Contacts of the helix formed by residues 513 - 529 (chain B) in PDB entry 4Y5U
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 THR 513 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B PHE 4.2 0.2 - - - -
503B ASN* 3.1 51.3 + - - +
504B LYS 4.1 8.3 - - - +
505B GLU 4.4 8.7 - - - +
506B ILE* 4.3 14.8 - - + -
507B LEU* 4.0 2.9 - - - -
512B PHE* 1.3 82.3 - - - +
514B PHE* 1.3 59.1 + - - +
515B TRP 3.6 0.5 + - - -
516B GLN* 2.7 34.3 + - - +
517B TRP* 3.1 21.1 + - - +
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Residues in contact with PHE 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B TRP* 4.6 7.2 - + - -
451B MET* 5.6 0.2 - - - -
455B LEU* 4.4 23.3 - - + -
477B LEU* 3.8 39.5 - - + -
480B LYS* 4.0 17.5 - - + -
481B ILE* 3.6 35.9 - - + -
501B GLN 3.8 11.9 - - - +
502B PHE* 3.6 32.1 + + - +
505B GLU 4.8 1.6 + - - -
507B LEU* 3.9 20.6 - - + +
513B THR* 1.3 76.3 - - - +
515B TRP* 1.3 58.9 + - - +
517B TRP* 3.3 5.6 + + - +
518B PHE* 2.9 34.5 + + + +
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Residues in contact with TRP 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ASN* 3.0 33.3 + - - +
423B LYS* 3.9 22.7 - - + -
424B ALA* 3.4 18.9 - - + +
427B LEU* 4.2 25.1 - - + -
455B LEU* 5.1 1.6 - - + -
458B LYS* 4.7 8.1 - - + -
502B PHE* 3.1 41.8 + + + +
503B ASN* 3.2 26.2 - - - +
513B THR 3.5 0.4 - - - -
514B PHE* 1.3 73.2 - - - +
516B GLN* 1.3 65.5 + - - +
517B TRP 3.2 0.2 - - - -
518B PHE* 4.0 29.4 - + - +
519B ASP* 3.0 53.5 + - + +
522B LEU* 4.4 8.5 - - + -
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Residues in contact with GLN 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ASN* 3.4 35.2 + - - +
421B ASN* 5.5 3.8 - - - +
503B ASN* 5.3 0.7 - - - -
506B ILE* 5.4 0.5 - - - +
511B GLY 4.7 1.0 + - - +
512B PHE* 3.3 16.2 - - + -
513B THR* 2.7 54.2 + - - +
515B TRP* 1.3 76.8 - - - +
517B TRP* 1.3 62.9 + - - +
519B ASP* 4.0 0.7 - - - +
520B GLY* 3.0 17.2 + - - -
568B ILE* 3.6 12.9 - - + +
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Residues in contact with TRP 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B LEU* 3.9 19.3 - - + -
480B LYS* 3.6 37.7 - - + -
507B LEU* 4.7 2.5 - - + -
512B PHE* 3.4 32.3 - + + -
513B THR 3.1 13.8 + - - +
514B PHE* 3.4 12.3 - + - +
516B GLN* 1.3 78.1 - - - +
518B PHE* 1.3 70.6 + + + +
520B GLY* 3.2 7.6 + - - -
521B VAL* 3.2 37.1 + - + +
541B PHE* 4.0 20.4 - + - -
563B PHE* 4.2 12.1 - - + -
564B SER 3.0 27.7 + - - -
565B ASP* 3.7 14.5 + - - -
567B GLU 3.8 9.1 + - - -
568B ILE* 3.6 9.4 - - + +
569B GLY 5.5 0.9 + - - +
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Residues in contact with PHE 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B LEU* 3.6 61.2 - - + -
458B LYS* 4.8 4.7 - - + -
459B PHE* 4.5 9.4 - + + -
469B LEU* 4.4 9.0 - - + -
477B LEU* 4.2 27.4 - - + -
514B PHE* 2.9 24.0 + + + +
515B TRP* 3.3 22.2 + + + +
517B TRP* 1.3 81.5 - + + +
519B ASP* 1.3 60.6 + - - +
521B VAL* 3.2 8.9 + - + +
522B LEU* 3.1 43.7 + - + +
541B PHE* 4.6 14.1 - + - -
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Residues in contact with ASP 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ASN* 3.9 16.1 + - - +
423B LYS* 3.7 31.4 + - - +
515B TRP* 3.0 44.5 + - + +
516B GLN 4.2 1.3 - - - +
518B PHE* 1.3 73.7 - - - +
520B GLY* 1.3 62.9 + - - +
521B VAL 3.4 0.2 - - - -
522B LEU* 3.6 20.9 - - - +
523B ASP* 3.3 29.1 + - - +
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Residues in contact with GLY 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B GLN 3.0 17.5 + - - -
517B TRP 3.2 5.6 + - - -
518B PHE 3.1 0.4 - - - -
519B ASP* 1.3 78.8 - - - +
521B VAL* 1.3 58.2 + - - +
523B ASP* 3.5 6.3 - - - +
524B LEU 3.4 15.8 + - - -
568B ILE* 3.7 19.7 - - - -
569B GLY* 3.5 18.6 - - - -
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Residues in contact with VAL 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B PHE* 4.4 8.1 - - + -
517B TRP* 3.2 48.5 - - + +
518B PHE* 3.2 7.8 + - + +
520B GLY* 1.3 72.4 - - - +
522B LEU* 1.3 64.3 + - - +
524B LEU* 4.0 5.8 - - + +
525B THR* 2.8 31.5 + - - +
541B PHE* 4.0 14.4 - - + -
563B PHE* 3.7 43.7 - - + -
569B GLY* 5.0 4.5 - - - +
570B GLY 6.1 1.3 - - - +
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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
----------------------------------------------------------
458B LYS* 4.4 5.8 - - + -
459B PHE* 3.6 46.0 - - + +
462B GLU* 4.1 29.6 - - + -
463B VAL* 3.6 10.2 + - + +
515B TRP* 4.4 10.1 - - + -
518B PHE* 3.1 30.6 + - + +
519B ASP* 3.5 32.1 - - - +
521B VAL* 1.3 76.9 - - - +
523B ASP* 1.3 57.3 + - - +
526B LYS* 2.9 34.5 + - - +
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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
----------------------------------------------------------
423B LYS* 5.0 6.1 + - - -
519B ASP* 3.3 19.0 + - - +
520B GLY* 3.5 12.5 - - - +
522B LEU* 1.3 78.8 - - - +
524B LEU* 1.3 58.7 + - + +
526B LYS* 3.8 18.9 + - - +
527B ARG* 3.1 63.7 + - - +
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Residues in contact with LEU 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B GLY 3.4 14.3 + - - +
521B VAL* 4.0 4.0 - - - +
523B ASP* 1.3 79.9 - - - +
525B THR* 1.3 60.3 + - - +
527B ARG* 4.0 2.9 - - - +
528B CYS* 3.2 29.7 + - - +
529B LEU* 3.2 32.4 - - + +
563B PHE* 4.4 9.4 - - + -
569B GLY* 3.5 20.6 - - - +
570B GLY 4.0 23.8 - - - +
571B ILE* 4.1 6.1 - - + +
592B PHE 4.5 0.4 - - - +
593B SER* 4.0 4.0 - - - -
594B ALA* 3.7 37.9 - - + +
597B LEU* 4.4 5.2 - - + -
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Residues in contact with THR 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B PHE* 3.9 14.4 - - + -
463B VAL* 3.5 30.5 - - + -
521B VAL* 2.8 20.6 + - - +
524B LEU* 1.3 74.5 - - - +
526B LYS* 1.3 65.8 + - - +
529B LEU* 3.1 33.3 + - + +
530B ARG* 3.1 13.0 + - - -
533B TRP* 4.1 14.8 - - + -
538B ILE* 5.8 0.7 - - + -
563B PHE* 3.6 25.8 - - + -
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Residues in contact with LYS 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LYS* 5.7 4.6 - - - +
462B GLU* 3.2 42.7 + - - +
463B VAL* 4.0 15.3 - - - +
522B LEU* 2.9 22.1 + - - +
523B ASP* 3.8 23.0 + - - +
525B THR* 1.3 79.0 - - - +
527B ARG* 1.3 70.9 + - + +
530B ARG* 4.4 12.6 - - - +
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Residues in contact with ARG 527 (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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523B ASP* 3.1 41.5 + - - +
524B LEU* 5.1 0.4 - - - +
526B LYS* 1.3 91.7 - - + +
528B CYS* 1.3 67.0 + - - +
594B ALA* 3.7 31.6 + - - +
595B LYS 5.3 0.4 - - - +
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Residues in contact with CYS 528 (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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524B LEU* 3.2 15.3 + - - +
527B ARG* 1.3 86.0 - - - +
529B LEU* 1.3 70.2 + - + +
530B ARG 3.8 1.3 - - - -
532B TYR* 4.0 12.6 - - - -
594B ALA* 3.7 40.4 - - - -
597B LEU* 4.0 22.8 - - + +
598B SER* 5.4 0.7 - - - -
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Residues in contact with LEU 529 (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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524B LEU* 3.2 42.0 - - + +
525B THR* 3.1 27.0 + - + +
528B CYS* 1.3 84.1 - - + +
530B ARG* 1.3 59.6 + - - +
531B SER 3.5 1.6 - - - -
532B TYR* 3.1 31.5 + - + +
533B TRP* 2.9 26.2 + - - +
538B ILE* 4.1 9.9 - - + -
563B PHE* 4.5 1.8 - - + -
571B ILE* 4.1 16.8 - - + -
597B LEU* 4.3 10.5 - - + -
602B LEU* 3.8 21.1 - - + -
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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