Contacts of the helix formed by residues 532 - 553 (chain A) in PDB entry 5E2Q
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 532 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A GLU* 1.3 71.3 - - - +
533A ALA* 1.3 65.3 + - - -
535A ALA* 3.1 18.3 + - - +
536A GLU* 3.4 12.0 + - - +
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Residues in contact with ALA 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A GLU 3.4 1.6 + - - -
532A GLY* 1.3 71.3 - - - +
534A ASP* 1.3 67.4 + - - +
536A GLU* 3.6 5.0 + - - +
537A ASP* 2.9 32.4 + - - +
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Residues in contact with ASP 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A TRP* 3.6 33.0 - - + -
530A PHE* 4.6 7.6 - - + -
531A GLU 3.5 14.1 + - - +
532A GLY 3.3 0.4 - - - -
533A ALA* 1.3 79.9 - - - +
535A ALA* 1.3 63.8 + - - +
537A ASP* 3.4 9.7 + - - +
538A VAL* 3.1 29.6 + - - +
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Residues in contact with ALA 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A PRO* 6.3 1.1 - - + -
525A LEU* 3.2 28.1 - - + +
530A PHE* 3.6 26.9 - - - +
531A GLU* 3.6 10.5 + - - +
532A GLY 3.1 12.9 + - - +
534A ASP* 1.3 78.9 - - - +
536A GLU* 1.3 64.5 + - + +
538A VAL* 3.3 2.3 + - - +
539A ILE* 3.1 20.2 + - + +
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Residues in contact with GLU 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A GLY 3.4 9.7 + - - +
533A ALA* 4.2 6.3 - - - +
534A ASP 3.5 0.2 - - - -
535A ALA* 1.3 80.7 - - + +
537A ASP* 1.3 57.4 + - - +
539A ILE* 3.4 9.7 + - + +
540A TYR* 2.9 29.3 + - - +
607A ARG* 3.5 23.6 + - - +
611A ARG* 4.6 22.8 + - - +
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Residues in contact with ASP 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A LEU* 3.9 16.3 - - + +
438A TRP* 3.6 24.7 + - + +
533A ALA* 2.9 22.3 + - - +
534A ASP* 3.5 14.6 - - - +
535A ALA 3.2 0.6 - - - -
536A GLU* 1.3 74.5 - - - +
538A VAL* 1.3 60.1 + - - +
540A TYR* 3.3 1.7 + - - +
541A VAL* 3.0 36.3 + - - +
607A ARG* 3.2 27.8 + - - +
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Residues in contact with VAL 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A TRP* 3.7 28.3 - - + -
441A PRO* 5.0 1.3 - - + -
442A SER* 4.1 23.0 - - - +
445A VAL* 4.8 9.6 - - + -
519A SER* 6.5 1.3 - - - -
525A LEU* 4.7 10.1 - - + -
530A PHE* 3.7 34.5 - - + -
534A ASP 3.1 15.9 + - - +
535A ALA 3.3 7.2 + - - +
537A ASP* 1.3 75.4 - - - +
539A ILE* 1.3 58.8 + - - +
541A VAL* 3.4 5.5 + - - +
542A ASN* 2.9 31.9 + - + +
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Residues in contact with ILE 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519A SER* 3.2 26.9 - - - +
520A LEU* 3.7 31.0 - - + +
525A LEU* 3.7 13.0 - - + -
535A ALA* 3.1 16.2 + - + +
536A GLU* 3.5 15.0 - - + +
538A VAL* 1.3 76.5 - - - +
540A TYR* 1.3 64.3 + - - +
542A ASN* 3.3 5.0 + - - +
543A TRP* 3.1 36.9 + - + +
610A ILE* 4.8 9.9 - - + -
611A ARG* 3.4 31.2 - - + +
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Residues in contact with TYR 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A ASP* 2.7 41.2 + - - -
434A LEU* 4.3 13.5 - - + -
536A GLU 2.9 17.6 + - - +
537A ASP 3.8 3.1 - - - +
539A ILE* 1.3 76.0 - - - +
541A VAL* 1.3 66.0 + - + +
543A TRP* 3.4 1.6 + - - +
544A LEU* 2.8 41.1 + - + +
605A LEU* 3.3 38.6 + - + +
607A ARG* 3.6 59.0 - - + +
610A ILE* 4.2 13.2 - - + -
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Residues in contact with VAL 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A LEU* 3.5 33.9 - - + +
435A TYR* 4.3 18.8 - - + +
438A TRP* 3.6 37.0 - - + +
439A LYS* 4.0 7.6 - - - +
442A SER* 4.1 7.9 - - - +
537A ASP 3.0 20.8 + - - +
538A VAL 3.9 2.9 - - - +
540A TYR* 1.3 79.2 - - + +
542A ASN* 1.3 56.4 + - - +
544A LEU* 3.5 7.3 - - + +
545A ASN* 2.7 35.1 + - + +
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Residues in contact with ASN 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A SER* 4.3 23.4 + - - +
443A PHE* 5.5 0.2 - - - -
445A VAL* 6.0 0.8 - - - +
446A GLN* 3.0 40.0 + - - +
516A LEU* 3.7 10.4 - - - +
519A SER* 3.3 29.3 + - - -
538A VAL* 2.9 21.9 + - + +
539A ILE* 3.3 6.9 + - - +
541A VAL* 1.3 76.4 - - - +
543A TRP* 1.3 58.2 + - - +
545A ASN* 3.7 10.0 + - - +
546A MET* 3.3 25.5 + - - +
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Residues in contact with TRP 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516A LEU* 3.5 47.9 + - + +
519A SER* 3.8 5.6 + - - -
520A LEU* 3.6 21.0 - - + +
539A ILE* 3.1 34.3 + - + +
540A TYR 3.9 1.1 - - - +
542A ASN* 1.3 74.9 - - + +
544A LEU* 1.3 65.3 + - - +
545A ASN 3.2 0.4 - - - -
546A MET* 3.4 1.8 + - - +
547A VAL* 3.1 29.8 + - - +
579A LEU* 4.0 31.4 - - + -
586A LEU* 5.2 1.6 - - + -
605A LEU* 3.6 20.2 - - + -
610A ILE* 3.7 30.7 - - + -
614A GLY* 3.9 31.9 - - - -
615A LYS* 4.1 3.8 - - - -
618A LEU* 3.9 25.8 - - + -
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Residues in contact with LEU 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A LEU* 4.0 23.1 - - + -
431A ASP* 3.8 39.0 - - + +
435A TYR* 3.9 25.1 - - + +
540A TYR* 2.8 30.7 + - + +
541A VAL* 3.5 7.6 - - + +
543A TRP* 1.3 78.0 - - - +
545A ASN* 1.3 56.0 + - - +
547A VAL* 3.9 2.0 - - + +
548A ARG* 2.9 30.8 + - - +
603A VAL* 4.6 20.2 - - + +
605A LEU* 3.5 20.3 - - + +
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Residues in contact with ASN 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A TYR* 2.7 37.6 + - + -
439A LYS* 4.6 7.0 - - + +
442A SER* 5.3 5.2 - - - +
443A PHE* 5.9 5.2 - - - +
541A VAL* 2.7 22.6 + - + +
542A ASN* 3.8 12.1 + - - +
544A LEU* 1.3 71.6 - - - +
546A MET* 1.3 58.7 + - - +
548A ARG* 3.3 4.6 + - - +
549A ALA* 2.8 33.3 + - - +
572A ARG* 4.4 18.6 - - - +
6B HIS 4.4 10.1 + - - +
7B PRO* 5.1 0.7 - - - +
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Residues in contact with MET 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A GLN* 4.0 7.6 - - + +
512A GLU* 3.8 34.1 - - + +
516A LEU* 3.5 41.1 - - + -
542A ASN* 3.3 14.0 + - - +
543A TRP 3.8 4.9 - - - +
544A LEU 3.4 0.2 - - - -
545A ASN* 1.3 82.8 - - - +
547A VAL* 1.3 61.9 + - + +
549A ALA* 3.3 5.5 + - - +
550A GLY* 3.0 24.6 + - - -
572A ARG* 3.6 36.5 - - + +
575A ILE* 3.8 23.6 - - + -
576A LEU* 5.1 1.1 - - - +
579A LEU* 5.5 0.9 - - + -
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Residues in contact with VAL 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A TRP* 3.1 18.0 + - + +
544A LEU* 3.9 5.4 - - - +
546A MET* 1.3 73.8 - - + +
548A ARG* 1.3 65.9 + - - +
550A GLY* 3.3 9.9 + - - +
551A LEU* 3.5 9.4 + - - +
576A LEU* 3.6 22.0 - - + +
579A LEU* 4.1 19.3 - - + -
587A VAL* 3.6 40.6 - - + -
589A ILE* 4.7 1.9 - - + +
603A VAL* 3.5 25.9 - - + +
604A ARG 5.3 0.9 - - - +
605A LEU* 4.6 9.2 - - + -
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Residues in contact with ARG 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A LYS 4.8 2.2 + - - -
424A LEU* 4.1 11.0 - - - +
425A THR* 3.0 50.2 + - - +
426A PHE* 4.7 6.7 - - + +
427A LEU* 3.8 31.2 - - + +
435A TYR* 2.7 47.6 + - - -
439A LYS* 5.4 0.6 - - - +
544A LEU 2.9 19.7 + - - +
545A ASN* 3.6 4.0 - - - +
547A VAL* 1.3 78.9 - - - +
549A ALA* 1.3 62.1 + - - +
551A LEU* 3.1 14.7 + - - +
552A LEU* 3.2 29.7 + - + +
603A VAL* 4.6 10.9 - - + +
7B PRO* 3.8 25.8 - - - +
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Residues in contact with ALA 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A ASN* 2.8 22.7 + - - +
546A MET* 3.7 3.4 - - - +
548A ARG* 1.3 72.2 - - - +
550A GLY* 1.3 59.7 + - - +
552A LEU* 3.2 13.8 + - + +
553A ALA* 2.9 30.5 + - - +
569A MET* 3.8 7.3 - - + +
572A ARG* 3.6 40.8 - - - +
6B HIS 4.6 7.4 - - - +
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Residues in contact with GLY 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A MET 3.0 11.2 + - - -
547A VAL 3.3 5.3 + - - -
548A ARG 3.2 0.6 - - - -
549A ALA* 1.3 78.2 - - - +
551A LEU* 1.3 59.3 + - - +
553A ALA* 3.5 8.1 - - - +
554A LEU* 4.4 1.0 + - - +
572A ARG* 3.6 28.0 - - - +
573A PHE* 3.4 24.4 - - - -
576A LEU* 3.5 14.0 - - - +
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Residues in contact with LEU 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A PHE* 3.7 40.4 - - + -
547A VAL 3.5 7.7 + - - +
548A ARG 3.1 10.4 + - - +
550A GLY* 1.3 75.6 - - - +
552A LEU* 1.3 64.9 + - + +
553A ALA 3.1 2.1 + - - -
554A LEU* 3.3 30.9 + - + +
576A LEU* 3.8 5.4 - - + +
589A ILE* 4.5 9.2 - - + -
601A ALA* 4.2 11.7 - - + -
603A VAL* 4.0 18.2 - - + -
655A PHE* 4.8 4.9 - - + -
658A LEU* 3.9 24.5 - - + -
662A VAL* 3.3 30.7 - - + +
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Residues in contact with LEU 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A THR* 4.0 9.0 - - - +
426A PHE* 3.6 35.2 - - + -
548A ARG* 3.2 34.3 + - - +
549A ALA* 3.2 12.8 + - + +
551A LEU* 1.3 78.3 - - - +
553A ALA* 1.3 63.1 + - - +
554A LEU 3.1 0.9 + - - -
555A GLU* 3.2 24.2 + - - +
556A PHE* 4.2 3.3 - - - -
569A MET* 4.3 1.6 - - - -
662A VAL* 3.5 11.1 - - + +
665A ARG 6.0 1.3 - - - +
666A LYS* 6.2 3.4 - - - -
6B HIS* 4.4 18.8 - - + +
7B PRO* 3.9 29.4 - - + -
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Residues in contact with ALA 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A ALA 2.9 17.0 + - - +
550A GLY* 3.5 11.9 - - - +
551A LEU 3.1 0.8 - - - -
552A LEU* 1.3 72.8 - - - +
554A LEU* 1.3 56.8 + - - +
555A GLU 3.0 6.1 - - - -
556A PHE* 2.8 24.0 + - - +
564A TRP* 3.1 23.5 - - + -
569A MET* 3.2 45.1 - - + +
573A PHE* 4.1 1.8 - - + -
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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) + - + + + + + -
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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