Contacts of the helix formed by residues 491 - 510 (chain A) in PDB entry 3QHE
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 ASP 491 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489A THR* 2.8 22.1 + - + +
490A ASN* 1.3 76.6 - - - +
492A HIS* 1.3 66.8 + - - +
493A TYR* 3.1 33.0 + - - +
494A SER* 3.4 9.1 + - - +
495A ILE* 3.1 23.4 + - - +
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Residues in contact with HIS 492 (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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490A ASN 3.3 6.3 + - - +
491A ASP* 1.3 74.6 + - - +
493A TYR* 1.3 56.1 + - - +
495A ILE* 3.5 7.9 + - + +
496A THR* 2.7 55.5 + - + -
499A ARG* 5.8 2.9 - - - -
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Residues in contact with TYR 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A PRO* 3.2 39.0 + - + -
442A VAL* 3.4 43.2 - - + -
445A GLN* 4.1 1.6 - - - -
446A ILE 3.3 4.0 + - - -
447A CYS* 2.9 47.5 + - + +
448A PRO* 4.0 6.3 - - + +
491A ASP* 3.1 12.3 + - - +
492A HIS* 1.3 79.6 + - - +
494A SER* 1.3 60.7 + - - +
496A THR* 3.3 6.5 + - - -
497A LEU* 3.0 29.5 + - + +
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Residues in contact with SER 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A PRO* 4.2 9.5 - - - +
482A ASP* 3.0 31.2 + - - +
486A TYR* 3.8 12.4 - - - -
489A THR* 4.0 23.6 - - - -
491A ASP* 3.4 11.6 + - - -
493A TYR* 1.3 76.2 - - - +
495A ILE* 1.3 64.6 + - - +
497A LEU* 3.4 6.7 + - - +
498A ARG* 3.0 31.9 + - - +
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Residues in contact with ILE 495 (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 THR* 3.4 26.5 - - + +
490A ASN* 3.7 27.6 - - + +
491A ASP 3.1 12.7 + - - +
492A HIS* 3.8 8.1 - - + +
494A SER* 1.3 72.5 - - - +
496A THR* 1.3 68.2 + - - +
498A ARG* 3.1 10.7 + - - +
499A ARG* 2.8 35.5 + - + +
535A SER* 4.9 2.7 - - - +
537A SER* 3.5 37.5 - - - +
540A LEU* 4.6 12.0 - - + +
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Residues in contact with THR 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A CYS* 3.5 12.1 - - - -
492A HIS* 2.7 44.7 + - + -
493A TYR* 3.3 6.7 + - - -
495A ILE* 1.3 76.1 - - - +
497A LEU* 1.3 64.0 + - - +
499A ARG* 3.2 19.7 + - - +
500A TYR* 3.0 60.4 + - + +
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Residues in contact with LEU 497 (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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416A TYR* 5.5 0.7 - - + -
441A PRO* 4.1 20.6 - - + -
446A ILE* 3.7 25.8 - - + -
447A CYS* 3.8 15.0 - - - +
450A VAL* 4.1 14.9 - - + +
478A LEU* 4.1 25.4 - - + +
479A LEU* 5.1 1.8 - - - -
482A ASP* 4.2 28.3 - - + +
493A TYR* 3.0 23.9 + - + +
494A SER* 3.6 4.7 - - - +
496A THR* 1.3 76.5 - - - +
498A ARG* 1.3 65.2 + - + +
500A TYR* 3.3 4.7 + - - +
501A ALA* 3.0 28.0 + - + +
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Residues in contact with ARG 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A LEU* 4.3 12.8 - - + +
482A ASP* 2.8 46.5 + - + +
483A CYS* 3.6 26.8 - - - +
486A TYR* 3.6 11.7 - - - +
487A GLY 2.9 30.9 + - - -
488A LEU* 4.5 1.4 - - - +
489A THR* 3.8 14.5 + - - +
494A SER* 3.0 19.9 + - - +
495A ILE* 3.1 5.7 + - - +
497A LEU* 1.3 81.3 - - + +
499A ARG* 1.3 64.4 + - - +
501A ALA* 3.5 4.7 + - - +
502A GLY* 2.9 21.5 + - - -
532A GLN* 2.8 36.9 + - + +
540A LEU* 3.8 25.0 - - + +
543A VAL* 4.6 0.2 - - - +
544A ILE* 5.5 0.2 - - - +
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Residues in contact with ARG 499 (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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492A HIS* 5.8 3.0 - - - -
495A ILE* 2.8 28.3 + - - +
496A THR* 3.4 23.0 + - - +
498A ARG* 1.3 77.0 - - - +
500A TYR* 1.3 81.4 + - + +
502A GLY 3.3 1.0 + - - -
503A MET* 2.8 46.2 + - - +
537A SER* 4.7 0.2 - - - -
539A ASP* 3.7 35.3 + - - +
540A LEU* 3.9 28.9 - - + +
543A VAL* 3.5 13.0 - - + +
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Residues in contact with TYR 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A CYS* 4.2 12.3 - - - -
450A VAL* 3.9 14.1 - - + +
451A CYS* 3.6 45.0 - - + -
454A MET* 3.6 35.0 - - + +
496A THR* 3.0 45.5 + - + +
497A LEU 3.8 3.6 - - - +
499A ARG* 1.3 94.1 + - + +
501A ALA* 1.3 66.2 + - - +
503A MET* 3.4 12.7 + - + -
504A ALA* 3.1 23.2 + - - +
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Residues in contact with ALA 501 (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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450A VAL* 3.6 10.8 - - + +
475A ILE* 3.6 24.1 - - + +
478A LEU* 5.0 4.9 - - + -
479A LEU* 4.2 23.6 - - + +
497A LEU* 3.0 18.2 + - + +
498A ARG* 3.8 5.2 - - - +
500A TYR* 1.3 77.3 - - - +
502A GLY* 1.3 56.9 + - - +
504A ALA* 3.2 4.6 + - - +
505A LEU* 2.9 33.1 + - - +
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Residues in contact with GLY 502 (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* 4.3 10.5 - - - +
498A ARG 2.9 13.7 + - - -
501A ALA* 1.3 73.3 - - - +
503A MET* 1.3 60.5 + - - +
505A LEU* 3.2 3.4 + - - -
506A THR* 2.8 32.2 + - - -
543A VAL* 3.4 21.5 - - - -
544A ILE* 5.6 1.3 - - - -
547A VAL* 3.3 12.8 - - - +
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Residues in contact with MET 503 (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 MET* 3.8 29.8 - - + -
457A SER* 4.7 0.2 - - - -
458A PHE* 4.8 7.2 - - + -
499A ARG* 2.8 37.0 + - - +
500A TYR* 3.8 26.0 - - + +
501A ALA 3.3 0.2 - - - -
502A GLY* 1.3 75.3 - - - +
504A ALA* 1.3 57.9 + - - +
506A THR* 3.4 8.2 + - - -
507A ASN* 3.1 32.8 + - - -
543A VAL* 3.5 13.7 - - + +
388B SER* 3.6 48.0 - - - +
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Residues in contact with ALA 504 (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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450A VAL* 5.7 1.1 - - + +
453A LEU* 4.5 2.0 - - + +
454A MET* 4.1 13.2 - - - +
457A SER* 3.6 22.0 - - - +
475A ILE* 4.2 23.6 - - + -
500A TYR 3.1 16.7 + - - +
501A ALA* 3.5 5.4 - - - +
502A GLY 3.2 0.2 - - - -
503A MET* 1.3 75.6 - - - +
505A LEU* 1.3 59.1 + - - +
507A ASN* 3.3 1.7 + - - +
508A LEU* 2.9 36.2 + - - +
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Residues in contact with LEU 505 (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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472A LEU* 3.6 42.2 - - + +
475A ILE* 4.1 9.4 - - + -
476A ALA* 4.0 25.4 - - + +
479A LEU* 4.1 24.2 - - + -
501A ALA 2.9 19.8 + - - +
502A GLY* 3.7 7.4 - - - +
504A ALA* 1.3 73.4 - - - +
506A THR* 1.3 61.5 + - - +
508A LEU* 3.8 3.5 - - + +
509A THR* 2.8 36.4 + - - +
519A LEU* 4.3 21.5 - - + -
525A CYS* 5.1 1.1 - - - -
529A LEU* 4.8 7.6 - - + -
547A VAL* 4.1 9.0 - - + -
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Residues in contact with THR 506 (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 2.8 20.1 + - - -
503A MET* 3.4 11.8 - - - -
505A LEU* 1.3 76.1 - - - +
507A ASN* 1.3 63.0 + - - +
509A THR* 2.8 20.0 + - - -
510A PHE* 3.1 4.9 + - - +
543A VAL 3.9 0.7 + - - -
546A SER* 3.7 16.7 - - - +
547A VAL* 3.2 20.0 + - - +
549A ARG* 3.7 13.5 - - - +
550A ASN* 3.0 26.2 + - - +
385B GLY 3.7 10.5 - - - +
386B TYR 3.9 12.3 - - - +
387B TYR 4.0 2.5 - - - +
388B SER 4.6 2.0 - - - -
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Residues in contact with ASN 507 (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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457A SER* 2.8 44.7 + - - +
458A PHE* 3.3 32.0 - - - -
463A ARG* 3.5 15.3 - - - -
503A MET 3.1 10.9 + - - +
504A ALA 3.3 3.1 + - - +
506A THR* 1.3 79.3 - - - +
508A LEU* 1.3 59.8 + - - +
509A THR 3.7 0.3 + - - -
510A PHE* 3.8 7.6 + - - +
386B TYR* 2.6 59.6 + - + +
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Residues in contact with LEU 508 (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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457A SER* 4.7 3.6 - - - -
463A ARG* 4.0 30.3 - - + +
466A MET* 4.1 22.9 - - + -
467A ASN* 3.6 22.7 - - - +
471A GLY 4.7 0.4 - - - -
472A LEU* 4.0 29.2 - - + +
475A ILE* 3.9 27.1 - - + -
504A ALA* 2.9 23.5 + - + +
505A LEU* 4.9 0.7 - - - +
507A ASN* 1.3 74.4 - - - +
509A THR* 1.3 63.7 + - - +
510A PHE 4.9 0.4 - - - -
512A ASP* 3.5 7.3 - - - +
515A ASN* 2.8 31.9 + - - +
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Residues in contact with THR 509 (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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472A LEU* 4.3 9.6 - - + -
505A LEU 2.8 24.5 + - - +
506A THR* 2.8 13.5 + - - -
508A LEU* 1.3 79.5 - - - +
510A PHE* 1.3 64.6 + - - +
511A GLY 3.1 1.4 + - - -
512A ASP 2.9 15.6 + - - +
515A ASN* 4.4 4.0 - - - -
516A LYS* 3.3 25.8 - - - +
519A LEU* 4.0 15.3 - - + -
547A VAL* 4.9 2.9 + - + -
550A ASN* 3.1 23.3 + - - +
551A LEU* 3.7 25.1 - - + -
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Residues in contact with PHE 510 (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 3.1 10.4 + - - +
507A ASN 4.0 10.6 - - - +
508A LEU 3.5 1.5 - - - +
509A THR* 1.3 75.1 + - - +
511A GLY* 1.3 62.9 + - - +
512A ASP* 2.9 10.0 + - - +
550A ASN* 3.6 6.1 - - - +
384B GLU* 3.6 38.4 - - + -
385B GLY* 3.6 40.2 - - - +
386B TYR* 3.2 47.1 + + + -
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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