Contacts of the helix formed by residues 506 - 527 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480B VAL* 5.7 1.2 - - - +
505B LEU* 1.3 78.6 - - - +
507B HIS* 1.3 61.8 + - - +
508B GLY* 3.4 4.1 + - - -
509B PHE* 3.0 38.3 + - - +
510B ARG* 3.0 28.4 + - - +
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Residues in contact with HIS 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B LEU 5.4 1.1 + - - -
506B SER* 1.3 74.1 - - - +
508B GLY* 1.3 60.8 + - - +
510B ARG* 3.5 26.3 + - - +
511B LYS* 3.0 26.7 + - - +
680B GLU 5.7 1.1 - - - +
681B GLN* 3.4 47.9 + - + +
939B GLU* 2.7 57.5 + - + +
940B THR* 4.1 4.0 - - + +
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Residues in contact with GLY 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B SER* 3.3 4.8 + - - -
507B HIS* 1.3 77.6 - - - +
509B PHE* 1.3 60.9 + - - +
511B LYS* 3.4 13.9 + - - +
512B ALA* 2.8 30.6 + - - +
680B GLU 5.9 0.7 - - - -
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Residues in contact with PHE 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B VAL* 4.3 12.6 - - + -
483B VAL* 4.2 10.3 - - + -
484B ALA* 3.5 43.3 - - + -
487B LEU* 3.7 20.5 - - + +
505B LEU* 4.1 17.5 - - + -
506B SER* 3.0 36.1 + - - +
508B GLY* 1.3 77.7 - - - +
510B ARG* 1.3 62.9 + - - +
512B ALA* 3.0 7.6 + - + +
513B ILE* 3.0 28.3 + - - +
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Residues in contact with ARG 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B PRO* 5.8 0.7 - - - +
500B SER* 3.0 46.1 + - - +
501B MET* 3.7 10.7 + - - +
503B TYR 3.0 22.2 + - - -
504B PRO* 4.5 2.2 - - - +
505B LEU* 3.5 26.3 + - + +
506B SER 3.0 20.5 + - - +
507B HIS* 3.5 35.9 + - - +
508B GLY 3.3 0.2 - - - -
509B PHE* 1.3 77.0 - - - +
511B LYS* 1.3 62.2 + - - +
513B ILE* 3.3 9.7 + - - +
514B ALA* 3.2 21.8 + - - +
658B THR* 5.2 4.0 - - + +
940B THR* 3.7 23.6 - - - +
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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
----------------------------------------------------------
507B HIS 3.0 16.5 + - - +
508B GLY* 3.8 11.4 - - - +
510B ARG* 1.3 76.4 - - - +
512B ALA* 1.3 57.4 + - - +
514B ALA* 3.4 2.0 + - - +
515B GLU* 2.8 34.4 + - + +
658B THR* 4.4 15.0 - - + +
660B GLY* 4.3 3.3 - - - +
680B GLU* 2.9 30.4 + - - +
681B GLN 3.7 20.2 + - - +
682B TYR 3.9 17.5 + - - +
683B SER* 4.0 16.8 - - - +
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Residues in contact with ALA 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B LEU* 3.7 24.5 - - + -
508B GLY 2.8 19.7 + - - +
509B PHE* 3.0 8.0 + - - +
511B LYS* 1.3 78.4 - - - +
513B ILE* 1.3 57.7 + - - +
515B GLU* 3.1 23.3 - - - +
516B ARG* 3.1 18.0 + - - +
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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
----------------------------------------------------------
483B VAL* 4.0 23.1 - - + -
487B LEU* 4.9 1.6 - - + -
493B PRO* 4.2 22.4 - - + -
495B VAL* 3.5 38.6 - - + +
497B PRO* 4.0 15.7 - - + -
500B SER* 4.2 16.8 - - - -
505B LEU* 4.5 10.8 - - + -
509B PHE 3.0 17.5 + - - +
510B ARG* 3.6 7.0 - - - +
511B LYS 3.2 0.2 - - - -
512B ALA* 1.3 73.4 - - - +
514B ALA* 1.3 60.0 + - - +
516B ARG* 2.8 22.5 + - - +
517B HIS* 3.2 29.5 + - + -
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Residues in contact with ALA 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B PRO* 4.3 12.3 - - + +
510B ARG 3.2 9.4 + - - +
511B LYS* 3.5 10.3 - - - +
513B ILE* 1.3 78.9 - - - +
515B GLU* 1.3 64.5 + - - +
516B ARG 3.0 0.5 + - - -
517B HIS* 3.1 2.8 + - - -
518B GLY 2.8 19.6 + - - -
632B TYR* 3.1 16.8 + - + -
655B TYR* 5.4 0.4 - - - +
658B THR* 3.7 19.3 - - + +
659B SER 3.6 20.4 - - - +
660B GLY* 3.9 2.2 - - - -
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Residues in contact with GLU 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* 2.8 21.4 + - + +
512B ALA* 3.1 18.8 - - - +
514B ALA* 1.3 72.2 - - - +
516B ARG* 1.3 71.5 + - - +
518B GLY* 3.2 4.3 + - - -
519B ASN* 3.2 43.4 + - - +
660B GLY* 3.2 24.8 - - - +
661B ALA* 5.5 0.2 - - - -
662B LEU* 4.3 18.4 - - - +
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Residues in contact with ARG 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B GLN 4.0 1.2 + - - -
487B LEU* 2.7 42.3 + - + +
490B ASN* 3.5 34.6 + - - -
491B ARG 3.1 28.7 + - - -
492B LEU* 3.9 21.8 - - + +
493B PRO* 4.0 13.0 - - + +
512B ALA* 3.1 15.8 + - - +
513B ILE 2.8 14.8 + - - +
515B GLU* 1.3 79.1 + - - +
517B HIS* 1.3 59.1 + - - +
518B GLY 3.1 1.3 - - - -
519B ASN* 2.9 27.4 + - - +
520B LEU* 3.3 12.6 + - - +
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Residues in contact with HIS 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B LEU* 4.0 28.2 - - + +
493B PRO* 4.1 8.4 + - + +
495B VAL 4.0 11.2 + - - -
496B HIS* 4.9 11.4 + + - -
497B PRO* 3.4 34.6 - - + +
513B ILE* 3.2 25.2 + - + +
514B ALA 3.1 6.1 + - - +
516B ARG* 1.3 73.6 - - + +
518B GLY* 1.3 65.7 + - - +
520B LEU* 3.3 34.5 + - + +
521B CYS* 3.9 10.9 + - - -
632B TYR* 3.7 23.5 - - + -
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Residues in contact with GLY 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B ALA 2.8 11.2 + - - -
515B GLU 3.3 7.4 - - - -
516B ARG 3.1 0.2 - - - -
517B HIS* 1.3 78.5 - - - +
519B ASN* 1.3 62.4 + - - +
520B LEU 3.3 0.7 + - - -
521B CYS* 3.6 9.2 + - - +
522B LEU* 3.7 13.9 + - - +
632B TYR* 3.1 15.6 + - - -
661B ALA* 4.3 16.4 - - - -
663B PHE* 4.0 13.3 - - - -
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Residues in contact with ASN 519 (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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515B GLU* 3.2 38.2 + - - +
516B ARG* 2.9 20.2 + - - +
518B GLY* 1.3 76.2 - - - +
520B LEU* 1.3 61.4 + - - +
521B CYS 3.3 0.4 - - - -
522B LEU* 3.2 30.1 + - + +
523B ASP* 2.9 30.7 - - - +
662B LEU* 4.8 5.0 - - - +
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Residues in contact with LEU 520 (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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363B GLN* 5.1 7.7 - - + +
492B LEU* 4.1 26.7 - - + -
516B ARG 3.3 10.8 + - - +
517B HIS* 3.3 32.2 + - + +
518B GLY 3.2 1.2 - - - -
519B ASN* 1.3 74.3 - - - +
521B CYS* 1.3 68.9 + - - +
523B ASP* 3.7 11.3 + - - +
524B LYS* 3.6 26.2 + - - +
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Residues in contact with CYS 521 (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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517B HIS 4.0 12.8 - - - -
518B GLY* 3.6 6.9 + - - +
519B ASN 3.3 0.2 - - - -
520B LEU* 1.3 77.2 - - - +
522B LEU* 1.3 60.7 + - - +
524B LYS* 2.8 22.4 + - - +
525B ILE* 3.2 16.1 + - - +
632B TYR* 5.4 2.9 - - - -
638B ASN* 4.0 28.5 - - + -
639B GLU* 4.0 39.5 - - + +
642B ALA* 4.4 6.7 - - + -
663B PHE* 4.9 3.6 - - + -
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Residues in contact with LEU 522 (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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518B GLY 3.7 11.6 + - - +
519B ASN* 3.2 36.1 + - + +
521B CYS* 1.3 77.6 - - - +
523B ASP* 1.3 64.2 + - - +
525B ILE* 3.6 17.8 - - + +
526B ASN* 2.8 39.0 + - - +
642B ALA* 4.9 7.2 - - + +
662B LEU* 4.9 15.7 - - + -
663B PHE* 4.9 16.6 - - + -
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Residues in contact with ASP 523 (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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333B ILE* 5.6 6.3 - - + +
363B GLN* 4.7 24.8 + - - +
364B GLN* 4.5 5.4 - - + +
519B ASN* 2.9 21.5 + - - +
520B LEU* 4.1 12.5 - - - +
521B CYS 3.1 0.8 - - - -
522B LEU* 1.3 80.5 - - - +
524B LYS* 1.3 64.4 + - - +
525B ILE 3.2 1.4 + - - -
526B ASN* 3.6 12.4 + - - +
527B VAL* 3.5 22.9 - - - +
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Residues in contact with LYS 524 (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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362B GLN 4.7 2.4 + - - -
363B GLN* 3.8 19.5 + - - +
364B GLN 3.8 15.5 - - - +
365B GLY* 3.8 18.1 - - - -
397B GLU* 3.4 25.8 + - - -
520B LEU* 3.6 15.2 + - - +
521B CYS 2.8 9.5 + - - +
523B ASP* 1.3 80.6 - - - +
525B ILE* 1.3 60.1 + - - +
527B VAL* 3.7 14.7 - - - +
528B LEU* 4.4 4.9 - - - +
611B ASN* 5.6 2.2 + - - +
639B GLU* 3.2 30.4 + - + +
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Residues in contact with ILE 525 (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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521B CYS 3.2 10.3 + - - +
522B LEU* 3.6 20.2 - - + +
524B LYS* 1.3 80.3 - - - +
526B ASN* 1.3 75.1 + - - +
527B VAL 3.0 2.9 - - - -
528B LEU* 2.8 30.8 + - + +
529B HIS 3.8 1.7 + - - -
530B LYS* 5.2 1.6 + - - +
611B ASN* 4.8 2.7 - - + +
639B GLU* 3.6 40.8 - - + +
642B ALA* 4.3 22.0 - - + +
643B LEU* 3.9 32.5 - - + +
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Residues in contact with ASN 526 (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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334B GLU* 6.1 0.9 - - - +
522B LEU* 2.8 35.1 + - - +
523B ASP* 3.6 14.1 + - - +
525B ILE* 1.3 83.4 - - - +
527B VAL* 1.3 58.4 - - + +
528B LEU 3.1 0.2 - - - -
529B HIS* 3.2 30.8 + - - -
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Residues in contact with VAL 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLU* 6.1 0.7 - - - +
364B GLN* 3.7 46.4 - - + +
366B LYS* 4.2 26.8 - - + +
523B ASP 3.5 16.2 - - - +
524B LYS 3.7 17.7 - - - +
525B ILE 3.0 1.4 + - - -
526B ASN* 1.3 77.0 - - + +
528B LEU* 1.3 65.6 + - + +
529B HIS* 3.4 17.2 + - - -
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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