Contacts of the helix formed by residues 501 - 523 (chain B) in PDB entry 3PLZ
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 LEU 501 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A TYR* 3.8 18.4 - - - +
537A HIS* 4.3 16.8 - - + +
497B GLY 3.0 17.4 + - - +
498B GLN* 3.8 6.3 - - + +
499B LEU 3.2 0.4 - - - -
500B LEU* 1.3 75.6 - - - +
502B ARG* 1.3 89.6 + - - +
503B LEU 3.2 0.2 - - - -
504B PRO* 3.4 20.0 - - + +
505B GLU* 3.5 15.5 - - - +
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Residues in contact with ARG 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B LEU* 5.2 6.3 - - + -
437B LYS* 3.7 35.0 - - - +
438B LEU* 4.0 36.3 - - + -
441B LEU* 4.2 9.5 - - - +
451B LEU* 5.2 4.7 - - + -
498B GLN* 2.7 42.5 + - - +
499B LEU 3.3 17.0 - - - +
500B LEU 3.1 0.6 - - - -
501B LEU* 1.3 103.1 - - - +
503B LEU* 1.3 57.7 + - - +
504B PRO 3.6 0.2 - - - -
505B GLU* 3.0 45.4 + - - +
506B ILE* 2.9 45.7 + - + +
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Residues in contact with LEU 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B GLU* 4.8 2.6 - - - +
388B LEU* 5.2 0.7 - - + -
451B LEU* 4.0 36.8 - - + -
454B LEU* 4.1 31.2 - - + +
455B VAL* 3.7 28.0 - - + -
474B GLN* 6.0 0.2 - - - +
499B LEU 4.5 0.4 - - - +
500B LEU* 3.0 19.8 + - + +
502B ARG* 1.3 77.6 - - - +
504B PRO* 1.4 65.1 - - + +
506B ILE* 3.2 14.7 + - + +
507B ARG* 2.9 28.3 + - - +
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Residues in contact with PRO 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A TYR* 3.7 31.8 - - + +
500B LEU 3.2 13.5 - - - +
501B LEU* 3.4 18.2 - - + +
503B LEU* 1.4 91.9 - - + +
505B GLU* 1.3 54.3 + - - +
507B ARG* 3.5 8.4 + - + +
508B ALA* 3.0 28.8 + - - +
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Residues in contact with GLU 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A TYR* 4.0 9.2 + - + +
522A LEU* 3.9 38.6 - - + +
434B LEU* 3.9 25.2 - - + +
437B LYS* 4.7 9.2 + - - +
501B LEU* 3.5 16.5 - - - +
502B ARG* 3.0 49.8 + - - +
503B LEU 3.2 0.4 - - - -
504B PRO* 1.3 73.5 - - - +
506B ILE* 1.3 66.8 + - - +
508B ALA* 3.2 2.4 + - - +
509B ILE* 3.0 31.3 + - + +
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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
----------------------------------------------------------
384B GLU* 3.9 29.4 - - + +
387B ILE* 4.1 10.0 - - + +
388B LEU* 3.9 29.6 - - + -
391B ILE* 4.1 11.9 - - + -
434B LEU* 3.8 23.8 - - + -
438B LEU* 5.6 2.9 - - + -
451B LEU* 5.6 0.4 - - + -
455B VAL* 5.8 2.2 - - + -
502B ARG* 2.9 32.4 + - + +
503B LEU* 3.6 14.8 - - + +
505B GLU* 1.3 75.8 - - - +
507B ARG* 1.3 53.9 + - - +
509B ILE* 3.5 3.1 + - - +
510B SER* 2.6 47.8 + - - +
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Residues in contact with ARG 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A GLU* 2.6 44.0 + - + +
380B ASN* 2.7 45.7 + - - +
384B GLU* 2.7 50.3 + - - +
503B LEU 2.9 17.1 + - - +
504B PRO* 3.7 9.9 - - + +
506B ILE* 1.3 76.5 - - - +
508B ALA* 1.3 63.4 + - - +
510B SER* 3.2 2.4 + - - -
511B MET* 3.1 46.0 + - - +
539B LYS* 3.9 6.9 - - - +
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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
----------------------------------------------------------
515A GLU* 3.7 25.9 - - - +
518A TYR* 3.9 11.7 - - + -
519A TYR* 3.7 24.5 - - - +
522A LEU* 4.4 2.9 - - + -
504B PRO 3.0 17.7 + - - +
505B GLU 3.2 3.6 + - - +
507B ARG* 1.3 78.4 - - - +
509B ILE* 1.3 63.4 + - - +
511B MET* 3.5 6.3 + - - +
512B GLN* 3.4 24.1 + - - +
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Residues in contact with ILE 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A TYR* 4.7 11.0 - - + -
522A LEU* 4.8 9.9 - - + -
1B 470 5.4 2.2 - - + -
387B ILE* 4.2 17.5 - - + -
427B LEU* 4.2 28.3 - - + +
430B HIS* 3.7 32.3 - - + +
431B ALA* 4.7 3.6 - - + +
434B LEU* 3.5 35.9 - - + -
505B GLU* 3.0 23.3 + - + +
506B ILE* 3.9 3.6 - - - +
508B ALA* 1.3 76.4 - - - +
510B SER* 1.3 57.3 + - - +
512B GLN* 3.3 4.8 + - - +
513B ALA* 2.9 26.5 + - + +
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Residues in contact with SER 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B SER* 3.4 22.9 + - - -
384B GLU* 3.4 26.2 - - - -
387B ILE* 3.3 23.8 - - - +
506B ILE* 2.6 25.9 + - - +
507B ARG 3.2 4.9 + - - -
509B ILE* 1.3 76.4 - - - +
511B MET* 1.3 59.7 + - - +
513B ALA* 3.3 3.1 + - - +
514B GLU* 2.9 32.7 + - - +
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Residues in contact with MET 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A GLN* 5.6 7.9 - - + +
515A GLU* 3.7 35.0 - - + +
383B SER* 5.4 0.9 - - - -
384B GLU* 5.6 0.2 - - - +
507B ARG* 3.1 33.6 + - - +
508B ALA* 3.9 6.1 - - - +
509B ILE 3.3 0.2 - - - -
510B SER* 1.3 76.8 - - - +
512B GLN* 1.3 68.8 + - - +
514B GLU* 3.4 10.5 + - + +
515B GLU* 3.1 22.7 + - - +
539B LYS* 3.6 44.2 - - + -
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Residues in contact with GLN 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A THR* 2.9 36.7 + - - +
516A TYR* 3.7 21.6 - - - +
519A TYR* 3.7 38.2 - - + -
423B THR* 5.6 0.7 - - - +
427B LEU* 3.9 21.0 - - + +
508B ALA 3.4 6.1 + - - +
509B ILE 3.3 7.8 + - - +
511B MET* 1.3 81.0 + - + +
513B ALA* 1.3 59.7 + - - +
515B GLU* 3.3 7.2 + - - +
516B TYR* 3.0 28.4 + - - +
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Residues in contact with ALA 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 470 3.9 48.2 - - + -
387B ILE* 4.5 2.0 - - + -
427B LEU* 3.7 12.7 - - + +
509B ILE* 2.9 16.9 + - + +
510B SER* 3.3 7.4 + - - +
512B GLN* 1.3 73.5 - - - +
514B GLU* 1.3 59.5 + - - +
516B TYR* 3.3 1.8 + - - +
517B LEU* 2.9 35.3 + - + +
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Residues in contact with GLU 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 470 3.8 6.9 - - + +
382B TRP* 3.4 29.2 + - + -
383B SER* 2.6 28.3 + - - +
510B SER 2.9 16.9 + - - +
511B MET* 3.6 12.7 - - + +
512B GLN 3.3 0.2 - - - -
513B ALA* 1.3 75.6 - - - +
515B GLU* 1.3 63.6 + - - +
518B TYR* 3.0 25.3 + - - +
535B MET 4.7 0.2 - - - +
536B LEU* 3.6 19.6 - - + +
539B LYS* 2.8 46.5 + - - +
540B ARG* 5.7 1.0 - - - +
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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
----------------------------------------------------------
422A ALA* 3.6 27.3 - - + +
423A THR* 3.7 26.6 + - - +
426A ASN* 4.0 9.0 - - - +
511B MET 3.1 14.4 + - - +
512B GLN* 3.6 13.0 - - - +
513B ALA 3.3 0.2 - - - -
514B GLU* 1.3 76.7 - - - +
516B TYR* 1.3 58.3 + - - +
518B TYR* 3.4 7.2 + - - +
519B TYR* 3.0 27.4 + - - +
540B ARG* 3.2 35.1 + - - +
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Residues in contact with TYR 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B PHE* 4.1 4.7 - + - -
420B ALA* 5.0 1.2 - - - +
421B GLY* 4.5 10.6 + - - -
423B THR* 3.5 33.4 - - + -
424B LEU* 3.4 55.1 + - + +
427B LEU* 4.1 9.6 - - + -
512B GLN 3.0 16.5 + - - +
513B ALA* 3.7 3.6 - - - +
515B GLU* 1.3 77.4 - - - +
517B LEU* 1.3 66.0 + - + +
519B TYR* 3.2 22.0 + + - +
520B LYS* 2.9 68.7 + - + +
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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
----------------------------------------------------------
1B 470 3.7 61.5 - - + -
342B PHE* 3.8 31.4 - - + -
346B CYS* 4.5 4.5 - - - -
349B ALA* 5.5 0.7 - - + -
424B LEU* 5.3 0.7 - - + -
513B ALA* 2.9 17.2 + - - +
516B TYR* 1.3 83.6 - - + +
518B TYR* 1.3 60.1 + - - +
520B LYS* 3.4 1.9 + - - -
521B HIS* 2.9 29.1 + - - +
526B VAL* 3.7 7.8 - - + +
532B LEU* 4.6 22.0 - - + -
536B LEU* 4.0 16.9 - - + +
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Residues in contact with TYR 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B GLU 3.0 18.5 + - - +
515B GLU* 3.6 6.7 - - - +
517B LEU* 1.3 77.6 - - - +
519B TYR* 1.3 62.5 + - - +
521B HIS* 3.2 19.8 + + - +
522B LEU* 3.0 55.6 + - + +
533B ILE* 4.9 1.3 - - + -
536B LEU* 4.3 20.3 - - + +
537B HIS* 3.6 32.8 - + - -
540B ARG* 3.3 55.2 + - - +
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Residues in contact with TYR 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B GLU* 3.0 14.0 + - + +
516B TYR* 3.3 27.1 - + - +
518B TYR* 1.3 78.9 - - - +
520B LYS* 1.3 78.0 + - + +
522B LEU* 3.1 13.1 + - + +
523B ASN* 3.0 38.2 + - + +
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Residues in contact with LYS 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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342B PHE* 3.7 31.7 - - + -
419B GLN 5.5 4.9 + - - -
420B ALA* 6.2 0.6 - - - +
516B TYR* 2.9 63.4 + - + +
517B LEU* 3.8 5.2 - - - +
519B TYR* 1.3 86.9 - - + +
521B HIS* 1.3 59.4 + - - +
523B ASN* 3.3 4.7 + - + -
524B GLY 3.2 4.3 + - - -
525B ASP* 2.8 61.2 + - + +
526B VAL* 3.8 4.7 - - + -
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Residues in contact with HIS 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B LEU 2.9 18.3 + - - +
518B TYR* 3.4 14.2 + + - +
520B LYS* 1.3 75.7 - - - +
522B LEU* 1.3 78.8 + - + +
524B GLY* 3.1 13.9 + - - -
526B VAL* 3.5 30.1 - - + +
529B ASN* 6.1 0.4 - - - -
533B ILE* 3.3 41.9 - - + +
536B LEU* 5.0 1.8 - - + -
537B HIS* 4.9 6.5 - + - -
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Residues in contact with LEU 522 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B TYR* 3.0 53.2 + - + +
519B TYR* 3.1 11.9 + - + +
521B HIS* 1.3 91.5 - - + +
523B ASN* 1.3 58.5 + - - +
524B GLY* 3.2 1.1 + - - -
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Residues in contact with ASN 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B TYR* 3.0 29.9 + - + +
520B LYS* 3.3 7.2 + - - +
521B HIS 3.2 0.4 - - - -
522B LEU* 1.3 76.6 - - - +
524B GLY* 1.3 60.0 + - - +
525B ASP* 3.3 21.7 + - - +
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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