Contacts of the helix formed by residues 496 - 517 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491C PHE* 3.8 31.2 - - + -
492C SER 3.3 19.7 + - - +
493C TRP* 4.6 6.3 - - - +
494C MET* 3.3 0.6 - - - +
495C GLU* 1.3 77.9 - - - +
497C LEU* 1.3 63.3 + - + +
498C ILE 3.2 1.1 - - - -
499C ILE* 3.2 18.0 + - + +
500C SER* 2.9 27.5 + - - -
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Residues in contact with LEU 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456C LEU* 3.8 22.2 - - + -
493C TRP* 3.3 33.9 - - + +
494C MET* 3.8 7.9 + - - +
496C MET* 1.3 79.8 - - + +
498C ILE* 1.3 59.8 + - - +
500C SER* 2.6 25.6 + - - +
501C TRP* 2.9 42.4 + - + -
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Residues in contact with ILE 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C PHE* 3.9 18.8 - - + -
456C LEU* 4.2 22.7 - - + +
457C LEU* 4.1 15.7 - - + -
460C ASN* 4.1 20.9 - - + +
494C MET 3.3 20.1 + - - +
495C GLU* 4.4 8.1 - - - +
496C MET 3.2 0.4 - - - -
497C LEU* 1.3 75.1 - - - +
499C ILE* 1.3 59.0 + - - +
501C TRP* 3.4 6.3 + - - +
502C VAL* 2.9 37.0 + - + +
537C PHE* 4.6 4.0 - - + -
541C PHE* 3.8 22.9 - - + -
599C TYR* 3.9 22.0 - - + +
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Residues in contact with ILE 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C PHE* 3.7 30.3 - - + -
495C GLU 3.3 19.5 - - - +
496C MET* 3.2 25.4 + - + +
498C ILE* 1.3 77.7 - - - +
500C SER* 1.3 55.5 + - - +
502C VAL* 3.3 2.2 + - - +
503C ILE* 2.9 47.6 + - + +
541C PHE* 3.9 36.3 - - + -
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Residues in contact with SER 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496C MET 2.9 12.3 + - - -
497C LEU* 2.6 31.5 + - - +
499C ILE* 1.3 77.4 - - - +
501C TRP* 1.3 64.2 + - - +
503C ILE* 3.4 7.9 + - - +
504C GLY* 3.0 25.8 + - - -
763C PRO* 5.1 8.1 - - - +
766C LEU* 4.4 8.7 - - - +
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Residues in contact with TRP 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C LEU* 5.3 2.0 - - + -
449C SER* 3.1 26.7 + - - -
452C ILE* 3.6 37.5 - - + -
453C PHE* 3.8 36.6 - + + +
456C LEU* 4.1 12.8 - - + -
497C LEU* 2.9 53.0 + - + +
498C ILE 3.4 5.1 + - - +
500C SER* 1.3 90.0 + - - +
502C VAL* 1.3 57.5 + - - +
504C GLY* 3.5 1.1 + - - -
505C MET* 2.9 37.5 + - + +
762C VAL* 3.6 20.8 - - + +
763C PRO* 3.7 35.4 - - + -
764C PHE* 6.1 1.6 - + - -
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Residues in contact with VAL 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C PHE* 4.3 14.4 - - + -
498C ILE* 2.9 22.7 + - + +
499C ILE* 3.9 3.8 - - - +
501C TRP* 1.3 75.8 - - - +
503C ILE* 1.3 58.9 + - + +
505C MET* 3.7 7.2 - - + +
506C ILE* 2.9 46.2 + - + +
534C LEU* 4.3 11.9 - - + +
537C PHE* 3.9 44.0 - - + -
538C ALA* 4.9 3.1 - - - +
541C PHE* 4.1 15.7 - - + -
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Residues in contact with ILE 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499C ILE* 2.9 37.9 + - + +
500C SER* 3.8 6.5 - - - +
502C VAL* 1.3 78.1 - - + +
504C GLY* 1.3 57.8 + - - +
506C ILE* 3.3 9.7 + - + +
507C TRP* 3.0 27.8 + - + +
766C LEU* 3.8 22.4 - - + -
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Residues in contact with GLY 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500C SER 3.0 14.6 + - - -
501C TRP 3.9 0.2 - - - -
503C ILE* 1.3 78.5 - - - +
505C MET* 1.3 55.8 + - - +
507C TRP* 3.8 0.3 - - - +
508C ALA* 2.9 30.3 + - - +
762C VAL* 3.5 22.7 - - - -
765C ASN* 3.5 12.4 + - - -
766C LEU* 4.0 14.5 - - - +
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Residues in contact with MET 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450C PHE* 6.2 1.3 - - + -
453C PHE* 4.3 24.9 - - + -
501C TRP* 2.9 43.1 + - + +
502C VAL* 3.7 6.1 - - - +
504C GLY* 1.3 73.7 - - - +
506C ILE* 1.3 62.4 + - - +
508C ALA* 4.0 2.5 - - - +
509C GLU* 3.5 15.9 + - - +
533C MET* 4.7 6.5 - - - +
534C LEU* 3.5 35.4 - - + +
609C ARG* 3.5 45.3 + - - +
762C VAL* 3.7 20.4 - - + +
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Residues in contact with ILE 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C VAL* 2.9 34.8 + - + +
503C ILE* 3.3 9.4 + - + +
505C MET* 1.3 74.6 - - - +
507C TRP* 1.3 61.4 + - - +
509C GLU* 3.2 3.9 + - - +
510C CYS* 2.9 40.6 + - - -
534C LEU* 3.9 35.2 - - + +
538C ALA* 4.5 12.6 - - + -
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Residues in contact with TRP 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C ILE* 3.0 16.6 + - + +
504C GLY 3.8 2.7 - - - +
506C ILE* 1.3 79.9 - - - +
508C ALA* 1.3 55.7 + - - +
510C CYS* 3.3 7.1 + - + +
511C LYS* 3.0 56.1 + - + +
514C TRP* 3.6 35.7 - + - -
765C ASN* 3.9 28.0 + - + +
766C LEU* 3.9 26.6 - - + +
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Residues in contact with ALA 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504C GLY 2.9 17.9 + - - +
505C MET* 4.2 4.3 - - - +
507C TRP* 1.3 76.0 - - - +
509C GLU* 1.3 58.0 + - - +
511C LYS* 4.1 9.2 - - - +
512C GLU* 3.7 16.8 + - - +
762C VAL* 4.3 13.0 - - + -
765C ASN* 3.4 17.0 - - - +
1002C R0G 4.3 11.9 - - + +
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Residues in contact with GLU 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C MET 3.5 14.6 + - - +
506C ILE* 3.2 6.4 + - - +
507C TRP 3.1 0.4 - - - -
508C ALA* 1.3 76.5 - - - +
510C CYS* 1.3 61.2 + - - +
511C LYS 3.3 0.9 - - - -
512C GLU* 3.2 5.1 + - - +
513C ILE* 2.9 34.0 + - + +
521C TYR* 2.4 34.2 + - + +
527C ASN 3.8 8.3 - - - +
530C ASP* 3.5 15.4 - - - +
531C PHE* 4.4 15.6 + - + -
534C LEU* 4.1 10.2 - - + +
609C ARG* 4.3 2.9 + - - -
1002C R0G 3.1 38.6 + - - -
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Residues in contact with CYS 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506C ILE* 2.9 32.4 + - - +
507C TRP* 3.3 10.7 + - + +
509C GLU* 1.3 74.3 - - - +
511C LYS* 1.3 60.9 + - - +
513C ILE* 3.1 15.6 + - - +
514C TRP* 3.0 57.9 + - + -
531C PHE* 6.3 2.7 - - - -
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Residues in contact with LYS 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507C TRP* 3.0 48.6 + - + +
508C ALA* 4.4 7.9 - - - +
510C CYS* 1.3 77.3 - - - +
512C GLU* 1.3 59.2 + - - +
514C TRP* 3.7 20.1 + - - +
515C THR* 2.7 36.3 + - - -
758C ARG* 5.5 12.9 - - - +
765C ASN* 6.2 0.2 - - - +
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Residues in contact with GLU 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508C ALA 3.7 13.0 + - - +
509C GLU* 3.2 9.9 + - - +
510C CYS 3.2 0.4 - - - -
511C LYS* 1.3 78.1 - - - +
513C ILE* 1.3 63.4 + - - +
515C THR* 4.7 3.7 - - - -
516C GLN* 3.2 35.2 + - + +
521C TYR* 4.0 19.0 - - + -
527C ASN* 4.4 8.1 + - - -
758C ARG* 4.1 18.5 + - - -
1002C R0G 3.8 32.1 - - + +
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Residues in contact with ILE 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509C GLU* 2.9 21.0 + - + +
510C CYS* 3.1 20.8 + - - +
512C GLU* 1.3 77.0 - - - +
514C TRP* 1.3 63.1 + - + +
517C GLY* 3.1 30.0 + - - -
518C PRO* 3.8 20.1 - - + +
521C TYR* 3.7 43.5 - - + +
531C PHE* 5.2 12.1 - - + -
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Residues in contact with TRP 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507C TRP* 3.6 42.0 - + - -
510C CYS* 3.0 40.3 + - + -
511C LYS* 3.7 23.6 - - + +
512C GLU 3.5 0.2 - - - -
513C ILE* 1.3 79.9 - - + +
515C THR* 1.3 59.1 + - - +
517C GLY* 4.7 1.8 - - - -
518C PRO* 5.8 1.6 - - - -
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Residues in contact with THR 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511C LYS* 2.7 29.0 + - - -
512C GLU* 4.3 4.9 - - - +
513C ILE 3.2 0.8 - - - -
514C TRP* 1.3 84.3 + - - +
516C GLN* 1.3 63.3 + - - +
517C GLY 3.4 1.1 - - - -
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Residues in contact with GLN 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512C GLU* 3.2 29.0 + - - +
515C THR* 1.3 75.8 - - + +
517C GLY* 1.3 65.5 + - - +
520C GLU* 3.7 20.8 - - + +
521C TYR* 4.9 10.5 - - + +
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Residues in contact with GLY 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513C ILE 3.1 13.7 + - - -
514C TRP* 5.3 1.1 - - - -
515C THR 3.4 3.4 + - - +
516C GLN* 1.3 82.1 - - - +
518C PRO* 1.3 70.0 - - - +
519C LYS 3.1 10.9 + - - -
520C GLU 4.2 0.4 - - - -
521C 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