Contacts of the helix formed by residues 522 - 540 (chain A) in PDB entry 3I5Y
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 522 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520A THR 3.6 4.6 + - - +
521A GLU* 1.3 75.9 - - - +
523A PRO* 1.3 75.1 - - + +
524A GLU* 3.2 21.1 - - + +
525A ASP* 3.0 29.0 + - - +
526A ILE* 3.0 11.9 + - - +
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Residues in contact with PRO 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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521A GLU 4.6 0.7 - - - +
522A GLU* 1.3 88.9 - - + +
524A GLU* 1.3 65.2 + - - +
526A ILE* 3.3 10.5 + - + +
527A SER* 2.9 29.5 + - - -
559A TYR* 3.7 19.6 - - - +
563A LEU* 4.1 25.3 - - + -
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Residues in contact with GLU 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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522A GLU* 3.2 18.3 - - + +
523A PRO* 1.3 89.4 - - - +
525A ASP* 1.3 64.9 + - - +
527A SER* 3.4 7.5 + - - -
528A ASP* 3.2 29.0 + - - +
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Residues in contact with ASP 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A GLU* 3.9 23.7 - - + +
522A GLU* 3.0 34.8 + - - +
524A GLU* 1.3 80.5 - - - +
526A ILE* 1.3 62.5 + - - +
528A ASP* 3.3 12.5 + - - +
529A ILE* 3.2 29.4 + - + +
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Residues in contact with ILE 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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388A PHE* 3.9 27.6 - - + -
519A VAL* 4.5 7.6 - - + -
521A GLU* 3.9 25.4 - - + +
522A GLU 3.0 20.1 + - - +
523A PRO* 3.7 10.3 - - + +
525A ASP* 1.3 73.2 - - - +
527A SER* 1.3 65.8 + - - +
529A ILE* 3.4 6.9 + - + +
530A VAL* 3.1 27.2 + - + +
559A TYR* 3.9 20.4 - - + +
562A LEU* 4.1 32.8 - - + -
563A LEU* 4.9 10.8 - - + -
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Residues in contact with SER 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A PRO 2.9 17.6 + - - -
524A GLU* 3.6 8.5 - - - -
526A ILE* 1.3 74.4 - - - +
528A ASP* 1.3 58.6 + - - +
530A VAL* 3.2 2.8 + - - +
531A ILE* 2.8 57.1 + - - +
559A TYR* 3.9 20.3 - - - -
570A ILE* 3.5 12.3 - - - +
571A PRO* 4.9 4.4 + - - -
1B U 4.9 6.6 - - - -
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Residues in contact with ASP 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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384A LYS* 3.9 22.8 - - + +
524A GLU* 3.2 16.7 + - - +
525A ASP* 3.3 13.4 + - - +
527A SER* 1.3 79.4 + - - +
529A ILE* 1.3 57.6 + - - +
532A SER* 3.0 29.5 + - - -
1B U 3.3 41.9 + - - +
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Residues in contact with ILE 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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384A LYS* 3.7 24.0 - - + +
385A PHE* 3.8 37.0 - - + -
388A PHE* 3.8 36.6 - - + -
521A GLU* 4.7 9.6 - - + -
525A ASP* 3.2 22.9 + - + +
526A ILE* 3.7 13.0 - - + +
527A SER 3.2 0.2 - - - -
528A ASP* 1.3 76.3 - - - +
530A VAL* 1.3 64.5 + - + +
532A SER* 2.7 24.5 + - - -
533A LEU* 3.2 10.0 + - + +
562A LEU* 5.8 3.4 - - + -
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Residues in contact with VAL 530 (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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526A ILE* 3.1 22.4 + - + +
527A SER* 3.9 2.5 - - - +
529A ILE* 1.3 75.5 - - + +
531A ILE* 1.3 61.8 + - - +
533A LEU* 3.0 12.0 + - + +
534A ILE* 2.9 26.8 + - + +
555A ILE* 3.5 26.0 - - + +
556A ALA* 3.8 21.3 - - - +
558A THR* 4.2 13.5 - - + -
559A TYR* 3.7 28.7 - - + +
562A LEU* 4.8 2.5 - - + -
570A ILE* 3.9 12.1 - - + -
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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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527A SER* 2.8 38.8 + - - +
528A ASP 3.8 2.9 - - - +
530A VAL* 1.3 76.7 - - - +
532A SER* 1.3 63.9 + - - +
534A ILE* 3.1 27.9 + - + +
535A SER* 3.1 18.1 + - - +
570A ILE* 4.5 14.1 - - + -
572A VAL* 5.0 2.0 - - + -
576A PHE* 4.4 20.6 - - + -
592A PHE* 4.8 5.4 - - + -
1B U 3.6 53.2 - - + +
3B U 4.6 3.6 - - - +
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Residues in contact with SER 532 (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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382A THR* 3.0 28.1 + - - +
384A LYS* 4.0 9.9 - - - +
528A ASP 3.0 15.6 + - - -
529A ILE 2.7 18.5 + - - -
531A ILE* 1.3 76.9 - - - +
533A LEU* 1.3 55.4 + - - +
535A SER* 3.6 4.0 + - - -
536A SER* 3.0 27.4 + - - -
3B U 3.4 39.4 + - - +
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Residues in contact with LEU 533 (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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352A PHE* 3.8 26.7 - - + -
381A PRO* 3.7 39.3 - - + -
382A THR* 4.2 5.2 - - + -
385A PHE* 3.8 30.1 - - + -
529A ILE* 3.2 14.5 + - + +
530A VAL* 3.0 16.6 + - + +
532A SER* 1.3 79.6 + - - +
534A ILE* 1.3 59.4 + - - +
536A SER* 4.2 1.8 - - - -
537A TYR* 2.9 40.5 + - + +
555A ILE* 3.5 17.0 - - + -
558A THR* 5.0 7.6 - - + -
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Residues in contact with ILE 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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530A VAL 2.9 19.1 + - - +
531A ILE* 3.1 15.9 + - + +
533A LEU* 1.3 75.0 - - - +
535A SER* 1.3 55.3 + - - +
537A TYR* 3.7 2.4 - - - +
538A ARG* 2.7 43.8 + - + +
552A LEU* 4.4 16.0 - - + +
555A ILE* 4.3 16.2 - - + -
556A ALA* 4.0 17.9 - - + +
570A ILE* 4.1 11.0 - - + -
580A LEU* 6.3 2.5 - - + -
591A MET* 3.4 37.2 - - + -
592A PHE* 4.0 16.2 - - + -
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Residues in contact with SER 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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531A ILE* 3.1 16.8 + - - +
532A SER* 3.6 6.9 - - - -
534A ILE* 1.3 80.5 - - - +
536A SER* 1.3 61.2 + - - +
538A ARG* 3.2 10.9 + - - +
539A SER* 3.1 21.8 + - - -
3B U 3.3 37.6 + - - -
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Residues in contact with SER 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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381A PRO* 3.8 19.7 + - - +
382A THR* 3.7 11.7 - - - -
453A VAL* 5.9 1.9 - - - +
532A SER 3.0 19.8 + - - -
533A LEU* 3.6 5.6 - - - -
534A ILE 3.3 0.2 - - - -
535A SER* 1.3 78.9 - - - +
537A TYR* 1.3 66.7 + - - +
539A SER* 3.3 15.4 + - - -
540A CYS* 3.7 10.3 - - - -
3B U 3.5 28.2 + - - -
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Residues in contact with TYR 537 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A PHE* 3.2 24.8 - + - -
381A PRO* 4.3 8.3 - - + -
452A GLY* 3.2 13.0 - - - -
453A VAL* 3.5 20.4 + - + -
484A GLU* 2.5 38.2 + - + -
533A LEU* 2.9 43.1 + - + +
534A ILE 4.0 2.5 - - - +
536A SER* 1.3 78.4 + - - +
538A ARG* 1.3 64.8 + - - +
539A SER 3.4 0.3 + - - -
540A CYS* 3.4 14.6 + - - -
541A ILE* 3.3 19.0 + - - +
546A PHE* 3.9 21.8 - + - -
551A ILE* 4.1 7.0 - - + -
552A LEU* 4.3 9.0 - - + -
555A ILE* 3.7 33.0 - - + -
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Residues in contact with ARG 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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534A ILE* 2.7 29.9 + - - +
535A SER* 3.2 10.7 + - - +
537A TYR* 1.3 74.8 - - - +
539A SER* 1.3 62.2 + - - +
540A CYS 3.3 0.7 + - - -
541A ILE* 3.6 21.6 + - + +
548A GLU* 4.2 16.1 + - - +
552A LEU* 4.2 19.2 - - + +
579A LYS 5.2 0.2 + - - -
580A LEU* 2.7 44.9 + - - +
581A GLY 4.6 0.8 + - - -
582A LEU* 3.3 33.9 - - - +
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Residues in contact with SER 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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455A SER 5.5 2.3 + - - -
535A SER 3.1 10.6 + - - -
536A SER 3.5 11.3 + - - -
537A TYR 3.3 0.2 - - - -
538A ARG* 1.3 78.1 - - - +
540A CYS* 1.3 61.6 + - - +
541A ILE 3.8 0.5 + - - -
542A LYS* 5.0 3.5 + - - +
543A GLU* 5.3 2.1 + - - +
3B U 4.2 30.0 + - - -
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Residues in contact with CYS 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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453A VAL* 4.2 11.7 - - - -
454A PRO 5.0 2.0 - - - +
455A SER* 5.3 5.2 - - - +
536A SER* 3.7 12.8 - - - +
537A TYR* 3.7 17.3 - - - -
538A ARG 3.3 0.4 - - - -
539A SER* 1.3 80.4 - - - +
541A ILE* 1.3 59.3 + - - +
542A LYS 3.4 2.5 - - - -
543A GLU* 3.9 16.2 - - - +
544A TYR* 2.9 68.2 + - + +
546A PHE* 4.3 5.8 - - - -
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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