Contacts of the helix formed by residues 537 - 553 (chain A) in PDB entry 4YK6
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 SER 537 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490A ASN* 4.9 1.6 + - - -
495A ILE* 3.7 33.7 - - - +
499A ARG* 4.5 0.3 - - - -
535A SER* 3.0 13.3 + - - -
536A GLU* 1.3 75.1 - - - +
538A GLU* 1.3 63.3 + - - +
539A ASP* 3.4 9.0 + - - +
540A LEU* 3.0 20.1 + - - +
541A GLN* 3.0 22.7 + - - +
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Residues in contact with GLU 538 (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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536A GLU 3.3 7.0 + - - +
537A SER* 1.3 72.8 - - - +
539A ASP* 1.3 57.9 + - - +
541A GLN* 3.2 16.8 + - - +
542A GLN* 2.9 26.9 + - - +
578A GLU 4.8 0.2 - - - +
579A VAL* 3.8 7.0 - - - -
580A LYS* 2.9 35.4 + - - +
581A LYS* 2.7 36.7 + - + +
584A THR* 2.7 34.0 + - + +
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Residues in contact with ASP 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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499A ARG* 3.9 25.2 + - - +
537A SER* 3.2 7.1 + - - +
538A GLU* 1.3 79.1 - - - +
540A LEU* 1.3 62.6 + - - +
542A GLN* 3.2 8.4 + - - +
543A VAL* 3.0 25.5 + - + +
581A LYS* 4.2 25.2 + - - +
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Residues in contact with LEU 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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495A ILE* 4.5 12.8 - - + -
498A ARG* 3.9 24.0 - - + +
499A ARG* 3.7 39.5 - - + +
532A GLN* 3.8 24.7 - - + +
535A SER* 3.8 19.5 - - - +
537A SER* 3.0 23.3 + - - +
539A ASP* 1.3 73.3 - - - +
541A GLN* 1.3 66.4 + - - +
543A VAL* 3.1 4.8 + - + -
544A ILE* 2.9 46.5 + - + +
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Residues in contact with GLN 541 (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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532A GLN 4.2 9.9 - - - +
533A LEU* 3.4 29.0 + - + +
534A LYS* 4.5 1.0 - - - +
535A SER 2.6 26.3 + - - +
536A GLU* 4.8 1.4 - - - +
537A SER 3.0 13.5 + - - +
538A GLU* 3.2 18.5 + - - +
540A LEU* 1.3 74.7 - - - +
542A GLN* 1.3 58.3 + - - +
544A ILE* 3.3 6.1 + - - +
545A ALA* 2.9 31.4 + - - +
575A CYS* 3.7 11.6 - - - -
579A VAL* 3.6 24.9 - - - +
584A THR* 4.3 7.2 - - + -
588A VAL* 5.1 0.4 - - - +
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Residues in contact with GLN 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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538A GLU 2.9 13.9 + - - +
539A ASP* 3.5 10.0 - - - +
540A LEU 3.1 0.2 - - - -
541A GLN* 1.3 77.4 - - - +
543A VAL* 1.3 69.3 + - - +
545A ALA* 3.3 5.0 + - - +
546A SER* 2.8 54.4 + - - -
583A SER* 3.7 23.2 + - - +
584A THR* 3.8 21.5 - - - +
587A SER* 3.0 12.9 + - - +
372B MET 5.9 0.4 + - - -
374B LEU* 3.5 42.2 + - + +
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Residues in contact with VAL 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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498A ARG 4.6 0.7 - - - +
499A ARG* 3.5 18.6 - - + +
502A GLY* 3.4 40.2 - - - +
503A MET* 3.4 27.1 - - + +
506A THR* 3.8 1.1 + - - +
539A ASP* 3.0 16.4 + - + +
540A LEU* 3.1 13.6 + - + +
542A GLN* 1.3 86.0 - - - +
544A ILE* 1.3 62.2 + - + +
546A SER* 3.2 8.3 + - - -
547A VAL* 3.1 22.0 + - - +
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Residues in contact with ILE 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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479A LEU* 4.8 7.2 - - + -
498A ARG 5.4 0.9 - - - +
502A GLY* 5.5 1.1 - - - -
529A LEU* 3.1 53.6 - - + +
532A GLN* 3.6 32.5 - - + -
533A LEU* 3.6 20.0 - - + -
540A LEU* 2.9 34.5 + - + +
541A GLN 3.7 5.6 - - - +
543A VAL* 1.3 78.4 - - + +
545A ALA* 1.3 64.4 + - - +
547A VAL* 3.1 7.5 + - + +
548A LEU* 3.0 29.6 + - + +
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Residues in contact with ALA 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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533A LEU* 4.6 0.7 - - + -
541A GLN 2.9 18.0 + - - +
542A GLN* 3.7 5.4 - - - +
544A ILE* 1.3 77.5 - - - +
546A SER* 1.3 53.0 + - - +
548A LEU* 3.3 6.7 + - - +
549A ARG* 2.7 34.8 + - - +
572A LEU* 4.1 12.1 - - + -
587A SER* 3.8 15.8 - - - +
588A VAL* 3.6 32.8 - - + +
591A ALA* 4.0 0.9 - - - +
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Residues in contact with SER 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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506A THR* 3.6 23.6 - - - -
542A GLN* 2.8 41.8 + - - -
543A VAL* 3.2 11.9 + - - -
545A ALA* 1.3 72.3 - - - +
547A VAL* 1.3 67.0 + - - +
549A ARG* 3.4 10.0 + - - +
550A ASN* 3.1 28.8 + - - +
587A SER* 3.2 8.5 + - - -
371B GLU* 5.3 2.7 - - - -
372B MET 5.3 3.3 + - - -
373B ALA* 5.6 2.7 - - - -
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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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502A GLY* 3.4 19.7 - - - +
505A LEU* 4.1 7.0 - - + -
506A THR* 3.3 25.1 - - - +
509A THR* 5.2 3.6 - - - +
519A LEU* 3.8 29.4 - - + -
529A LEU* 4.0 20.9 - - + -
543A VAL 3.1 12.2 + - - +
544A ILE* 3.1 9.6 + - - +
546A SER* 1.3 77.6 - - - +
548A LEU* 1.3 58.0 + - + +
550A ASN* 3.2 7.5 + - - +
551A LEU* 2.9 37.3 + - + +
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Residues in contact with LEU 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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526A MET* 4.2 13.9 - - + -
529A LEU* 4.8 11.2 - - + -
530A VAL* 4.6 12.1 - - + -
533A LEU* 4.0 20.9 - - + -
544A ILE* 3.0 35.0 + - + +
545A ALA* 3.8 4.7 - - - +
547A VAL* 1.3 75.9 - - + +
549A ARG* 1.3 58.7 + - - +
551A LEU* 3.9 7.8 - - + +
552A SER* 2.9 30.2 + - - -
563A LEU* 4.0 24.4 - - + +
568A SER* 4.5 13.0 - - - -
572A LEU* 4.1 27.6 - - + -
591A ALA* 4.1 2.4 - - - +
595A LEU* 5.4 0.8 - - + +
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Residues in contact with ARG 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 ALA 2.7 22.4 + - - +
546A SER* 3.5 9.2 - - - +
548A LEU* 1.3 72.5 - - - +
550A ASN* 1.3 65.7 + - - +
552A SER* 2.9 16.1 + - - -
553A TRP* 3.2 10.0 + - - +
586A LYS* 4.6 14.5 - - - +
587A SER* 4.2 14.0 + - - +
590A SER* 3.3 31.0 + - - -
591A ALA* 3.6 18.1 - - + +
594A ASN* 3.2 9.4 + - - +
368B GLY 2.8 26.5 + - - -
369B GLY* 3.3 16.8 + - - +
370B GLU* 3.9 14.3 + - - +
371B GLU* 3.1 42.1 + - - +
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Residues in contact with ASN 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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506A THR* 3.0 32.1 + - - +
509A THR* 3.3 19.3 + - - +
510A PHE* 3.8 9.8 - - - +
516A LYS* 3.0 30.5 + - - -
546A SER 3.1 12.9 + - - +
547A VAL* 3.6 6.5 - - - +
549A ARG* 1.3 78.4 - - - +
551A LEU* 1.3 62.9 + - - +
553A TRP* 3.3 5.9 + - - +
370B GLU* 3.3 15.3 - - + -
371B GLU 2.9 41.3 + - - +
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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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509A THR* 3.8 20.0 - - + -
516A LYS* 3.7 41.9 - - + +
519A LEU* 3.8 20.0 - - + -
520A CYS* 4.0 10.9 - - - -
526A MET* 3.6 36.3 - - + -
547A VAL* 2.9 29.4 + - + +
548A LEU* 4.0 8.1 - - + +
550A ASN* 1.3 76.9 - - - +
552A SER* 1.3 60.4 + - - +
553A TRP 3.6 2.1 + - - +
555A ALA* 3.6 17.7 - - - +
559A SER* 4.6 4.7 - - - -
563A LEU* 3.7 11.8 - - + +
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Residues in contact with SER 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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548A LEU 2.9 19.6 + - - -
549A ARG* 2.9 11.4 + - - -
551A LEU* 1.3 76.7 - - - +
553A TRP* 1.3 62.1 + - - +
554A ARG 3.5 2.3 + - - -
555A ALA 3.7 1.9 + - - -
563A LEU* 3.7 9.2 - - - -
591A ALA 3.7 4.0 + - - -
594A ASN* 3.1 26.7 + - - +
595A LEU* 3.8 29.2 - - - -
598A HIS* 3.0 26.2 + - - -
366B GLN* 3.8 1.4 - - - +
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Residues in contact with TRP 553 (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 LYS* 3.1 36.6 + - - +
549A ARG 3.2 4.5 + - - +
550A ASN 3.3 11.6 + - - +
551A LEU 4.1 0.3 - - - +
552A SER* 1.3 72.8 - - - +
554A ARG* 1.3 111.7 + - + +
555A ALA* 3.1 2.1 + - - -
594A ASN* 3.5 11.0 - - - +
365B TYR* 6.3 0.4 - + - -
366B GLN* 2.6 39.3 - - + -
367B GLY* 4.5 1.6 - - - -
369B GLY* 3.3 48.0 - - - +
370B GLU* 3.5 27.5 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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