Contacts of the helix formed by residues 513 - 529 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502A PHE 4.4 0.4 - - - -
503A ASN* 3.2 47.5 + - - +
504A LYS 4.0 3.8 - - - +
505A GLU 3.5 22.4 - - - +
506A ILE* 3.9 15.3 - - + -
507A LEU* 4.1 4.3 - - - +
512A PHE* 1.3 81.5 - - - +
514A PHE* 1.3 63.2 + - - +
515A TRP 3.8 0.5 + - - -
516A GLN* 2.9 33.4 + - - +
517A TRP* 3.2 16.3 + - - +
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Residues in contact with PHE 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A TRP* 4.9 2.2 - + - -
455A LEU* 4.3 21.5 - - + -
477A LEU* 3.9 44.4 - - + -
480A LYS* 3.9 21.3 - - + -
481A ILE* 3.6 42.4 - - + -
501A GLN 4.0 4.2 + - - +
502A PHE* 3.8 30.0 + + - +
505A GLU 4.6 2.0 + - - -
507A LEU* 4.0 18.1 - - + +
513A THR* 1.3 72.8 - - - +
515A TRP* 1.3 64.0 + - - +
517A TRP* 3.3 5.5 + + - +
518A PHE* 2.9 35.9 + + + +
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Residues in contact with TRP 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A ASN* 2.9 33.3 + - - +
423A LYS* 4.0 23.1 - - + -
424A ALA* 3.5 19.1 - - + +
427A LEU* 4.7 14.6 - - + -
455A LEU* 5.2 1.8 - - + -
458A LYS* 4.4 16.2 - - + -
502A PHE* 3.2 40.8 + + + +
503A ASN* 3.3 24.9 - - - +
513A THR* 3.5 0.4 + - - -
514A PHE* 1.3 76.9 - - - +
516A GLN* 1.3 59.6 + - - +
518A PHE* 3.9 30.7 - + + +
519A ASP* 2.7 58.1 + - + +
522A LEU* 4.2 9.0 - - + -
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Residues in contact with GLN 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A ASN* 3.3 36.5 + - - +
421A ASN* 4.5 8.9 - - - +
503A ASN* 4.6 2.0 + - - -
506A ILE* 4.6 3.0 - - - +
511A GLY 4.4 2.1 - - - +
512A PHE* 3.3 17.8 - - + +
513A THR* 2.9 50.4 + - - +
515A TRP* 1.3 79.5 - - - +
517A TRP* 1.3 58.8 + - - +
519A ASP* 4.4 1.0 - - - +
520A GLY* 3.2 15.8 + - - -
568A ILE* 3.8 15.5 - - + +
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Residues in contact with TRP 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A LEU* 3.9 18.4 - - + -
480A LYS* 3.6 39.3 - - + -
507A LEU* 4.6 2.5 - - + -
512A PHE* 3.5 28.9 - + + -
513A THR 3.2 10.2 + - - +
514A PHE* 3.6 10.1 - + - +
515A TRP 3.2 0.2 - - - -
516A GLN* 1.3 77.7 - - - +
518A PHE* 1.3 72.8 + + + +
520A GLY* 3.3 1.9 + - - -
521A VAL* 3.2 47.6 + - + +
541A PHE* 3.9 21.1 - + - -
563A PHE* 4.2 10.3 - - + -
564A SER 3.0 28.8 + - - -
565A ASP* 3.8 13.4 + - - -
567A GLU 3.6 14.2 + - - -
568A ILE* 3.8 8.2 - - + +
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Residues in contact with PHE 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A LEU* 3.7 50.3 - - + -
458A LYS* 5.0 3.6 - - + -
459A PHE* 4.3 14.8 - + + -
469A LEU* 4.3 7.2 - - + -
477A LEU* 4.2 33.9 - - + -
514A PHE* 2.9 26.4 + + + +
515A TRP* 3.8 23.3 - + + +
517A TRP* 1.3 81.6 - + + +
519A ASP* 1.3 63.2 + - - +
521A VAL* 3.2 14.3 + - + +
522A LEU* 3.3 35.8 + - + +
541A PHE* 4.4 15.5 - + - -
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Residues in contact with ASP 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A GLN* 4.9 5.9 + - - -
420A ASN* 4.1 12.7 + - - +
423A LYS* 3.1 34.1 + - - -
462A GLU* 5.8 1.4 - - - +
515A TRP* 2.7 43.5 + - + +
516A GLN 4.4 2.0 - - - +
518A PHE* 1.3 72.7 - - - +
520A GLY* 1.3 57.7 + - - +
522A LEU* 3.1 33.2 - - - +
523A ASP* 3.2 12.8 + - - +
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Residues in contact with GLY 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516A GLN 3.2 14.3 + - - -
517A TRP 3.6 4.9 - - - -
518A PHE 3.2 1.0 - - - -
519A ASP* 1.3 79.6 - - - +
521A VAL* 1.3 59.0 + - - +
523A ASP* 4.1 4.2 - - - +
524A LEU 3.3 15.2 + - - -
568A ILE* 3.9 18.2 - - - -
569A GLY* 3.5 17.9 - - - -
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Residues in contact with VAL 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A PHE* 4.2 8.5 - - + -
517A TRP* 3.2 49.6 + - + +
518A PHE* 3.2 7.7 + - + +
520A GLY* 1.3 71.7 - - - +
522A LEU* 1.3 58.2 + - + +
524A LEU* 3.9 7.1 - - + +
525A THR* 2.4 38.2 + - - +
541A PHE* 3.8 26.5 - - + -
563A PHE* 3.8 30.7 - - + -
569A GLY* 5.0 3.6 - - - +
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Residues in contact with LEU 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A LYS* 4.4 10.5 - - + +
459A PHE* 3.6 43.3 - - + -
462A GLU* 4.4 21.0 - - + +
463A VAL* 3.8 14.6 + - + +
515A TRP* 4.2 11.0 - - + -
518A PHE* 3.3 29.3 + - + +
519A ASP* 3.1 32.3 - - - +
521A VAL* 1.3 78.5 - - + +
523A ASP* 1.3 57.2 + - - +
526A LYS* 3.0 32.8 + - - +
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Residues in contact with ASP 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519A ASP* 3.2 15.1 + - - +
520A GLY* 4.1 5.3 - - - +
522A LEU* 1.3 74.4 - - - +
524A LEU* 1.3 66.7 + - - +
526A LYS* 4.0 17.7 + - - +
527A ARG* 3.2 65.5 + - - +
594A ALA* 5.4 1.0 - - - +
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Residues in contact with LEU 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A GLY 3.3 16.5 + - - +
521A VAL* 3.9 4.0 - - + +
522A LEU 3.4 0.2 - - - -
523A ASP* 1.3 82.1 + - - +
525A THR* 1.3 57.8 + - - +
527A ARG* 5.0 1.3 - - - -
528A CYS* 3.1 29.4 + - - +
529A LEU* 3.8 19.2 + - + +
563A PHE* 4.2 11.2 - - + -
569A GLY* 3.6 24.7 - - - +
570A GLY 3.6 30.1 - - - +
571A ILE* 3.9 4.9 - - + +
592A PHE 4.2 2.9 - - - +
593A SER 4.0 4.7 - - - +
594A ALA* 3.7 30.7 - - + +
597A LEU* 4.5 12.3 - - + -
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Residues in contact with THR 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A PHE* 4.6 8.0 - - + -
463A VAL* 4.0 26.0 - - + -
521A VAL* 2.4 26.8 + - - +
524A LEU* 1.3 73.3 - - - +
526A LYS* 1.3 65.4 + - - +
529A LEU* 3.2 45.5 + - + +
530A ARG* 3.3 12.3 + - - -
533A TRP* 4.3 14.1 - - + -
538A ILE* 5.2 0.4 - - + -
563A PHE* 4.0 19.9 - - + -
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Residues in contact with LYS 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A GLU* 3.2 49.5 + - - +
463A VAL* 4.0 16.4 - - - +
522A LEU 3.0 23.2 + - - +
523A ASP* 4.0 21.0 + - - +
525A THR* 1.3 76.9 - - - +
527A ARG* 1.3 67.6 + - + +
530A ARG* 4.5 10.2 - - - +
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Residues in contact with ARG 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523A ASP* 3.2 49.6 + - - +
524A LEU* 4.4 0.4 - - - +
526A LYS* 1.3 85.1 - - + +
528A CYS* 1.3 67.2 + - - +
594A ALA* 3.4 32.5 + - - +
595A LYS* 4.6 2.2 - - - +
598A SER* 6.4 0.2 - - - -
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Residues in contact with CYS 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A LEU* 3.1 13.6 + - - +
527A ARG* 1.3 84.9 - - - +
529A LEU* 1.3 61.7 + - + +
530A ARG 3.7 1.8 - - - -
531A SER* 5.3 1.6 + - - -
532A TYR* 3.8 16.5 - - - -
594A ALA* 3.7 38.6 - - - -
597A LEU* 3.7 35.6 - - + +
598A SER* 5.0 2.0 - - - -
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Residues in contact with LEU 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A LEU* 3.8 37.5 - - + +
525A THR* 3.2 27.6 + - + +
528A CYS* 1.3 82.4 - - + +
530A ARG* 1.3 64.4 + - - +
531A SER* 3.4 2.5 - - - -
532A TYR* 3.2 12.6 + - + +
533A TRP* 3.0 20.1 + - - +
538A ILE* 4.0 11.4 - - + -
563A PHE* 4.2 5.2 - - + -
571A ILE* 4.0 18.4 - - + -
597A LEU* 3.8 25.1 - - + -
602A LEU* 4.0 24.2 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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