Contacts of the helix formed by residues 508 - 526 (chain B) in PDB entry 4Z4Q
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 ASP 508 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B GLU* 4.3 1.9 - - - +
506B ASP* 2.8 38.5 + - + +
507B ALA* 1.3 79.5 - - - +
509B THR* 1.3 65.2 + - - +
510B ASP* 3.6 11.8 + - - +
511B GLY 3.1 18.9 + - - -
512B ALA* 3.0 19.8 + - - +
581B LYS 3.7 16.7 - - - +
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Residues in contact with THR 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B ASP* 1.3 75.7 - - - +
510B ASP* 1.3 65.3 + - - +
512B ALA* 3.0 10.7 - - - +
513B HIS 2.9 22.7 + - - -
1019B ARG* 3.9 19.5 - - + +
1020B TYR* 3.7 17.4 - - - +
1023B TYR* 3.4 57.5 - - + -
1028B ARG* 4.8 0.3 + - - -
1076B HIS* 5.9 0.5 - - - -
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Residues in contact with ASP 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B GLU* 4.6 8.1 - - - +
458B LYS* 3.1 26.8 + - + +
508B ASP* 3.3 10.8 + - - +
509B THR* 1.3 78.5 + - - +
511B GLY* 1.3 60.3 + - - +
513B HIS* 3.5 8.5 + - - +
514B ILE* 3.1 30.1 + - + +
1020B TYR* 3.7 5.6 - - - -
1028B ARG* 2.6 34.7 + - - -
1076B HIS* 4.4 13.9 + - - -
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Residues in contact with GLY 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B GLU* 3.7 16.4 - - - -
505B THR* 3.7 21.9 + - - -
506B ASP 3.7 4.9 - - - -
508B ASP* 3.1 13.3 + - - -
510B ASP* 1.3 74.7 - - - +
512B ALA* 1.3 67.8 + - - +
514B ILE* 3.1 3.8 + - - +
515B GLN* 2.9 28.1 + - - +
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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
----------------------------------------------------------
506B ASP 4.6 0.4 + - - -
508B ASP 3.0 11.9 + - - +
509B THR* 3.0 18.4 - - - +
511B GLY* 1.3 77.3 - - - +
513B HIS* 1.3 59.8 + - - +
515B GLN* 3.3 8.7 + - - +
516B THR* 3.2 16.0 + - - -
1016B ARG* 3.7 51.5 - - - +
1019B ARG* 4.4 9.2 - - + -
1020B TYR 4.8 0.2 - - - +
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Residues in contact with HIS 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B LYS* 3.0 29.0 + - + +
509B THR 2.9 5.9 + - - -
510B ASP 3.6 8.5 - - - +
511B GLY 3.1 0.2 - - - -
512B ALA* 1.3 76.1 - - - +
514B ILE* 1.3 57.8 + - - +
516B THR* 2.9 37.4 - - + +
517B LEU* 3.0 36.3 + - + +
622B MET* 5.1 1.2 - - - +
1016B ARG 5.5 0.4 - - - -
1017B PHE* 4.6 9.5 - + - -
1020B TYR* 3.1 59.9 - + + +
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Residues in contact with ILE 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B GLU* 3.7 35.9 - - + +
455B LEU* 4.7 9.9 - - + +
457B GLY 4.7 11.9 - - - +
458B LYS* 4.5 26.2 - - + +
459B VAL* 4.7 8.5 - - + +
505B THR* 3.8 15.5 - - + -
510B ASP* 3.1 16.5 + - + +
511B GLY 3.1 7.0 + - - +
513B HIS* 1.3 78.1 - - - +
515B GLN* 1.3 63.7 + - - +
517B LEU* 3.2 9.3 + - + +
518B LEU* 3.0 46.6 + - + +
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Residues in contact with GLN 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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503B ILE* 4.4 14.5 - - + +
505B THR* 3.1 29.7 + - + +
506B ASP 4.8 1.2 + - - -
507B ALA* 6.1 0.8 - - - +
511B GLY 2.9 21.6 + - - +
512B ALA* 3.5 7.0 - - - +
514B ILE* 1.3 76.5 - - - +
516B THR* 1.3 62.1 + - - +
518B LEU* 4.0 1.1 - - - +
519B LEU* 3.1 33.0 + - + +
537B ILE* 3.5 44.2 - - + +
538B ALA 5.2 2.4 + - - -
1016B ARG* 3.1 37.9 + - + +
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Residues in contact with THR 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B ALA 3.2 9.1 + - - -
513B HIS* 2.9 17.9 + - + +
515B GLN* 1.3 80.6 - - - +
517B LEU* 1.3 54.5 + - + +
519B LEU* 5.2 0.7 - - - -
520B THR* 2.6 35.1 + - + +
622B MET* 2.8 44.2 - - + -
1013B MET* 3.7 18.3 - - - +
1016B ARG* 3.9 5.4 - - - +
1017B PHE* 3.8 32.1 + - + +
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Residues in contact with LEU 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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458B LYS* 4.9 4.7 - - + -
459B VAL* 3.4 45.9 - - + +
460B ILE 4.8 4.4 - - - +
461B ASN* 3.8 25.7 - - + +
462B THR* 4.7 2.3 + - - -
513B HIS* 3.0 50.8 + - + +
514B ILE* 3.2 9.2 + - + +
516B THR* 1.3 80.6 - - - +
518B LEU* 1.3 62.4 - - - +
520B THR* 3.3 9.6 + - - -
521B PHE* 3.2 20.1 + - - +
622B MET* 3.6 19.5 - - + -
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Residues in contact with LEU 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B LEU* 4.4 6.1 - - + -
455B LEU* 3.5 28.0 - - + -
459B VAL* 4.5 15.0 - - + -
476B ILE* 6.4 0.2 - - + -
479B MET* 3.8 33.4 - - + -
503B ILE* 3.8 31.4 - - + -
514B ILE* 3.0 40.9 + - + +
515B GLN 4.0 2.7 - - - +
517B LEU* 1.3 76.3 - - - +
519B LEU* 1.3 57.7 + - - +
521B PHE* 3.0 11.2 + - + +
522B PHE* 3.0 34.0 + - + -
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Residues in contact with LEU 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B ILE* 4.1 11.4 - - + -
515B GLN* 3.1 26.8 + - + +
516B THR* 3.8 3.6 - - - +
518B LEU* 1.3 75.0 - - - +
520B THR* 1.3 59.0 + - - +
522B PHE* 3.4 7.2 + - + +
523B TYR* 2.9 30.7 + - - +
530B VAL* 6.2 3.4 - - + -
535B VAL* 4.1 26.0 - - + -
537B ILE* 4.1 23.1 - - + -
606B VAL* 4.5 11.2 - - + -
1009B LEU* 4.2 29.2 - - + +
1012B ILE* 4.2 20.2 - - + -
1013B MET* 4.3 10.1 - - + -
1016B ARG* 6.2 0.2 - - + -
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Residues in contact with THR 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B ASN* 4.2 6.1 + - - -
462B THR* 3.9 6.1 + - - -
463B ALA* 4.0 16.1 - - - +
516B THR 2.6 30.9 + - - +
517B LEU* 3.7 5.6 + - - +
518B LEU 3.3 0.2 - - - -
519B LEU* 1.3 74.7 - - - +
521B PHE* 1.3 58.3 + - - +
523B TYR* 4.0 6.5 - - - -
524B ARG* 2.8 34.1 + - - +
618B VAL* 3.9 20.2 - - - -
622B MET* 3.6 17.2 - - + +
1013B MET* 3.3 24.2 - - + -
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Residues in contact with PHE 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B VAL* 6.1 1.6 - - + -
460B ILE 5.6 0.7 - - - +
462B THR* 3.4 27.6 - - + +
470B ILE* 5.2 1.6 - - + -
476B ILE* 3.2 58.1 - - + -
479B MET* 5.0 13.5 - - + -
480B ILE* 5.6 4.0 - - + -
487B VAL* 5.4 6.5 - - + -
517B LEU 3.2 9.6 + - - +
518B LEU* 3.0 13.9 + - + +
520B THR* 1.3 75.8 + - - +
522B PHE* 1.3 80.2 + + - +
523B TYR 3.0 1.6 - - - -
524B ARG* 3.3 1.0 + - - -
525B TYR* 2.8 54.5 + + + +
526B MET* 4.1 25.4 - - + -
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Residues in contact with PHE 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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431B LEU* 3.7 22.4 - - + -
479B MET* 3.6 26.7 - - + -
483B ILE* 4.5 11.2 - - + -
501B ILE* 4.1 16.4 - - + -
503B ILE* 4.6 10.1 - - + -
518B LEU* 3.0 27.1 + - + +
519B LEU* 3.4 9.8 + - + +
521B PHE* 1.3 90.9 - + - +
523B TYR* 1.3 56.4 + - - +
526B MET* 2.8 63.3 + - + +
527B ARG* 3.1 2.3 + - - -
529B LEU* 5.8 2.0 - - + -
530B VAL* 4.7 9.6 - - + +
535B VAL* 4.3 28.3 - - + -
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Residues in contact with TYR 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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519B LEU 2.9 19.3 + - - +
520B THR* 4.1 6.3 - - - +
522B PHE* 1.3 79.7 - - - +
524B ARG* 1.3 84.1 + - + +
525B TYR 3.3 0.5 + - - -
527B ARG* 3.5 25.2 - - + +
530B VAL* 5.4 4.9 - - + -
608B ILE* 4.2 22.0 - - + -
611B LEU* 3.7 23.8 - - + +
614B ALA* 4.4 10.1 - - + -
615B GLU* 2.8 41.5 + - - +
618B VAL* 4.7 13.5 - - + -
619B ASN* 6.0 0.2 - - - -
1009B LEU* 3.1 34.1 - - + -
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Residues in contact with ARG 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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462B THR 2.9 26.3 + - - +
463B ALA* 3.9 26.5 - - + +
488B GLY* 5.5 1.4 - - - -
520B THR* 2.8 26.5 + - - +
521B PHE* 4.0 0.4 - - - +
523B TYR* 1.3 97.9 - - + +
525B TYR* 1.3 88.0 + - + +
527B ARG* 5.2 1.2 + - - +
615B GLU* 5.7 2.9 - - - -
618B VAL* 5.1 6.3 - - - -
619B ASN* 5.0 9.2 + - - -
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Residues in contact with TYR 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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462B THR* 3.9 15.2 + - + -
467B MET* 3.9 26.9 - - + +
470B ILE* 4.0 15.9 - - + +
487B VAL* 3.9 8.5 - - + -
488B GLY* 3.0 45.2 + - - +
491B PHE* 4.5 0.7 - - - -
521B PHE* 2.8 45.2 + + + +
524B ARG* 1.3 109.3 + - + +
526B MET* 1.3 69.8 + - - +
527B ARG 3.9 1.1 - - - -
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Residues in contact with MET 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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479B MET 5.3 0.7 - - - +
480B ILE* 5.3 9.4 - - - -
483B ILE* 3.8 37.2 - - + -
486B GLY 4.5 8.3 - - - +
487B VAL* 4.9 2.5 - - - -
491B PHE* 3.2 42.4 - - + -
521B PHE* 3.8 26.7 + - + -
522B PHE* 2.8 36.5 + - + +
525B TYR* 1.3 90.6 - - + +
527B ARG* 1.3 65.5 + - - +
528B PRO* 3.2 8.3 - - - -
529B LEU* 3.1 25.1 + - + +
530B VAL 3.8 1.2 + - - -
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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