Contacts of the helix formed by residues 496 - 517 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B PHE* 3.8 31.4 - - + -
492B SER 3.3 19.2 + - - +
493B TRP* 4.6 6.3 - - - +
494B MET 3.3 0.6 - - - -
495B GLU* 1.3 77.7 - - - +
497B LEU* 1.3 63.1 + - + +
498B ILE 3.2 1.3 - - - -
499B ILE* 3.2 19.1 + - + +
500B SER* 2.9 27.0 + - - -
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Residues in contact with LEU 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B LEU* 3.8 21.5 - - + -
493B TRP* 3.3 33.0 - - + +
494B MET* 3.8 7.9 + - + +
496B MET* 1.3 79.7 - - + +
498B ILE* 1.3 59.6 + - - +
500B SER* 2.6 25.9 + - - +
501B TRP* 2.9 42.7 + - + -
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Residues in contact with ILE 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B PHE* 3.9 19.3 - - + -
456B LEU* 4.2 23.1 - - + +
457B LEU* 4.1 15.3 - - + -
460B ASN* 4.1 20.9 - - + +
494B MET 3.3 19.9 + - - +
495B GLU* 4.4 8.1 - - + +
496B MET 3.2 0.2 - - - -
497B LEU* 1.3 76.4 - - - +
499B ILE* 1.3 57.7 - - - +
501B TRP* 3.4 6.2 + - - +
502B VAL* 2.9 36.8 + - + +
537B PHE* 4.6 4.0 - - + -
541B PHE* 3.8 22.0 - - + -
599B TYR* 3.9 21.1 - - + +
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Residues in contact with ILE 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B PHE* 3.7 31.0 - - + -
495B GLU 3.3 18.8 - - - +
496B MET* 3.2 25.4 + - + +
498B ILE* 1.3 77.4 - - - +
500B SER* 1.3 57.0 + - - +
502B VAL* 3.3 2.5 + - - +
503B ILE* 2.9 47.4 + - + +
541B PHE* 3.9 36.8 - - + -
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Residues in contact with SER 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B MET 2.9 12.7 + - - -
497B LEU* 2.6 32.4 + - - +
499B ILE* 1.3 78.3 - - - +
501B TRP* 1.3 64.6 + - - +
503B ILE* 3.4 8.5 + - - +
504B GLY* 3.0 25.6 + - - -
763B PRO* 5.1 8.6 - - - +
766B LEU* 4.4 9.4 - - - +
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Residues in contact with TRP 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B LEU* 5.3 2.0 - - + -
449B SER* 3.1 26.7 + - - -
452B ILE* 3.6 37.9 - - + -
453B PHE* 3.8 36.6 - + + +
456B LEU* 4.1 11.2 - - + -
497B LEU* 2.9 53.5 + - + +
498B ILE 3.4 4.7 + - - +
500B SER* 1.3 90.1 + - - +
502B VAL* 1.3 56.8 + - - +
504B GLY* 3.5 1.5 + - - -
505B MET* 2.9 37.5 + - + +
762B VAL* 3.6 21.2 - - + +
763B PRO* 3.7 34.8 - - + -
764B PHE* 6.1 1.3 - + - -
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Residues in contact with VAL 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B PHE* 4.3 14.1 - - + -
498B ILE* 2.9 23.5 + - + +
499B ILE* 3.9 3.8 - - - +
501B TRP* 1.3 76.4 - - - +
503B ILE* 1.3 58.3 + - + +
505B MET* 3.7 6.6 - - + +
506B ILE* 2.9 44.4 + - + +
534B LEU* 4.3 12.1 - - + +
537B PHE* 3.9 43.5 - - + -
538B ALA* 4.9 3.6 - - - +
541B PHE* 4.1 16.2 - - + -
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Residues in contact with ILE 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B ILE* 2.9 37.8 + - + +
500B SER* 3.8 6.5 - - - +
502B VAL* 1.3 77.7 - - + +
504B GLY* 1.3 58.8 + - - +
506B ILE* 3.3 11.1 + - + +
507B TRP* 3.0 27.4 + - + +
766B LEU* 3.8 21.5 - - + -
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Residues in contact with GLY 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B SER 3.0 14.8 + - - -
501B TRP 3.9 0.2 - - - -
503B ILE* 1.3 78.2 - - - +
505B MET* 1.3 55.2 + - - +
507B TRP* 3.4 0.3 + - - +
508B ALA* 2.9 30.3 + - - +
762B VAL* 3.5 24.5 - - - -
765B ASN* 3.5 12.2 + - - -
766B LEU* 4.0 13.7 - - - -
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Residues in contact with MET 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B PHE* 6.2 1.6 - - + -
453B PHE* 4.3 24.2 - - + -
501B TRP* 2.9 44.2 + - + +
502B VAL* 3.7 5.8 - - - +
503B ILE 3.3 0.2 - - - -
504B GLY* 1.3 73.0 - - - +
506B ILE* 1.3 62.6 + - - +
508B ALA* 4.0 3.2 - - + +
509B GLU* 3.5 15.8 + - - +
533B MET* 4.7 6.1 - - - +
534B LEU* 3.5 35.1 - - + +
609B ARG* 3.5 47.4 + - - +
762B VAL* 3.7 20.1 - - + +
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Residues in contact with ILE 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B VAL* 2.9 34.1 + - + +
503B ILE* 3.3 9.2 + - + +
505B MET* 1.3 75.2 - - - +
507B TRP* 1.3 62.5 + - - +
509B GLU* 3.2 4.1 + - - +
510B CYS* 2.9 40.4 + - - -
534B LEU* 3.9 35.0 - - + +
538B ALA* 4.5 12.8 - - + -
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Residues in contact with TRP 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B ILE* 3.0 18.3 + - + +
504B GLY 3.4 3.1 + - - +
506B ILE* 1.3 79.8 - - - +
508B ALA* 1.3 54.9 + - - +
510B CYS* 3.3 6.5 + - + +
511B LYS* 3.0 56.6 + - + +
514B TRP* 3.6 35.4 - + - -
765B ASN* 3.9 29.1 + - + +
766B LEU* 3.9 26.6 - - + +
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Residues in contact with ALA 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B GLY 2.9 17.2 + - - +
505B MET* 3.9 4.2 + - + +
506B ILE 3.3 0.2 - - - -
507B TRP* 1.3 76.4 - - - +
509B GLU* 1.3 58.2 + - - +
511B LYS* 4.1 8.4 - - - +
512B GLU* 3.7 16.8 + - - +
762B VAL* 4.3 12.8 - - + -
765B ASN* 3.4 17.7 - - - +
1002B R0G 4.3 11.9 - - + +
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Residues in contact with GLU 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B MET 3.5 13.7 + - - +
506B ILE* 3.2 6.7 + - - +
507B TRP 3.1 0.6 - - - -
508B ALA* 1.3 77.3 - - - +
510B CYS* 1.3 61.1 + - - +
511B LYS 3.3 1.1 - - - -
512B GLU* 3.2 5.9 + - - +
513B ILE* 2.9 33.8 + - + +
521B TYR* 2.4 34.9 + - + +
527B ASN 3.8 8.0 - - - +
530B ASP* 3.5 16.1 - - - +
531B PHE* 4.4 15.4 + - + -
534B LEU* 4.1 10.1 - - + +
609B ARG* 4.3 2.9 + - - -
1002B R0G 3.1 37.8 + - - -
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Residues in contact with CYS 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B ILE* 2.9 32.2 + - - +
507B TRP* 3.9 10.5 - - + +
509B GLU* 1.3 74.8 - - - +
511B LYS* 1.3 59.9 + - - +
513B ILE* 3.1 15.5 + - - +
514B TRP* 3.0 58.7 + - + -
531B PHE* 6.3 2.2 - - - -
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Residues in contact with LYS 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B TRP* 3.0 50.2 + - + +
508B ALA* 4.4 7.6 - - - +
510B CYS* 1.3 77.3 - - - +
512B GLU* 1.3 58.6 + - - +
514B TRP* 3.7 19.8 + - + +
515B THR* 2.7 36.9 + - - -
758B ARG* 5.5 13.3 - - - +
765B ASN* 6.2 0.9 - - + +
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Residues in contact with GLU 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B ALA 3.7 13.2 + - - +
509B GLU* 3.2 10.7 + - - +
510B CYS 3.2 0.4 - - - -
511B LYS* 1.3 77.2 - - - +
513B ILE* 1.3 63.2 + - - +
515B THR* 4.7 4.3 - - - +
516B GLN* 3.2 35.2 + - + +
521B TYR* 4.0 20.2 - - + +
527B ASN* 4.4 8.3 + - - -
758B ARG* 4.1 18.2 + - - -
1002B R0G 3.8 30.9 - - + +
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Residues in contact with ILE 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B GLU* 2.9 21.9 + - + +
510B CYS* 3.1 21.0 + - - +
512B GLU* 1.3 76.4 - - - +
514B TRP* 1.3 63.6 + - + +
515B THR 3.2 0.2 - - - -
517B GLY* 3.1 30.3 + - - -
518B PRO* 3.8 20.3 - - + +
521B TYR* 3.7 42.4 - - + +
531B PHE* 5.2 12.6 - - + -
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Residues in contact with TRP 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B TRP* 3.6 42.4 - + - -
510B CYS* 3.0 39.8 + - + -
511B LYS* 3.7 24.6 - - + +
513B ILE* 1.3 81.9 - - + +
515B THR* 1.3 60.3 + - - +
517B GLY* 4.7 2.0 - - - -
518B PRO* 5.8 1.1 - - - -
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Residues in contact with THR 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511B LYS* 2.7 30.0 + - - -
512B GLU* 4.3 4.9 - - - +
513B ILE 3.2 0.8 - - - -
514B TRP* 1.3 84.4 + - - +
516B GLN* 1.3 61.7 + - - +
517B GLY 3.4 1.3 - - - -
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Residues in contact with GLN 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B GLU* 3.2 28.9 + - - +
515B THR* 1.3 76.6 - - - +
517B GLY* 1.3 64.1 + - - +
520B GLU* 3.7 20.0 - - + +
521B TYR* 4.9 11.2 - - + +
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Residues in contact with GLY 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B ILE 3.1 12.9 + - - -
514B TRP* 4.7 1.3 - - - -
515B THR 3.4 3.2 + - - +
516B GLN* 1.3 83.3 - - - +
518B PRO* 1.3 68.9 - - - +
519B LYS 3.1 11.9 + - - -
520B GLU 5.0 0.2 - - - -
521B TYR* 3.2 21.0 + - - +
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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