Contacts of the helix formed by residues 568 - 593 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C SER* 4.0 22.8 + - - +
226C ILE* 3.9 18.4 - - + -
245C ILE* 4.1 12.1 - - + -
246C LYS* 3.9 35.4 - - + +
249C VAL* 5.2 7.0 - - + -
566C ILE 3.7 1.6 + - - -
567C PRO* 1.3 72.0 - - + +
569C LYS* 1.3 58.2 + - - +
571C VAL* 3.0 2.8 + - - +
572C MET* 2.8 61.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 569 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527C TYR* 3.5 17.5 - - + +
567C PRO* 4.3 7.8 - - + +
568C ILE* 1.3 81.5 - - - +
570C ILE* 1.3 58.3 + - + +
572C MET* 3.3 9.0 + - - +
573C GLU* 3.0 60.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 570 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C LEU* 4.0 23.8 - - + -
524C ILE* 4.0 14.6 - - + -
527C TYR* 3.8 43.5 - - + +
529C LEU* 3.9 14.3 - - + +
543C MET* 5.2 1.3 - - + -
566C ILE* 4.3 17.7 - - + -
567C PRO* 3.0 36.6 + - + +
569C LYS* 1.3 76.1 - - + +
571C VAL* 1.3 61.0 + - - +
573C GLU* 3.4 8.5 + - - +
574C ALA* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 571 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C ILE* 3.5 31.2 - - + -
229C LEU* 3.7 24.9 - - + -
245C ILE* 4.2 1.8 - - + -
543C MET* 6.3 0.2 - - - -
545C PHE* 4.1 11.2 - - + -
561C ILE* 5.0 1.3 - - + -
566C ILE* 3.8 28.3 - - + -
567C PRO 3.4 2.4 + - - +
568C ILE 3.0 7.5 + - - +
570C ILE* 1.3 77.3 - - - +
572C MET* 1.3 78.7 + - + +
574C ALA* 3.0 8.1 + - - +
575C ILE* 3.0 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 572 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C GLN* 5.2 0.5 - - - +
242C CYS* 3.5 33.5 - - + +
245C ILE* 3.9 11.2 - - + -
246C LYS* 3.9 18.2 - - - +
568C ILE* 2.8 50.6 + - + +
569C LYS* 3.6 9.0 - - - +
571C VAL* 1.3 89.0 - - + +
573C GLU* 1.3 63.4 + - + +
575C ILE* 3.3 19.2 + - + +
576C GLN* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 573 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527C TYR* 2.6 33.9 + - - -
529C LEU* 3.5 14.5 - - + +
569C LYS* 3.0 55.3 + - + +
570C ILE* 3.7 1.4 - - - +
572C MET* 1.3 78.2 - - + +
574C ALA* 1.3 57.1 + - - +
576C GLN* 3.6 5.6 + - - +
577C GLN* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 574 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511C ILE* 3.3 16.0 - - + +
529C LEU* 3.7 23.3 - - + +
543C MET* 4.0 15.7 - - + -
545C PHE* 4.1 17.3 - - + -
570C ILE 2.9 16.9 + - - +
571C VAL* 3.0 6.7 + - - +
573C GLU* 1.3 73.9 - - - +
575C ILE* 1.3 60.6 + - - +
577C GLN* 4.4 2.7 - - - -
578C ALA* 2.8 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 575 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C GLN* 3.9 28.3 - - + +
241C PHE* 4.3 10.1 - - + -
242C CYS* 4.0 8.1 - - - -
245C ILE* 3.7 29.8 - - + -
545C PHE* 3.6 20.6 - - + -
547C ILE* 4.3 8.9 - - + +
554C ILE* 4.1 17.0 - - + -
557C LEU* 5.0 0.2 - - + -
571C VAL* 3.0 21.2 + - + +
572C MET* 3.6 18.2 - - + +
573C GLU 3.3 0.2 - - - -
574C ALA* 1.3 77.1 - - - +
576C GLN* 1.3 62.1 + - - +
578C ALA* 3.3 6.6 + - - +
579C SER* 3.0 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 576 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C GLN* 2.9 30.0 + - - +
572C MET 3.2 14.0 + - - +
573C GLU* 4.0 5.6 - - - +
575C ILE* 1.3 78.8 - - - +
577C GLN* 1.3 64.1 + - - +
579C SER* 2.8 37.0 + - - -
580C VAL* 3.2 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 577 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C LEU 3.3 4.2 + - - -
365C THR* 3.9 18.0 - - + +
511C ILE* 4.0 5.0 - - + +
529C LEU* 3.2 51.7 + - - +
530C LEU 3.8 0.8 - - - +
531C THR* 2.7 37.0 - - + +
573C GLU 3.0 17.3 + - - +
574C ALA* 3.8 5.6 - - - +
576C GLN* 1.3 76.4 - - - +
578C ALA* 1.3 62.7 + - - +
580C VAL* 3.5 9.0 + - + +
581C ALA* 3.4 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 578 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C VAL* 3.9 8.4 - - + +
511C ILE* 3.0 26.4 - - + +
547C ILE* 3.3 32.8 - - + -
574C ALA 2.8 16.0 + - - +
575C ILE 3.6 4.9 - - - +
576C GLN 3.2 0.2 - - - -
577C GLN* 1.3 72.4 - - - +
579C SER* 1.3 53.5 + - - +
581C ALA* 3.1 3.7 + - - +
582C LYS* 2.7 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 579 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C GLN* 3.7 19.7 - - - -
575C ILE* 3.0 8.8 + - - -
576C GLN* 2.8 35.1 + - - -
578C ALA* 1.3 75.8 - - - +
580C VAL* 1.3 62.9 + - - +
582C LYS* 3.4 20.9 + - - +
583C LYS* 3.1 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 580 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C THR* 6.1 3.6 - - - +
576C GLN* 3.2 26.2 + - - +
577C GLN* 3.7 10.5 - - + +
578C ALA 3.2 0.4 - - - -
579C SER* 1.3 82.5 + - - +
581C ALA* 1.3 62.0 + - - +
583C LYS* 3.4 9.2 + - - +
584C GLU* 3.2 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 581 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C THR 5.3 2.0 - - - +
367C LEU* 3.8 23.7 - - + +
509C VAL* 4.2 15.7 - - + -
531C THR* 4.6 14.1 - - + +
577C GLN 3.4 8.7 + - - +
578C ALA* 3.1 7.9 + - - +
580C VAL* 1.3 76.8 - - - +
582C LYS* 1.3 66.3 + - - +
584C GLU* 3.2 11.3 + - - +
585C ILE* 3.0 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 582 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C ALA* 3.7 16.6 - - + +
508C GLY* 5.8 0.4 - - - -
509C VAL* 4.6 6.6 - - + +
547C ILE 5.7 1.6 - - - +
548C ALA* 4.5 2.8 - - - -
549C GLY* 3.6 24.5 - - - +
550C THR 2.8 27.5 + - - +
551C ASN* 4.8 5.9 + - - +
552C LYS 5.0 0.4 - - - -
553C GLY* 2.8 24.4 + - - +
554C ILE* 4.6 7.9 - - - +
578C ALA 2.7 18.4 + - - +
579C SER* 3.6 23.1 - - - +
580C VAL 3.4 0.2 - - - -
581C ALA* 1.3 72.0 - - - +
583C LYS* 1.3 58.5 + - - +
585C ILE* 3.4 11.4 + - - +
586C LEU* 3.0 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 583 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551C ASN* 3.3 46.5 + - - +
552C LYS* 5.8 0.2 - - - +
579C SER* 3.1 29.5 + - - +
580C VAL* 3.7 7.4 - - - +
581C ALA 3.1 0.2 - - - -
582C LYS* 1.3 79.6 - - + +
584C GLU* 1.3 64.6 + - + +
586C LEU* 3.5 7.1 + - - +
587C GLN* 3.1 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 584 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C THR 5.1 5.7 - - - +
366C SER* 5.7 0.3 - - - -
367C LEU* 3.7 29.8 + - + +
580C VAL* 3.2 33.3 + - + +
581C ALA* 3.2 9.3 + - - +
583C LYS* 1.3 78.6 - - + +
585C ILE* 1.3 61.3 + - - +
587C GLN* 3.3 10.3 + - - +
588C ILE* 3.3 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 585 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C LEU* 3.6 24.9 - - + -
370C VAL* 4.8 9.0 - - + -
386C PHE* 3.9 20.9 - - + -
388C ARG* 4.7 8.3 - - - +
489C CYS* 4.0 1.6 - - - -
507C ALA* 3.9 7.2 - - + -
508C GLY 3.5 24.9 - - - +
509C VAL* 4.1 15.0 - - + -
581C ALA 3.0 23.4 + - - +
582C LYS* 3.7 6.1 - - - +
584C GLU* 1.3 75.7 - - - +
586C LEU* 1.3 59.7 + - - +
588C ILE* 3.0 11.0 + - - +
589C MET* 2.8 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 586 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C ALA* 3.7 31.2 - - + +
506C VAL 3.8 11.9 - - - +
507C ALA* 3.6 19.3 - - + -
549C GLY 4.7 0.2 - - - +
550C THR* 3.8 7.2 - - - -
551C ASN* 3.5 43.1 - - + +
582C LYS* 3.0 30.1 + - + +
583C LYS* 3.8 4.7 - - - +
585C ILE* 1.3 76.1 - - - +
587C GLN* 1.3 54.4 + - - +
589C MET* 3.5 8.5 - - + +
590C ASN* 2.7 47.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 587 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583C LYS 3.1 15.6 + - - +
584C GLU* 3.4 14.1 - - - +
586C LEU* 1.3 78.0 - - - +
588C ILE* 1.3 64.9 + - + +
590C ASN* 3.5 7.3 + - - +
591C LYS* 3.5 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 588 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C LEU* 5.2 4.3 - - + -
370C VAL* 3.5 59.2 - - + +
371C SER* 4.7 2.2 - - - -
372C CYS* 4.6 8.5 - - - -
584C GLU* 3.3 18.4 + - + +
585C ILE* 3.0 6.3 + - - +
587C GLN* 1.3 73.9 - - + +
589C MET* 1.3 68.0 + - - +
591C LYS* 3.0 32.0 + - + +
592C THR* 3.6 6.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 589 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C VAL* 5.7 0.2 - - + -
372C CYS* 4.0 13.9 - - - -
386C PHE* 4.0 17.5 - - + -
489C CYS* 3.5 32.1 - - - +
492C SER* 3.7 12.3 - - - +
493C LEU* 4.0 17.4 - - + +
505C ALA* 4.8 4.3 - - + -
506C VAL 3.4 26.2 - - - +
507C ALA* 4.0 6.1 - - - -
585C ILE* 2.8 35.4 + - - +
586C LEU* 3.5 17.0 - - + +
588C ILE* 1.3 73.5 - - + +
590C ASN* 1.3 59.6 + - - +
592C THR* 2.8 22.2 + - - -
593C ILE 3.2 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 590 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C ALA* 4.1 21.3 - - - +
586C LEU* 2.7 31.9 + - - +
587C GLN* 3.9 8.1 - - - +
588C ILE 3.2 0.4 - - - -
589C MET* 1.3 75.1 - - - +
591C LYS* 1.3 61.4 + - - +
592C THR 3.2 0.6 + - - -
593C ILE* 3.3 10.6 + - - +
594C SER* 3.5 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 591 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587C GLN* 3.5 21.7 + - - +
588C ILE* 3.0 20.8 + - + +
590C ASN* 1.3 79.0 - - - +
592C THR* 1.3 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 592 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C CYS* 3.2 31.7 + - - +
373C GLU* 3.8 26.9 - - - -
374C VAL* 4.1 25.0 - - + +
493C LEU* 4.8 2.0 - - + -
588C ILE* 3.6 2.6 + - - +
589C MET 2.8 10.2 + - - -
591C LYS* 1.3 82.6 - - - +
593C ILE* 1.3 60.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 593 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C VAL* 4.1 19.1 - - + -
493C LEU* 3.5 31.3 - - + +
496C MET* 3.8 27.9 - - + +
497C ASP* 3.8 22.0 - - + +
589C MET* 3.2 11.9 + - - +
590C ASN* 3.3 11.2 - - - +
591C LYS 3.6 0.4 - - - -
592C THR* 1.3 80.8 - - + +
594C SER* 1.3 60.0 + - - +
595C LYS 3.2 26.7 - - - +
597C ARG* 4.7 4.3 - - + +
----------------------------------------------------------
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