Contacts of the helix formed by residues 535 - 555 (chain D) in PDB entry 2BKU
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 VAL 535 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493D TYR* 3.8 26.7 - - + +
496D TYR* 3.7 40.6 - - + -
497D PRO* 4.8 4.3 - - + -
531D ALA* 4.5 1.7 - - + +
532D THR* 3.6 34.4 - - - +
533D ASP 3.1 0.4 - - - -
534D THR* 1.3 83.0 - - + +
536D ALA* 1.3 58.3 + - - +
537D GLU* 3.6 1.6 - - - +
538D THR* 3.4 19.3 - - + -
539D SER* 3.3 21.5 + - - -
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Residues in contact with ALA 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532D THR 4.7 2.0 - - - +
533D ASP* 3.3 17.0 + - - +
534D THR 3.7 1.8 + - - -
535D VAL* 1.3 73.3 - - - +
537D GLU* 1.3 56.5 + - - +
538D THR 3.2 1.8 - - - -
539D SER* 3.1 5.8 + - - -
540D ALA* 2.6 38.3 + - - +
587D SER* 6.3 3.1 - - - -
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Residues in contact with GLU 537 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535D VAL* 3.6 0.6 - - - -
536D ALA* 1.3 78.8 - - - +
538D THR* 1.3 56.5 + - + +
540D ALA* 3.5 8.0 + - - +
541D SER* 3.0 27.8 + - - +
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Residues in contact with THR 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496D TYR* 4.0 12.2 + - + -
497D PRO* 4.4 20.0 - - + -
500D VAL* 3.2 33.3 - - - +
535D VAL* 3.4 40.8 - - + +
537D GLU* 1.3 77.1 - - + +
539D SER* 1.3 65.0 + - - +
540D ALA 3.1 1.6 - - - -
541D SER* 3.0 20.1 + - - -
542D ILE* 3.1 14.7 + - - +
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Residues in contact with SER 539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496D TYR* 5.9 2.2 - - - -
528D VAL* 5.2 9.5 - - - +
531D ALA* 4.6 17.5 - - - +
532D THR 5.7 0.2 - - - -
535D VAL 3.3 17.5 + - - -
536D ALA* 3.1 7.3 + - - -
538D THR* 1.3 79.6 + - - +
540D ALA* 1.3 60.3 + - - +
542D ILE* 3.5 17.2 + - - +
543D SER* 3.4 19.1 + - - -
583D VAL* 4.8 5.2 - - - +
586D LYS* 6.1 0.5 - - - +
587D SER* 3.3 23.9 + - - -
590D SER* 4.5 1.1 + - - -
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Residues in contact with ALA 540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536D ALA 2.6 20.9 + - - +
537D GLU* 3.5 8.7 - - - +
539D SER* 1.3 70.5 - - - +
541D SER* 1.3 61.9 + - - +
542D ILE 3.2 1.6 - - - -
543D SER* 3.0 19.8 + - - -
544D THR* 3.1 19.2 + - - +
590D SER* 4.0 19.0 + - - -
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Residues in contact with SER 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500D VAL* 5.0 2.7 - - - -
504D ILE* 4.3 14.1 - - - +
537D GLU* 3.0 15.4 + - - +
538D THR* 3.0 14.2 + - - -
540D ALA* 1.3 76.1 - - - +
542D ILE* 1.3 56.9 + - - +
544D THR* 4.1 4.7 - - - -
545D PHE* 3.0 29.6 + - - +
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Residues in contact with ILE 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496D TYR* 5.9 1.1 - - + -
500D VAL* 3.5 40.6 - - + -
504D ILE* 4.7 2.9 - - + -
524D LEU* 4.3 18.4 - - + +
527D MET* 4.2 11.7 - - + -
528D VAL* 3.4 28.5 - - + +
538D THR 3.1 9.0 + - - +
539D SER* 3.5 13.7 - - - +
540D ALA 3.2 0.2 - - - -
541D SER* 1.3 74.6 - - - +
543D SER* 1.3 61.0 + - - +
545D PHE* 3.1 7.0 + - - +
546D VAL* 2.9 33.0 + - + +
579D VAL* 3.4 30.5 - - + -
583D VAL* 4.4 2.2 - - + -
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Residues in contact with SER 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539D SER 3.4 5.7 + - - -
540D ALA* 3.0 15.4 + - - -
542D ILE* 1.3 77.9 - - - +
544D THR* 1.3 55.9 + - - +
546D VAL* 3.1 11.7 - - - +
547D MET* 2.9 38.2 + - - +
580D LEU* 5.3 0.4 - - - -
583D VAL* 3.8 19.0 - - - +
590D SER* 3.4 20.8 + - - -
591D VAL* 3.7 26.7 - - - -
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Residues in contact with THR 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D ALA* 3.1 18.7 + - - +
541D SER* 4.1 5.6 - - - -
543D SER* 1.3 75.9 + - - +
545D PHE* 1.3 62.2 + - - +
547D MET* 4.0 12.4 - - - +
548D ASP* 3.3 24.7 + - + +
590D SER 5.3 2.4 + - - -
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Residues in contact with PHE 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504D ILE* 3.7 33.0 - - + -
507D ALA* 3.6 30.7 - - + -
508D ASN* 3.0 44.2 - - - -
521D PHE* 4.4 11.2 - + - -
524D LEU* 4.4 4.3 - - + -
541D SER 3.0 19.7 + - - +
542D ILE* 3.1 3.3 + - - +
544D THR* 1.3 79.2 - - - +
546D VAL* 1.3 67.6 + - + +
548D ASP* 3.7 5.7 - - - +
549D LYS* 2.9 45.5 + - + +
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Residues in contact with VAL 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521D PHE* 4.4 15.0 - - + -
524D LEU* 4.9 1.8 - - + -
542D ILE* 2.9 25.2 + - + +
543D SER* 3.1 19.1 - - - +
545D PHE* 1.3 89.9 - - + +
547D MET* 1.3 51.7 + - - +
549D LYS* 3.4 6.6 - - - +
550D LEU* 2.7 36.2 + - - +
576D ILE* 3.6 15.7 - - + +
579D VAL* 3.6 33.4 - - + -
580D LEU* 3.3 24.0 - - + -
583D VAL* 5.2 0.7 - - + -
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Residues in contact with MET 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543D SER* 2.9 32.5 + - - +
544D THR* 3.9 11.2 - - - +
546D VAL* 1.3 73.1 - - - +
548D ASP* 1.3 62.1 + - - +
550D LEU* 3.3 4.4 + - - -
551D GLY* 3.0 25.6 + - - -
580D LEU* 3.9 9.4 - - + -
590D SER 4.2 2.9 - - - +
591D VAL* 3.5 23.1 - - + -
594D VAL* 3.6 29.4 - - + -
597D MET* 4.5 17.0 - - + -
598D LEU* 3.8 33.7 - - + -
601D LEU* 3.4 16.4 - - + +
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Residues in contact with ASP 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D THR* 3.3 18.4 + - + +
545D PHE* 3.7 6.5 - - - +
547D MET* 1.3 79.0 - - - +
549D LYS* 1.3 62.3 + - - +
551D GLY* 3.6 1.7 + - - -
552D GLN* 3.1 37.5 + - - +
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Residues in contact with LYS 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507D ALA 4.1 13.9 + - - -
508D ASN* 3.0 39.9 + - - +
509D ARG 5.0 2.4 + - - -
517D ARG* 5.7 1.5 - - - +
521D PHE* 4.5 8.5 - - + -
545D PHE* 2.9 33.3 + - + +
546D VAL* 3.4 9.4 - - - +
548D ASP* 1.3 75.4 + - - +
550D LEU* 1.3 66.2 + - - +
552D GLN* 3.0 35.1 + - + +
553D THR* 3.1 17.9 + - + +
572D LEU* 4.6 17.3 - - + -
576D ILE* 4.1 17.5 - - + -
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Residues in contact with LEU 550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546D VAL 2.7 20.5 + - - +
547D MET* 3.6 5.4 - - - +
549D LYS* 1.3 72.1 - - - +
551D GLY* 1.3 63.5 + - - +
553D THR* 2.7 31.5 + - - +
554D MET* 3.3 21.9 + - + +
573D GLN* 4.7 11.9 - - + +
576D ILE* 4.0 21.9 - - + +
577D LEU* 4.9 4.7 - - + -
580D LEU* 3.5 29.6 - - + -
601D LEU* 4.0 18.8 - - + -
602D PHE* 4.4 4.7 - - + -
605D LEU* 4.0 30.7 - - + -
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Residues in contact with GLY 551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547D MET 3.0 15.4 + - - -
548D ASP* 3.9 2.2 - - - -
550D LEU* 1.3 75.9 - - - +
552D GLN* 1.3 61.3 + - - +
554D MET* 3.2 25.5 + - - +
555D SER* 3.3 12.0 + - - -
601D LEU* 3.9 11.6 - - - +
604D ARG* 4.7 4.9 + - - -
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Residues in contact with GLN 552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548D ASP* 3.1 29.6 + - - +
549D LYS* 3.0 32.8 + - + +
551D GLY* 1.3 77.5 - - - +
553D THR* 1.3 61.7 + - + +
555D SER* 2.7 25.5 + - - +
556D VAL* 5.8 0.3 - - - +
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Residues in contact with THR 553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D LYS* 3.1 13.9 + - + +
550D LEU* 2.7 21.8 + - - +
552D GLN* 1.3 75.9 - - + +
554D MET* 1.3 61.6 + - - +
555D SER 3.4 0.5 + - - -
556D VAL* 3.8 15.8 + - - +
569D LEU* 4.0 27.3 - - + +
572D LEU* 3.8 29.8 - - + -
573D GLN* 3.3 30.6 + - + +
576D ILE* 4.1 9.9 - - + -
608D LYS* 5.1 1.0 + - - -
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Residues in contact with MET 554 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550D LEU* 3.3 37.0 + - + +
551D GLY* 3.2 7.8 + - - +
553D THR* 1.3 77.8 + - - +
555D SER* 1.3 68.9 + - - +
556D VAL* 3.1 6.8 + - - -
573D GLN* 4.2 6.5 - - - +
601D LEU* 3.5 53.4 - - + +
604D ARG* 3.1 43.4 + - - +
605D LEU* 3.9 12.8 - - + -
608D LYS* 3.9 28.7 + - + +
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Residues in contact with SER 555 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551D GLY 3.3 11.8 + - - -
552D GLN* 2.7 27.7 + - - +
554D MET* 1.3 77.8 - - - +
556D VAL* 1.3 68.9 + - - +
604D ARG* 4.5 9.4 + - - +
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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