Contacts of the helix formed by residues 496 - 517 (chain A) in PDB entry 6UZA
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 MET 496 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491A PHE* 3.8 31.2 - - + -
492A SER 3.3 19.7 + - - +
493A TRP* 4.6 6.1 - - - +
494A MET 3.3 0.8 - - - -
495A GLU* 1.3 77.0 - - - +
497A LEU* 1.3 63.3 + - + +
498A ILE 3.2 1.8 - - - -
499A ILE* 3.2 19.3 + - + +
500A SER* 2.9 27.1 + - - -
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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
----------------------------------------------------------
456A LEU* 3.8 21.8 - - + -
493A TRP* 3.3 34.1 - - + +
494A MET* 3.8 7.5 + - + +
495A GLU 3.6 0.2 - - - -
496A MET* 1.3 79.2 - - + +
498A ILE* 1.3 59.6 + - - +
500A SER* 2.6 26.1 + - - +
501A TRP* 2.9 43.3 + - + -
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Residues in contact with ILE 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A PHE* 3.9 20.0 - - + -
456A LEU* 4.2 22.0 - - + +
457A LEU* 4.1 15.9 - - + -
460A ASN* 4.1 21.3 - - + +
494A MET 3.3 19.9 + - - +
495A GLU* 4.4 7.9 - - - +
496A MET 3.2 0.6 - - - -
497A LEU* 1.3 75.7 - - - +
499A ILE* 1.3 57.2 + - - +
501A TRP* 3.4 6.3 + - - +
502A VAL* 2.9 37.4 + - + +
537A PHE* 4.6 3.8 - - + -
541A PHE* 3.8 22.7 - - + -
599A TYR* 3.9 21.8 - - + +
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Residues in contact with ILE 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A PHE* 3.7 30.5 - - + -
495A GLU 3.3 19.5 - - - +
496A MET* 3.2 24.9 + - + +
498A ILE* 1.3 77.6 - - - +
500A SER* 1.3 57.4 + - - +
502A VAL* 3.3 2.6 + - - +
503A ILE* 2.9 47.2 + - + +
541A PHE* 3.9 37.7 - - + -
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Residues in contact with SER 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A MET 2.9 13.1 + - - -
497A LEU* 2.6 31.9 + - - +
499A ILE* 1.3 77.9 - - - +
501A TRP* 1.3 64.0 + - - +
503A ILE* 3.4 8.2 + - - +
504A GLY* 3.0 25.1 + - - -
763A PRO* 5.1 8.1 - - - +
766A LEU* 4.4 8.3 - - - +
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Residues in contact with TRP 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LEU* 5.3 1.6 - - + -
449A SER* 3.1 27.5 + - - -
452A ILE* 3.6 37.9 - - + -
453A PHE* 3.8 36.8 - + + +
456A LEU* 4.1 11.2 - - + -
497A LEU* 2.9 54.1 + - + +
498A ILE 3.7 3.8 - - - +
500A SER* 1.3 89.5 + - - +
502A VAL* 1.3 57.4 + - - +
504A GLY* 3.5 2.2 + - - -
505A MET* 2.9 38.2 + - + +
762A VAL* 3.6 21.4 - - + +
763A PRO* 3.7 34.8 - - + -
764A PHE* 6.2 0.9 - + - -
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Residues in contact with VAL 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A PHE* 4.3 14.4 - - + -
498A ILE* 2.9 22.4 + - + +
499A ILE 3.9 3.4 - - - +
501A TRP* 1.3 75.1 - - - +
503A ILE* 1.3 59.2 + - + +
505A MET* 3.3 6.5 + - + +
506A ILE* 2.9 44.7 + - + +
534A LEU* 4.3 11.2 - - + +
537A PHE* 3.9 44.4 - - + -
538A ALA* 4.9 3.6 - - - +
541A PHE* 4.1 16.2 - - + -
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Residues in contact with ILE 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A ILE* 2.9 38.5 + - + +
500A SER* 3.8 6.5 - - - +
502A VAL* 1.3 78.0 - - + +
504A GLY* 1.3 57.5 + - - +
506A ILE* 3.3 10.1 + - + +
507A TRP* 3.0 27.9 + - + +
766A LEU* 3.8 22.0 - - + -
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Residues in contact with GLY 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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500A SER 3.0 15.3 + - - -
501A TRP 3.9 0.4 - - - -
503A ILE* 1.3 77.1 - - - +
505A MET* 1.3 54.9 + - - +
507A TRP* 3.4 0.5 + - - +
508A ALA* 2.9 30.5 + - - +
762A VAL* 3.5 22.2 - - - -
765A ASN* 3.5 12.7 + - - -
766A LEU* 4.0 14.3 - - - +
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Residues in contact with MET 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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450A PHE* 6.2 2.0 - - + -
453A PHE* 4.3 24.0 - - + -
501A TRP* 2.9 43.6 + - + +
502A VAL* 3.7 6.3 - - - +
503A ILE 3.3 0.2 - - - -
504A GLY* 1.3 74.3 - - - +
506A ILE* 1.3 62.6 + - - +
508A ALA* 4.0 2.2 - - - +
509A GLU* 3.5 15.8 + - - +
533A MET* 4.7 6.5 - - - +
534A LEU* 3.5 33.7 - - + +
609A ARG* 3.5 47.0 + - - +
762A VAL* 3.7 20.4 - - + +
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Residues in contact with ILE 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A VAL* 2.9 34.4 + - + +
503A ILE* 3.7 9.2 - - + +
505A MET* 1.3 73.9 - - - +
507A TRP* 1.3 61.7 + - - +
509A GLU* 3.2 3.9 + - - +
510A CYS* 2.9 40.6 + - - -
534A LEU* 3.9 35.4 - - + +
538A ALA* 4.5 12.8 - - + -
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Residues in contact with TRP 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ILE* 3.0 17.4 + - + +
504A GLY 3.8 3.1 - - - +
506A ILE* 1.3 78.5 - - - +
508A ALA* 1.3 56.6 + - - +
510A CYS* 3.3 6.5 + - + +
511A LYS* 3.0 56.4 + - + +
514A TRP* 3.6 35.2 - + - -
765A ASN* 3.9 28.6 + - + +
766A LEU* 3.9 26.4 - - + +
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Residues in contact with ALA 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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504A GLY 2.9 18.7 + - - +
505A MET* 4.2 3.8 - - + +
507A TRP* 1.3 76.3 - - - +
509A GLU* 1.3 57.6 + - - +
511A LYS* 4.1 7.9 - - - +
512A GLU* 3.7 16.6 + - - +
762A VAL* 4.3 12.8 - - + -
765A ASN* 3.4 17.7 - - - +
1001A R0G 4.3 12.3 - - + +
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Residues in contact with GLU 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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505A MET 3.5 13.9 + - - +
506A ILE* 3.2 6.6 + - - +
507A TRP 3.1 0.8 - - - -
508A ALA* 1.3 77.3 - - - +
510A CYS* 1.3 60.9 + - - +
511A LYS 3.3 1.3 - - - -
512A GLU* 3.2 5.4 + - - +
513A ILE* 2.9 34.3 + - + +
521A TYR* 2.4 34.7 + - + +
527A ASN 3.8 8.0 - - - +
530A ASP* 3.5 16.1 - - - +
531A PHE* 4.4 15.7 + - + -
534A LEU* 4.1 10.1 - - + +
609A ARG* 4.3 2.9 + - - -
1001A R0G 3.1 38.8 + - - -
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Residues in contact with CYS 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 ILE* 2.9 32.2 + - - +
507A TRP* 3.9 9.9 - - + +
509A GLU* 1.3 73.1 - - - +
511A LYS* 1.3 61.6 + - - +
513A ILE* 3.1 17.1 + - - +
514A TRP* 3.0 56.9 + - + -
531A PHE* 6.3 2.5 - - - -
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Residues in contact with LYS 511 (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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507A TRP* 3.0 49.7 + - + +
508A ALA* 4.4 7.6 - - - +
509A GLU 3.3 0.2 - - - -
510A CYS* 1.3 76.3 - - - +
512A GLU* 1.3 58.5 + - - +
514A TRP* 3.7 20.6 + - + +
515A THR* 2.7 37.6 + - - -
758A ARG* 5.5 13.3 - - - +
765A ASN* 6.2 0.7 - - - +
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Residues in contact with GLU 512 (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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508A ALA 3.7 13.4 + - - +
509A GLU* 3.2 10.2 + - - +
510A CYS 3.2 0.4 - - - -
511A LYS* 1.3 77.5 - - - +
513A ILE* 1.3 63.3 + - - +
515A THR* 4.7 4.3 - - - +
516A GLN* 3.2 36.4 + - + +
521A TYR* 4.0 20.7 - - + -
527A ASN* 4.4 8.5 + - - -
758A ARG* 4.1 17.8 + - - -
1001A R0G 3.8 31.9 - - + +
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Residues in contact with ILE 513 (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 GLU* 2.9 21.7 + - + +
510A CYS* 3.1 20.8 + - - +
512A GLU* 1.3 75.7 - - - +
514A TRP* 1.3 64.5 + - + +
517A GLY* 3.1 30.1 + - - -
518A PRO* 3.8 20.4 - - + +
521A TYR* 3.7 42.8 - - + +
531A PHE* 5.2 12.6 - - + -
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Residues in contact with TRP 514 (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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507A TRP* 3.6 42.2 - + - -
510A CYS* 3.0 40.0 + - + -
511A LYS* 3.7 23.9 - - + +
513A ILE* 1.3 80.8 - - + +
515A THR* 1.3 60.6 + - - +
517A GLY* 4.7 1.8 - - - +
518A PRO* 5.8 1.3 - - - -
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Residues in contact with THR 515 (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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511A LYS* 2.7 29.1 + - - -
512A GLU* 4.3 5.4 - - - +
513A ILE 3.2 0.8 - - - -
514A TRP* 1.3 84.5 + - - +
516A GLN* 1.3 63.5 + - - +
517A GLY 3.4 0.9 - - - -
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Residues in contact with GLN 516 (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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512A GLU* 3.2 29.2 + - - +
515A THR* 1.3 75.8 - - + +
517A GLY* 1.3 64.0 + - - +
520A GLU* 3.7 20.3 - - + +
521A TYR* 4.9 11.0 - - + +
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Residues in contact with GLY 517 (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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513A ILE 3.1 13.1 + - - -
514A TRP* 4.7 1.8 - - - -
515A THR 3.4 3.0 - - - +
516A GLN* 1.3 83.4 - - - +
518A PRO* 1.3 68.3 - - - +
519A LYS 3.1 11.0 + - - -
520A GLU 4.2 0.4 - - - -
521A TYR* 3.2 21.5 + - - +
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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
------------------------------------------------------------
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