21.2 - - + +
547B ILE* 3.2 34.8 - - + -
574B ALA 2.8 19.3 + - - +
575B ILE 3.6 4.3 - - - +
577B GLN* 1.3 76.5 - - - +
579B SER* 1.3 58.2 + - - +
581B ALA* 3.3 1.5 + - - +
582B LYS* 2.8 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 579 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLN* 3.4 26.3 + - - -
575B ILE 2.9 9.6 + - - -
576B GLN* 2.9 19.9 + - - -
578B ALA* 1.3 77.9 - - - +
580B VAL* 1.3 61.4 + - - +
582B LYS* 3.4 18.1 + - - +
583B LYS* 3.2 46.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 580 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B THR* 5.6 9.0 - - - +
531B THR* 6.5 0.7 - - + -
576B GLN* 3.1 32.7 + - + +
577B GLN* 3.4 10.7 + - + +
578B ALA 3.3 0.2 - - - -
579B SER* 1.3 78.2 - - - +
581B ALA* 1.3 64.4 + - + +
583B LYS* 3.4 10.1 + - - +
584B GLU* 3.1 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 581 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B THR 5.4 1.3 - - - +
367B LEU* 3.8 14.1 - - + +
509B VAL* 4.2 13.5 - - + -
531B THR* 4.0 23.1 - - + +
577B GLN 3.3 10.7 + - - +
578B ALA* 3.7 6.7 - - - +
579B SER 3.3 0.2 - - - -
580B VAL* 1.3 81.8 - - + +
582B LYS* 1.3 63.8 + - - +
584B GLU* 3.2 13.4 + - - +
585B ILE* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 582 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B ALA* 3.8 15.7 - - + +
508B GLY* 5.7 0.7 - - - -
509B VAL* 4.6 6.2 - - + +
547B ILE 5.7 1.6 - - - +
548B ALA* 4.4 3.1 - - - -
549B GLY* 3.7 24.8 - - - +
550B THR 2.9 27.7 + - - +
551B ASN* 5.1 1.5 - - - +
553B GLY 3.0 22.2 + - - +
554B ILE* 4.4 10.1 - - - +
578B ALA 2.8 16.5 + - - +
579B SER* 3.6 20.9 + - - +
580B VAL 3.3 0.2 - - - -
581B ALA* 1.3 75.3 - - - +
583B LYS* 1.3 64.0 + - - +
585B ILE* 3.2 13.1 + - - +
586B LEU* 2.9 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 583 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B ASN* 3.6 37.9 - - + -
576B GLN* 6.1 0.8 - - - +
579B SER* 3.2 33.5 + - - +
580B VAL* 3.8 7.1 - - - +
582B LYS* 1.3 80.4 - - - +
584B GLU* 1.3 65.6 + - + +
586B LEU* 3.4 9.1 + - - +
587B GLN* 3.0 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 584 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B THR 4.8 8.1 - - - +
367B LEU* 3.5 30.7 + - + +
580B VAL* 3.1 35.2 + - + +
581B ALA* 3.5 10.0 - - - +
583B LYS* 1.3 78.0 - - + +
585B ILE* 1.3 62.2 + - - +
587B GLN* 3.2 8.5 + - - +
588B ILE* 3.2 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 585 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B LEU* 3.7 30.5 - - + -
370B VAL* 5.0 9.6 - - + -
386B PHE* 4.1 11.4 - - + -
388B ARG* 4.5 10.3 - - - +
489B CYS* 3.9 8.7 - - - -
507B ALA* 3.7 15.9 - - + -
508B GLY 3.4 25.6 - - - +
509B VAL* 4.0 11.0 - - + -
581B ALA 2.9 19.8 + - - +
582B LYS* 3.2 8.3 + - - +
584B GLU* 1.3 77.0 - - - +
586B LEU* 1.3 58.0 + - - +
588B ILE* 3.1 9.9 + - - +
589B MET* 2.8 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 586 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B ALA* 3.7 25.8 - - + +
506B VAL 3.7 8.1 - - - +
507B ALA* 3.5 28.0 - - + +
549B GLY 4.5 0.2 - - - +
550B THR* 3.7 7.4 - - - -
551B ASN* 3.4 42.2 - - + +
582B LYS* 2.9 30.2 + - + +
583B LYS* 3.8 7.4 - - - +
584B GLU 3.3 0.2 - - - -
585B ILE* 1.3 76.0 - - - +
587B GLN* 1.3 57.7 + - - +
589B MET* 3.7 8.2 - - + +
590B ASN* 2.9 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 587 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B LYS* 3.0 19.9 + - + +
584B GLU* 3.5 11.2 - - - +
585B ILE 3.2 0.2 - - - -
586B LEU* 1.3 76.6 - - + +
588B ILE* 1.3 63.5 + - + +
590B ASN* 3.6 12.5 + - - +
591B LYS* 3.4 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 588 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B LEU* 4.8 7.9 - - + -
368B ARG 5.7 1.1 - - - +
369B ASN* 6.3 0.2 - - - -
370B VAL* 3.4 52.9 - - + +
371B SER* 5.5 0.2 - - - -
372B CYS* 4.7 4.7 - - - -
584B GLU* 3.2 18.6 + - + +
585B ILE* 3.1 8.6 + - - +
587B GLN* 1.3 76.0 - - + +
589B MET* 1.3 65.1 + - - +
591B LYS* 3.1 26.6 + - + +
592B THR* 3.7 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 589 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B VAL* 5.6 0.2 - - + -
372B CYS* 4.2 11.7 - - - -
386B PHE* 4.1 18.4 - - + -
489B CYS* 3.5 31.6 - - - +
492B SER* 3.8 12.3 - - - +
493B LEU* 3.9 22.0 - - + +
505B ALA* 4.7 4.5 - - + -
506B VAL 3.4 25.4 - - - +
507B ALA* 4.0 6.7 - - - -
585B ILE* 2.8 38.4 + - - +
586B LEU* 3.7 13.2 - - + +
588B ILE* 1.3 74.6 - - + +
590B ASN* 1.3 60.8 + - - +
592B THR* 3.1 19.4 + - - -
593B ILE 3.1 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 590 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B MET* 5.2 0.2 - - - +
505B ALA* 4.0 21.3 - - - +
586B LEU* 2.9 33.8 + - - +
587B GLN* 4.0 14.4 + - - +
588B ILE 3.2 0.4 - - - -
589B MET* 1.3 74.9 - - - +
591B LYS* 1.3 64.5 + - - +
592B THR 3.2 0.4 + - - -
593B ILE* 3.4 16.6 + - - +
594B SER* 3.3 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 591 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A MET 5.7 1.0 + - - -
61A GLY 5.6 0.2 - - - +
65A ARG* 3.3 29.3 + - - +
587B GLN* 3.4 38.8 + - - +
588B ILE* 3.1 16.2 + - + +
590B ASN* 1.3 78.6 - - - +
592B THR* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 592 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A MET* 3.8 18.5 + - - -
44A ALA* 4.2 6.0 + - + -
61A GLY 5.0 3.6 - - - +
65A ARG* 4.8 5.4 + - - +
372B CYS* 3.5 47.2 + - + +
373B GLU* 4.3 8.5 - - - -
374B VAL* 4.4 19.4 - - + +
493B LEU* 5.0 0.7 - - + -
588B ILE 3.7 3.9 + - - -
589B MET 3.1 10.1 + - - -
590B ASN 4.3 0.2 - - - -
591B LYS* 1.3 81.4 - - - +
593B ILE* 1.3 61.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 593 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A MET* 3.7 32.1 - - + +
374B VAL* 4.2 19.3 - - + -
493B LEU* 3.6 31.4 - - + +
496B MET* 3.7 29.5 - - + +
497B ASP* 3.7 19.1 - - - +
589B MET 3.1 12.4 + - - +
590B ASN* 3.4 11.1 - - - +
591B LYS 3.7 0.2 - - - -
592B THR* 1.3 79.3 - - + +
594B SER* 1.3 60.5 + - - +
595B LYS 3.3 24.7 - - - +
597B ARG* 5.0 0.4 - - - +
----------------------------------------------------------
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