Contacts of the helix formed by residues 506 - 527 (chain C) in PDB entry 4AY6
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 SER 506 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480C VAL* 5.6 1.2 - - - +
505C LEU* 1.3 77.4 - - - +
507C HIS* 1.3 62.2 + - - +
508C GLY* 3.4 4.0 + - - -
509C PHE* 3.0 40.6 + - - +
510C ARG* 3.0 27.6 + - - +
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Residues in contact with HIS 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C LEU 5.4 1.3 + - - -
506C SER* 1.3 74.3 - - - +
508C GLY* 1.3 60.0 + - - +
510C ARG* 3.4 26.0 + - - +
511C LYS* 3.0 27.9 + - - +
680C GLU 5.8 0.9 - - - -
681C GLN* 3.5 48.9 + - + +
939C GLU* 2.8 51.7 + - + +
940C THR* 4.1 8.2 - - + +
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Residues in contact with GLY 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506C SER* 3.3 5.5 + - - -
507C HIS* 1.3 77.3 - - - +
509C PHE* 1.3 55.0 + - - +
511C LYS* 3.4 12.8 + - - +
512C ALA* 2.8 35.7 + - - +
680C GLU 6.0 0.4 - - - -
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Residues in contact with PHE 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C VAL* 4.4 13.0 - - + -
483C VAL* 4.1 10.8 - - + -
484C ALA* 3.5 43.1 - - + -
487C LEU* 3.7 19.8 - - + +
505C LEU* 4.1 17.5 - - + -
506C SER* 3.0 41.0 + - - +
508C GLY* 1.3 76.5 - - - +
510C ARG* 1.3 63.1 + - - +
512C ALA* 3.2 7.8 + - - +
513C ILE* 3.0 29.5 + - - +
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Residues in contact with ARG 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C PRO* 5.8 0.5 - - - +
500C SER* 3.0 48.2 + - - +
501C MET* 3.7 10.5 + - - +
503C TYR 3.0 22.8 + - - -
504C PRO* 4.5 1.6 - - - +
505C LEU* 3.4 30.6 + - + +
506C SER 3.0 14.9 + - - +
507C HIS* 3.4 37.4 + - - +
508C GLY 3.3 0.2 - - - -
509C PHE* 1.3 71.7 - - - +
511C LYS* 1.3 67.2 + - - +
513C ILE* 3.2 10.0 + - - +
514C ALA* 3.1 22.9 + - - +
658C THR* 5.3 4.3 - - + -
940C THR* 3.6 23.7 - - - +
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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
----------------------------------------------------------
507C HIS 3.0 17.0 + - - +
508C GLY* 3.7 9.8 - - - +
510C ARG* 1.3 77.1 - - - +
512C ALA* 1.3 57.7 + - - +
514C ALA* 3.4 2.4 + - - +
515C GLU* 2.8 33.3 + - + +
658C THR* 4.4 12.0 - - + +
660C GLY* 4.3 5.8 - - - -
680C GLU* 2.9 30.5 + - - +
681C GLN 3.6 20.4 - - - +
682C TYR 3.9 18.8 + - - +
683C SER* 4.0 17.0 - - - +
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Residues in contact with ALA 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C LEU* 3.7 21.8 - - + -
508C GLY 2.8 18.1 + - - +
509C PHE* 3.2 8.7 + - - +
511C LYS* 1.3 77.8 - - - +
513C ILE* 1.3 60.5 + - - +
515C GLU* 3.1 10.5 - - - +
516C ARG* 3.1 31.1 + - - +
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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
----------------------------------------------------------
483C VAL* 4.0 23.8 - - + -
487C LEU* 4.8 1.8 - - + -
493C PRO* 4.2 22.2 - - + -
495C VAL* 3.5 36.1 - - + +
497C PRO* 4.0 14.6 - - + -
500C SER* 4.3 20.0 - - - -
505C LEU* 4.4 10.8 - - + -
509C PHE 3.0 20.3 + - - +
510C ARG* 3.5 7.0 - - - +
512C ALA* 1.3 73.5 - - - +
514C ALA* 1.3 68.5 + - - +
516C ARG* 3.0 12.6 + - - +
517C HIS* 3.2 28.7 + - + +
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Residues in contact with ALA 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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497C PRO* 4.3 11.6 - - + +
510C ARG 3.1 9.5 + - - +
511C LYS* 3.5 10.1 - - - +
513C ILE* 1.3 80.6 - - - +
515C GLU* 1.3 52.1 + - - +
517C HIS* 3.2 4.1 + - - +
518C GLY 2.8 29.6 + - - -
632C TYR* 3.1 19.4 + - + -
655C TYR* 5.3 0.2 - - - +
658C THR* 3.7 20.0 - - + +
659C SER 3.4 19.0 - - - +
660C GLY* 3.9 2.2 - - - -
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Residues in contact with GLU 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* 2.8 20.7 + - + +
512C ALA* 3.1 16.4 - - - +
514C ALA* 1.3 71.2 - - - +
516C ARG* 1.3 69.7 + - - +
518C GLY* 3.0 15.4 + - - -
519C ASN* 3.1 38.7 + - - +
660C GLY* 3.3 24.6 - - - +
661C ALA* 5.5 0.3 - - - -
662C LEU* 4.3 15.9 - - - +
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Residues in contact with ARG 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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486C GLN 4.1 0.8 + - - -
487C LEU* 2.6 41.2 + - + +
490C ASN* 3.5 33.6 + - - -
491C ARG 3.0 28.7 + - - +
492C LEU* 3.8 21.3 - - + +
493C PRO* 4.0 12.3 - - + -
512C ALA* 3.1 15.9 + - - +
513C ILE 3.0 8.2 + - - +
515C GLU* 1.3 86.4 + - - +
517C HIS* 1.3 60.4 + - - +
519C ASN* 2.9 27.9 + - - +
520C LEU* 3.3 12.5 + - - +
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Residues in contact with HIS 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492C LEU* 4.0 27.7 - - + +
493C PRO* 4.1 8.9 + - + +
495C VAL 3.9 10.8 + - - -
496C HIS* 4.7 12.6 + + - -
497C PRO* 3.4 34.4 - - + +
513C ILE* 3.2 25.6 + - + +
514C ALA 3.2 7.0 + - - +
516C ARG* 1.3 73.8 - - + +
518C GLY* 1.3 65.1 + - - +
519C ASN 3.2 0.2 - - - -
520C LEU* 3.3 32.5 + - + +
521C CYS* 4.0 11.6 - - - -
632C TYR* 3.8 24.2 - - + -
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Residues in contact with GLY 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514C ALA 2.8 10.8 + - - -
515C GLU 3.0 8.9 + - - -
517C HIS* 1.3 78.7 - - - +
519C ASN* 1.3 60.9 + - - +
520C LEU 3.4 0.7 + - - -
521C CYS* 3.6 8.8 + - - +
522C LEU* 3.7 10.2 + - - +
632C TYR* 3.2 15.1 + - - -
661C ALA* 4.2 15.7 - - - -
663C PHE* 3.9 17.6 - - - -
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Residues in contact with ASN 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C GLU* 3.1 38.0 + - - +
516C ARG* 2.9 18.2 + - - +
518C GLY* 1.3 75.7 - - - +
520C LEU* 1.3 63.6 + - - +
521C CYS 3.3 0.2 - - - -
522C LEU* 3.3 29.0 + - + +
523C ASP* 2.9 32.0 - - - +
662C LEU* 4.9 4.9 - - - +
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Residues in contact with LEU 520 (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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363C GLN* 5.1 7.0 - - + +
492C LEU* 4.0 26.7 - - + -
516C ARG 3.3 10.4 + - - +
517C HIS* 3.5 33.2 - - + +
518C GLY 3.3 0.8 - - - -
519C ASN* 1.3 77.1 - - - +
521C CYS* 1.3 66.3 + - - +
523C ASP* 3.7 10.4 + - - +
524C LYS* 3.6 26.2 + - - +
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Residues in contact with CYS 521 (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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517C HIS 4.0 14.4 - - - -
518C GLY* 3.6 6.3 + - - +
519C ASN 3.3 0.2 - - - -
520C LEU* 1.3 75.1 - - - +
522C LEU* 1.3 67.4 + - - +
523C ASP 3.1 0.2 - - - -
524C LYS* 2.8 16.1 + - - +
525C ILE* 3.1 16.3 + - - +
632C TYR* 5.4 2.9 - - - -
638C ASN* 3.9 29.8 - - - -
639C GLU* 3.9 37.0 - - + +
642C ALA* 4.5 6.5 - - + -
663C PHE* 4.9 3.6 - - + -
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Residues in contact with LEU 522 (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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518C GLY 3.7 11.4 + - - +
519C ASN* 3.3 35.0 + - + +
520C LEU 3.3 0.2 - - - -
521C CYS* 1.3 78.9 - - - +
523C ASP* 1.3 61.3 + - - +
525C ILE* 3.5 18.7 - - + +
526C ASN* 3.0 42.0 + - - +
642C ALA* 4.8 7.2 - - + +
661C ALA* 6.4 0.4 - - + -
662C LEU* 5.0 14.4 - - + -
663C PHE* 4.8 18.8 - - + -
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Residues in contact with ASP 523 (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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333C ILE* 5.7 6.3 - - + +
363C GLN* 4.9 22.2 + - + +
364C GLN* 4.5 5.8 - - + +
519C ASN* 2.9 22.0 - - - +
520C LEU* 4.1 12.2 - - + +
521C CYS 3.1 1.0 - - - -
522C LEU* 1.3 79.2 - - - +
524C LYS* 1.3 64.5 + - - +
525C ILE 3.2 2.7 + - - -
526C ASN* 3.6 12.8 + - - +
527C VAL* 3.4 23.0 - - - +
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Residues in contact with LYS 524 (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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362C GLN 4.7 2.0 + - - -
363C GLN 3.7 19.0 + - - +
364C GLN 3.9 14.7 - - - +
365C GLY* 3.8 17.4 - - - -
367C LEU* 6.3 0.2 - - - -
397C GLU* 3.4 25.9 + - - -
520C LEU* 3.6 14.3 + - - +
521C CYS* 2.8 9.1 + - - +
523C ASP* 1.3 79.6 - - - +
525C ILE* 1.3 59.4 + - - +
527C VAL* 3.8 14.4 - - - +
528C LEU* 4.3 5.5 - - - +
611C ASN* 5.7 1.3 + - - +
639C GLU* 3.2 31.4 + - + +
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Residues in contact with ILE 525 (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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521C CYS 3.1 7.3 + - - +
522C LEU* 3.5 23.1 - - + +
524C LYS* 1.3 80.1 - - - +
526C ASN* 1.3 74.3 + - - +
527C VAL 3.0 3.1 - - - -
528C LEU* 2.9 31.5 + - + +
529C HIS 3.9 1.7 + - - -
530C LYS* 5.2 1.4 + - - +
611C ASN* 4.8 2.9 - - + +
639C GLU* 3.6 40.8 - - + +
642C ALA* 4.2 23.3 - - + +
643C LEU* 3.8 32.9 - - + +
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Residues in contact with ASN 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C GLU* 6.1 1.1 - - - +
522C LEU* 3.0 35.4 + - - +
523C ASP* 3.6 13.7 + - - +
525C ILE* 1.3 83.6 - - - +
527C VAL* 1.3 59.0 + - + +
528C LEU 3.1 0.2 - - - -
529C HIS* 3.2 32.0 + - - +
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Residues in contact with VAL 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C GLN* 3.6 50.5 - - + +
366C LYS* 4.2 28.7 - - + +
523C ASP 3.4 17.3 - - - +
524C LYS 3.8 11.2 - - - +
525C ILE 3.0 1.2 - - - -
526C ASN* 1.3 78.3 - - + +
528C LEU* 1.3 62.9 + - + +
529C HIS* 3.4 16.1 + - + -
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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
------------------------------------------------------------
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