Contacts of the helix formed by residues 520 - 541 (chain A) in PDB entry 5YD6
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 GLU 520 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A ASP 5.3 1.9 - - - +
430A LEU* 4.8 1.3 - - + -
431A PRO* 4.0 29.5 - - + +
434A ASP* 3.0 11.9 + - - +
518A LEU* 4.6 0.4 - - - -
519A LYS* 1.3 85.1 - - + +
521A PRO* 1.4 64.1 - - - +
522A LYS* 3.4 2.5 - - - -
523A ARG* 3.1 47.2 + - + +
524A VAL* 3.3 11.0 + - - +
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Residues in contact with PRO 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A GLU* 4.0 24.3 - - + +
515A ARG 5.7 0.9 - - - +
518A LEU* 3.6 31.6 - - + +
519A LYS 3.5 8.7 - - - +
520A GLU* 1.4 85.3 - - - +
522A LYS* 1.3 61.4 + - + +
524A VAL* 3.2 3.2 + - + +
525A GLU* 2.7 36.2 + - - +
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Residues in contact with LYS 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A GLU 3.4 0.6 - - - -
521A PRO* 1.3 83.8 - - + +
523A ARG* 1.3 53.3 + - - +
525A GLU* 3.5 16.2 - - - +
526A GLU* 2.8 48.2 + - - +
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Residues in contact with ARG 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A GLY* 4.1 8.9 + - - -
429A ASP* 3.3 42.3 + - - +
430A LEU* 3.9 17.9 - - + +
520A GLU* 3.1 38.8 + - + +
522A LYS* 1.3 78.1 - - - +
524A VAL* 1.3 56.7 + - - +
526A GLU* 3.3 14.9 + - - +
527A LEU* 2.9 29.5 + - - +
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Residues in contact with VAL 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 4.1 26.9 - - + -
434A ASP* 5.1 0.7 - - - +
438A LEU* 4.2 10.3 - - + -
512A VAL* 3.7 12.7 - - + +
513A THR* 3.5 42.4 - - - +
514A GLU* 4.1 2.2 - - + +
518A LEU* 3.9 23.3 - - + -
520A GLU 3.3 12.5 + - - +
521A PRO 3.2 7.7 + - - +
523A ARG* 1.3 72.9 - - - +
525A GLU* 1.3 60.3 + - - +
527A LEU* 3.3 2.1 + - - +
528A GLN* 2.9 30.4 + - - +
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Residues in contact with GLU 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A GLU* 3.2 30.3 + - - +
521A PRO 2.7 20.3 + - - +
522A LYS* 3.5 18.2 - - - +
524A VAL* 1.3 73.9 - - - +
526A GLU* 1.3 62.3 + - + +
528A GLN* 3.4 11.5 + - - +
529A ASN* 3.1 47.4 + - - +
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Residues in contact with GLU 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A LYS* 2.8 30.7 + - - +
523A ARG* 3.6 17.5 + - + +
524A VAL 3.3 0.4 - - - -
525A GLU* 1.3 74.9 - - + +
527A LEU* 1.3 61.1 + - - +
529A ASN* 3.5 6.0 + - - +
530A LYS* 3.2 38.2 + - + +
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Residues in contact with LEU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LEU* 4.8 11.4 - - + -
424A ILE* 4.2 6.7 - - + -
425A PRO* 3.3 29.2 - - + +
426A GLY* 4.3 5.6 - - - -
427A PHE* 4.1 15.9 - - + +
430A LEU* 5.8 4.7 - - + -
512A VAL* 3.8 29.2 - - + -
523A ARG 2.9 18.2 + - - +
524A VAL* 3.9 4.3 - - - +
526A GLU* 1.3 73.4 - - - +
528A GLN* 1.3 64.7 + - - +
530A LYS* 3.4 17.4 + - + +
531A ILE* 3.1 41.3 + - + +
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Residues in contact with GLN 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A LEU* 3.4 22.0 + - + +
512A VAL* 3.4 21.8 + - - +
513A THR* 3.3 34.3 + - - +
514A GLU* 4.4 9.9 - - - +
524A VAL 2.9 18.8 + - - +
525A GLU* 3.6 12.7 - - - +
527A LEU* 1.3 75.2 - - - +
529A ASN* 1.3 71.9 + - - +
531A ILE* 3.1 3.6 + - - -
532A VAL* 2.9 33.5 + - + +
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Residues in contact with ASN 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A GLU* 3.1 37.0 + - - +
526A GLU* 3.5 4.8 + - - +
528A GLN* 1.3 94.1 - - - +
530A LYS* 1.3 58.6 + - - +
532A VAL* 3.5 11.6 - - + +
533A ASN* 2.9 42.0 + - - +
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Residues in contact with LYS 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LEU* 3.8 20.9 - - + +
526A GLU* 3.2 28.1 + - + +
527A LEU* 3.4 23.1 - - + +
529A ASN* 1.3 75.4 - - - +
531A ILE* 1.3 56.7 + - - +
533A ASN* 3.6 7.0 + - - +
534A CYS* 3.1 29.8 + - - +
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Residues in contact with ILE 531 (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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364A LEU* 4.6 4.5 - - + -
368A LEU* 4.0 22.0 - - + -
424A ILE* 4.7 1.3 - - + -
505A CYS* 3.5 37.4 - - + +
508A ALA* 3.8 19.5 - - + -
509A LEU* 3.7 12.1 - - + -
512A VAL* 4.2 15.7 - - + -
527A LEU* 3.2 39.9 - - + +
528A GLN* 3.1 7.1 + - - +
530A LYS* 1.3 74.5 - - - +
532A VAL* 1.3 64.1 + - - +
534A CYS* 3.2 10.2 - - - +
535A LEU* 3.0 22.7 + - - +
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Residues in contact with VAL 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A LEU* 3.8 26.9 - - + -
528A GLN* 2.9 26.8 + - + +
529A ASN* 3.3 15.2 + - + +
531A ILE* 1.3 74.5 - - - +
533A ASN* 1.3 60.2 + - - +
535A LEU* 3.2 8.2 + - - +
536A LYS* 2.9 54.8 + - + +
552A LEU* 5.6 1.8 - - + -
556A LEU* 5.3 15.5 - - + -
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Residues in contact with ASN 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A ASN* 2.9 27.4 + - - +
530A LYS* 4.0 6.1 - - - +
532A VAL* 1.3 77.4 - - - +
534A CYS* 1.3 58.7 + - - +
536A LYS* 3.5 22.4 + - + +
537A ASP* 2.9 44.3 + - - +
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Residues in contact with CYS 534 (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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364A LEU* 3.8 31.0 - - - -
365A ILE* 3.8 30.4 - - + +
368A LEU* 4.8 1.1 - - - -
505A CYS* 4.0 11.7 - - - -
530A LYS 3.1 17.2 + - - +
531A ILE* 3.2 12.3 - - - +
533A ASN* 1.3 71.5 - - - +
535A LEU* 1.3 60.5 + - - +
537A ASP* 3.5 7.4 + - - +
538A HIS* 2.9 29.8 + - - +
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Residues in contact with LEU 535 (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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502A ALA* 3.8 41.5 - - + +
505A CYS* 3.9 13.4 - - + -
506A ILE* 3.7 25.4 - - + -
509A LEU* 4.2 18.6 - - + -
531A ILE 3.0 7.3 + - - +
532A VAL* 3.3 9.4 - - - +
534A CYS* 1.3 77.8 - - - +
536A LYS* 1.3 54.5 + - - +
538A HIS* 3.2 5.0 + - + +
539A VAL* 2.8 43.5 + - + +
552A LEU* 4.3 16.8 - - + -
555A LEU* 4.2 13.5 - - + -
556A LEU* 4.2 9.2 - - + -
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Residues in contact with LYS 536 (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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532A VAL* 2.9 38.8 + - + +
533A ASN* 3.5 23.4 + - - +
534A CYS 3.3 0.2 - - - -
535A LEU* 1.3 75.0 - - - +
537A ASP* 1.3 64.3 + - - +
539A VAL* 3.2 5.9 + - - +
540A THR* 2.9 29.9 + - - -
552A LEU* 3.6 33.9 - - + -
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Residues in contact with ASP 537 (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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533A ASN* 2.9 33.5 + - - +
534A CYS* 3.8 6.6 + - - +
536A LYS* 1.3 74.5 - - - +
538A HIS* 1.3 57.6 + - - +
540A THR* 3.5 7.8 + - - -
541A PHE 2.9 22.3 + - - -
541C PHE* 3.4 31.7 - - + -
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Residues in contact with HIS 538 (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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365A ILE* 3.8 19.7 - - + -
499A ASP* 2.9 41.4 + - - -
501A SER* 3.4 22.4 + - - -
502A ALA* 4.3 9.8 + - - +
534A CYS 2.9 18.5 + - - +
535A LEU* 3.6 6.7 - - + +
537A ASP* 1.3 74.7 - - - +
539A VAL* 1.3 67.7 + - - +
541A PHE* 3.1 24.3 + - + +
365C ILE* 6.1 2.2 - - - +
366C SER* 4.4 8.3 + - - -
541C PHE* 4.4 9.3 - + + -
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Residues in contact with VAL 539 (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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502A ALA* 5.6 2.0 - - + -
535A LEU* 2.8 30.6 + - + +
536A LYS* 3.6 6.7 - - - +
538A HIS* 1.3 74.5 - - - +
540A THR* 1.3 64.9 + - - +
541A PHE* 3.2 18.7 - - - -
549A PRO* 4.7 17.7 - - + -
551A TYR* 4.4 15.9 - - + -
552A LEU* 4.8 22.7 - - + +
555A LEU* 3.8 28.3 - - + -
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Residues in contact with THR 540 (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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536A LYS 2.9 18.7 + - - -
537A ASP* 3.8 6.9 - - - -
539A VAL* 1.3 77.4 - - - +
541A PHE* 1.3 80.4 + - - +
549A PRO* 6.0 2.3 - - + +
541C PHE* 6.1 0.4 - - - -
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Residues in contact with PHE 541 (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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537A ASP 2.9 12.7 + - - -
538A HIS* 3.1 19.6 + - + +
539A VAL 3.2 22.2 - - - -
540A THR* 1.3 88.0 - - - +
537C ASP* 5.5 2.1 - - - +
541C PHE* 3.6 32.0 - - - +
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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