Contacts of the helix formed by residues 533 - 551 (chain A) in PDB entry 3NC0
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 533 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532A ARG* 1.3 77.1 - - - +
534A LYS* 1.3 59.5 + - - -
535A ASP* 2.9 15.4 + - - -
536A ASN 3.2 11.7 + - - -
537A LYS* 3.3 21.2 + - - +
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Residues in contact with LYS 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A GLY* 1.3 70.3 - - - -
535A ASP* 1.3 63.5 + - - +
537A LYS* 4.1 5.8 - - - +
538A ALA* 3.4 19.1 + - - +
575A GLU* 3.4 28.0 + - - +
576A THR* 4.5 9.7 + - - -
577A HIS* 3.4 32.3 + - + +
14B LEU* 3.9 30.0 + - + +
15B SER* 4.4 22.2 - - - -
100B ASN* 5.1 4.9 + - - +
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Residues in contact with ASP 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A TRP* 3.1 37.8 - - + -
533A GLY* 2.9 5.0 + - - +
534A LYS* 1.3 81.6 - - - +
536A ASN* 1.3 66.6 + - - +
538A ALA* 3.7 6.4 + - - +
539A ILE* 3.7 9.7 + - - +
577A HIS* 3.8 19.6 + - - -
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Residues in contact with ASN 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A TRP* 3.4 17.8 + - + +
491A TRP* 2.9 31.7 + - - +
531A LYS* 3.8 29.6 - - + +
532A ARG 3.1 22.2 + - - +
533A GLY 3.2 4.6 + - - +
535A ASP* 1.3 79.8 - - - +
537A LYS* 1.3 67.3 + - - +
539A ILE* 3.1 5.2 + - - +
540A ILE* 3.1 26.1 + - - +
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Residues in contact with LYS 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A CYS* 2.9 40.7 + - - +
529A GLU* 3.7 11.7 + - - +
531A LYS* 2.9 30.9 + - + +
532A ARG* 4.1 2.0 - - - +
533A GLY 3.3 27.2 + - - +
534A LYS* 4.4 2.5 - - - +
536A ASN* 1.3 76.2 - - - +
538A ALA* 1.3 56.8 + - - +
540A ILE* 3.8 4.7 - - - +
541A ALA* 2.9 31.4 + - - +
13B THR 4.1 10.6 + - - +
14B LEU* 3.6 32.9 - - + +
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Residues in contact with ALA 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A LYS 3.4 18.7 + - - +
535A ASP 4.0 1.3 - - - +
536A ASN 3.2 0.8 - - - -
537A LYS* 1.3 77.7 - - - +
539A ILE* 1.3 60.3 + - + +
541A ALA* 4.0 1.2 - - - +
542A SER* 2.7 35.5 + - - -
577A HIS* 3.7 24.7 - - + +
578A ASP 5.6 0.2 - - - +
580A VAL* 4.0 12.8 - - + -
583A MET* 5.2 0.3 - - - +
14B LEU* 3.4 17.9 - - + +
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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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491A TRP* 3.8 53.4 - - + -
494A LEU* 4.2 13.9 - - + -
495A ASN* 4.0 29.4 - - - +
535A ASP 3.7 6.8 + - - +
536A ASN 3.1 8.3 + - - +
538A ALA* 1.3 78.6 - - + +
540A ILE* 1.3 60.1 + - + +
542A SER* 3.6 4.9 + - - +
543A ASN* 2.6 35.1 + - - +
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Residues in contact with ILE 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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489A TRP* 3.9 16.2 - - + -
494A LEU* 3.8 24.0 - - + -
524A LEU* 3.8 17.7 - - + +
527A LEU* 3.6 32.1 - - + +
528A CYS* 3.6 33.2 - - + -
531A LYS* 4.4 7.6 - - + -
536A ASN 3.1 14.1 + - - +
537A LYS* 3.8 7.0 - - - +
539A ILE* 1.3 74.7 - - - +
541A ALA* 1.3 65.4 + - - +
543A ASN* 3.0 6.8 + - - +
544A ILE* 3.0 29.0 + - + +
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Residues in contact with ALA 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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528A CYS* 4.9 0.2 - - - -
537A LYS 2.9 22.6 + - - +
538A ALA 4.0 3.6 - - - +
540A ILE* 1.3 73.8 - - - +
542A SER* 1.3 56.9 + - - +
544A ILE* 3.4 8.5 + - - +
545A MET* 2.9 31.9 + - - +
572A PHE* 4.0 21.5 - - + -
583A MET* 4.4 3.1 - - + +
12B LEU* 3.9 27.8 - - + +
14B LEU* 4.4 7.9 - - + -
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Residues in contact with SER 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 ALA* 2.7 22.8 + - - +
539A ILE* 3.7 9.5 - - - +
540A ILE 3.1 0.2 - - - -
541A ALA* 1.3 77.5 - - - +
543A ASN* 1.3 56.3 + - - +
545A MET* 3.1 3.8 + - - +
546A TYR* 2.7 34.5 + - - +
580A VAL* 5.3 4.3 - - - +
583A MET* 3.6 38.2 - - - +
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Residues in contact with ASN 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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494A LEU* 3.2 26.1 - - + +
495A ASN* 3.1 34.4 + - - +
498A CYS* 3.5 22.9 - - + +
499A TRP* 5.2 3.6 + - - +
524A LEU* 5.4 1.3 - - + -
539A ILE* 2.6 26.1 + - - +
540A ILE* 3.0 8.7 + - - +
542A SER* 1.3 77.0 - - - +
544A ILE* 1.3 61.5 + - - +
546A TYR* 3.5 8.2 - - - +
547A ILE* 2.8 37.1 + - - +
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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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521A ILE* 4.6 13.7 - - + +
524A LEU* 3.9 42.4 - - + +
525A LEU* 3.6 25.4 - - + -
528A CYS* 4.9 0.4 - - + -
540A ILE* 3.0 24.4 + - + +
541A ALA* 3.5 12.6 - - - +
543A ASN* 1.3 76.0 - - - +
545A MET* 1.3 61.6 + - - +
547A ILE* 3.3 5.4 + - - +
548A VAL* 3.0 39.4 + - + +
9B LEU* 4.2 21.5 - - + -
12B LEU* 4.5 9.6 - - + -
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Residues in contact with MET 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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541A ALA 2.9 17.2 + - - +
542A SER 3.1 5.4 + - - +
544A ILE* 1.3 80.8 - - - +
546A TYR* 1.3 64.2 + - - +
548A VAL* 4.1 4.5 - - - +
549A GLY* 3.2 14.6 + - - -
565A VAL* 4.4 10.5 - - + +
568A LYS* 3.8 26.9 - - + -
569A LEU* 4.0 22.0 - - + -
572A PHE* 3.7 30.1 - - + -
583A MET* 3.6 25.6 - - + -
587A THR* 3.5 32.8 + - + +
9B LEU* 4.9 9.4 - - + -
12B LEU* 4.7 4.0 - - + -
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Residues in contact with TYR 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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427A PRO* 3.5 30.7 - - + +
428A GLU* 3.7 22.0 - - - -
454A TYR* 4.2 8.3 + - - -
498A CYS* 3.6 28.9 - - + -
499A TRP* 4.1 20.8 + + - -
502A GLY* 4.3 5.2 - - - -
542A SER 2.7 16.4 + - - +
543A ASN* 3.1 10.9 + - - +
545A MET* 1.3 72.7 - - - +
547A ILE* 1.3 69.9 + - + +
549A GLY* 3.1 9.9 + - - -
550A GLN* 3.2 36.5 + - + +
587A THR* 5.2 2.0 - - - -
590A LYS* 4.0 16.6 + - - +
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Residues in contact with ILE 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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498A CYS* 3.7 48.0 - - + +
501A ILE* 4.4 12.6 - - + -
502A GLY* 5.3 1.1 - - - +
517A LEU* 4.2 19.7 - - + -
520A VAL* 4.2 12.1 - - + -
521A ILE* 4.0 18.8 - - + -
524A LEU* 3.7 20.9 - - + -
543A ASN 2.8 19.1 + - - +
544A ILE* 3.7 4.5 - - - +
546A TYR* 1.3 76.3 - - + +
548A VAL* 1.3 58.6 + - + +
549A GLY 3.0 0.2 - - - -
550A GLN* 3.0 19.7 + - - +
551A TYR* 3.3 20.7 - - + -
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Residues in contact with VAL 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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517A LEU* 6.2 1.3 - - - -
521A ILE* 4.3 18.2 - - + -
544A ILE* 3.0 27.0 + - + +
545A MET* 4.4 7.0 - - - +
547A ILE* 1.3 75.7 - - + +
549A GLY* 1.3 60.6 + - - +
550A GLN 3.3 0.4 + - - -
551A TYR* 3.8 9.5 + - - +
554A PHE* 6.0 2.2 - - + -
555A LEU* 3.4 43.0 - - + +
561A PHE* 4.0 22.7 - - + -
565A VAL* 3.8 27.4 - - + -
587A THR* 6.2 0.2 - - + -
591A ILE* 4.8 1.3 - - + -
9B LEU* 5.3 2.7 - - + -
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Residues in contact with GLY 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 MET 3.2 12.0 + - - -
546A TYR 3.1 8.4 + - - -
547A ILE 3.0 1.8 - - - -
548A VAL* 1.3 79.3 - - - +
550A GLN* 1.3 58.5 + - - +
551A TYR 3.4 0.8 + - - -
552A PRO* 4.1 2.7 - - - +
555A LEU* 5.6 0.4 - - - +
587A THR* 4.6 6.1 - - - -
590A LYS* 3.9 16.7 - - - +
591A ILE* 4.5 16.9 - - - +
594A LYS* 3.0 24.8 + - - -
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Residues in contact with GLN 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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454A TYR* 4.7 6.9 + - - -
458A ARG* 6.3 0.2 - - - +
502A GLY* 3.0 37.4 + - - +
503A SER* 4.9 0.4 - - - +
505A SER* 2.7 28.9 + - - -
546A TYR* 3.2 38.6 + - + +
547A ILE 3.0 11.0 + - - +
549A GLY* 1.3 74.8 - - - +
551A TYR* 1.3 56.2 + - + +
552A PRO* 3.1 13.6 - - - +
590A LYS* 3.1 28.2 + - - +
594A LYS* 4.3 4.8 + - - +
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Residues in contact with TYR 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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501A ILE* 2.7 28.9 + - + -
502A GLY* 4.4 8.3 - - - -
504A ILE* 3.7 7.3 - - - +
505A SER* 3.2 42.5 + - - -
506A GLY 4.2 0.7 - - - -
513A GLU* 3.4 33.4 - - + -
516A PHE* 4.2 10.0 - + - -
517A LEU* 3.3 44.2 - - + -
547A ILE* 3.3 27.9 + - + +
548A VAL* 3.8 7.2 + - - +
549A GLY 3.4 1.2 - - - -
550A GLN* 1.3 79.1 - - - +
552A PRO* 1.3 64.5 - - - +
553A ARG* 3.2 3.6 - - + +
554A PHE* 3.2 13.4 + - + +
555A LEU* 3.3 13.2 + - - +
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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
------------------------------------------------------------
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