Contacts of the helix formed by residues 494 - 509 (chain A) in PDB entry 4I5L
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 ASN 494 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492A ASP* 2.9 11.7 + - - +
493A PRO* 1.3 80.2 - - + +
495A TYR* 1.3 71.6 + - - +
496A LEU* 3.1 34.8 + - - +
497A HIS* 3.0 38.0 + - + +
498A ARG* 3.1 14.1 + - - +
277C GLU* 5.1 3.6 + - - -
279C ASP* 4.4 21.2 + - + +
280C ASP* 3.7 3.2 - - - +
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Residues in contact with TYR 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A ASN* 1.3 77.9 + - - +
496A LEU* 1.3 86.8 + - + +
498A ARG* 3.5 26.6 - - - +
499A MET* 2.9 56.1 + - + +
533A VAL* 3.6 22.0 - - + -
535A ASN* 3.8 14.6 - - + -
536A VAL* 4.2 2.9 - - + +
51C PRO* 3.2 36.5 + - + -
52C VAL 4.9 1.0 + - - -
53C THR* 4.9 2.9 + - - -
77C ASP 3.5 9.2 - - - -
78C THR* 3.3 10.2 + - - -
79C ASN* 3.1 32.8 + - - +
278C LEU 5.4 0.9 - - - -
279C ASP* 5.6 1.6 - - - -
280C ASP* 2.9 18.0 + - - +
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Residues in contact with LEU 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ARG* 4.2 26.3 + - - +
494A ASN* 3.1 21.2 + - - +
495A TYR* 1.3 110.1 - - + +
497A HIS* 1.3 66.0 + - + +
499A MET* 3.7 14.5 + - + +
500A THR* 2.9 23.6 + - - -
503A PHE* 5.6 0.9 - - - -
53C THR* 5.4 2.5 - - - +
72C GLY 4.3 4.9 - - - +
78C THR* 3.9 21.8 - - + -
277C GLU* 3.5 39.5 - - + +
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Residues in contact with HIS 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A LEU 4.9 0.2 - - - -
452A VAL* 3.8 44.0 + - + +
453A ASP 4.6 1.4 + - - -
454A HIS* 5.7 5.7 + + - -
459A ARG* 4.4 18.2 + - - -
489A MET* 4.0 10.3 - - - +
492A ASP* 2.8 42.0 + - + +
494A ASN* 3.0 21.9 + - + +
496A LEU* 1.3 88.6 - - + +
498A ARG* 1.3 65.2 + - - +
500A THR* 3.2 19.5 + - - -
501A THR* 3.5 7.3 + - - -
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Residues in contact with ARG 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A MET 3.7 10.8 - - - +
490A SER 3.1 24.2 - - - +
491A GLY* 4.6 0.9 - - - -
492A ASP 3.0 36.5 + - - +
493A PRO* 3.3 12.7 + - - +
494A ASN 3.1 1.9 + - - +
495A TYR* 3.1 19.7 + - - +
497A HIS* 1.3 76.9 - - - +
499A MET* 1.3 63.0 + - - +
501A THR* 3.1 20.7 + - - -
502A LEU 3.6 0.9 + - - -
528A MET* 3.4 22.2 - - + +
531A ASP* 2.6 43.1 + - - -
532A PRO* 4.6 5.4 - - - +
533A VAL* 3.1 12.1 - - - +
536A VAL* 4.0 4.4 - - + +
280C ASP* 2.9 29.1 + - - -
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Residues in contact with MET 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A TYR* 2.9 35.8 + - + +
496A LEU* 3.9 20.9 - - + +
497A HIS 3.3 0.2 - - - -
498A ARG* 1.3 76.8 - - - +
500A THR* 1.3 56.9 + - - +
502A LEU* 2.9 15.3 + - - +
503A PHE* 2.9 44.4 + - + -
535A ASN* 3.8 15.5 - - - +
536A VAL* 4.2 16.4 - - + -
539A ASN* 3.7 23.1 - - + +
77C ASP* 3.3 39.7 - - + +
78C THR* 5.1 0.9 - - + -
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Residues in contact with THR 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A LEU* 3.8 22.6 + - + +
459A ARG* 3.5 21.6 - - + +
463A THR* 3.8 25.8 - - + -
489A MET* 4.3 8.5 - - + -
496A LEU 2.9 15.5 + - - -
497A HIS* 3.2 11.7 + - - -
498A ARG 3.1 0.8 - - - -
499A MET* 1.3 75.7 - - - +
501A THR* 1.3 55.2 + - - +
503A PHE* 3.5 12.7 - - + -
504A CYS* 2.7 42.1 + - - -
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Residues in contact with THR 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A VAL* 3.2 27.9 + - + +
487A LEU* 4.3 4.3 - - - -
489A MET* 3.3 16.2 - - - +
490A SER* 3.2 38.1 + - - -
497A HIS 3.5 1.4 + - - -
498A ARG 3.1 11.9 + - - -
500A THR* 1.3 77.4 - - - +
502A LEU* 1.3 56.6 + - - +
504A CYS* 3.2 3.5 + - - +
505A ILE* 2.9 46.0 + - + +
524A THR* 4.4 6.1 - - + -
528A MET* 4.4 4.7 - - - -
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Residues in contact with LEU 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A ARG 3.6 1.5 + - - +
499A MET* 2.9 11.7 + - - +
501A THR* 1.3 78.7 - - - +
503A PHE* 1.3 62.4 + - + +
505A ILE* 3.3 7.0 + - + +
506A ASN* 2.9 35.0 + - - +
525A VAL* 4.1 33.2 - - + -
528A MET* 3.9 25.6 - - + -
536A VAL* 3.7 24.2 - - + +
539A ASN* 3.7 12.1 - - + +
540A VAL* 3.6 31.6 - - + +
543A SER* 3.6 16.8 + - - +
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Residues in contact with PHE 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A TYR* 4.4 27.1 - + - -
460A GLU* 6.5 0.9 - - - -
463A THR* 4.3 16.1 + - + +
496A LEU 5.6 0.7 - - - -
499A MET* 2.9 39.9 + - + -
500A THR* 3.1 17.5 + - + +
502A LEU* 1.3 79.5 - - + +
504A CYS* 1.3 61.8 + - - +
506A ASN* 3.3 30.6 - - - +
507A VAL* 3.3 13.5 + - - +
539A ASN* 3.4 28.0 - - + -
543A SER* 5.7 0.2 - - - -
77C ASP* 3.8 29.6 - - + -
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Residues in contact with CYS 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A LEU* 3.7 24.5 - - - -
463A THR* 3.7 22.2 - - - -
466A LEU* 4.1 12.1 - - + -
486A VAL* 3.5 23.3 - - + -
489A MET* 4.4 1.1 - - - -
500A THR* 2.7 26.9 + - - +
501A THR 3.5 4.5 - - - +
503A PHE* 1.3 69.4 - - - +
505A ILE* 1.3 62.6 + - - +
507A VAL* 3.2 9.6 + - - +
508A LEU* 2.8 39.4 + - + +
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Residues in contact with ILE 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A VAL* 4.7 2.5 - - + -
487A LEU* 4.1 13.5 - - + -
501A THR* 2.9 37.8 + - + +
502A LEU* 3.7 7.6 - - + +
504A CYS* 1.3 73.9 - - - +
506A ASN* 1.3 65.5 + - - +
509A SER* 3.0 26.3 + - - -
521A MET* 3.7 58.3 - - + +
524A THR* 4.7 3.8 - - + -
525A VAL* 3.8 25.6 - - + -
543A SER* 5.6 1.6 - - - -
547A ILE* 4.4 17.5 - - + -
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Residues in contact with ASN 506 (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 LEU 2.9 15.8 + - - +
503A PHE* 3.3 28.2 - - - +
505A ILE* 1.3 77.5 - - - +
507A VAL* 1.3 61.4 + - + +
509A SER* 3.2 13.7 + - - -
510A GLU* 3.9 4.0 - - - +
539A ASN* 5.6 1.2 + - - -
542A LYS* 5.5 2.0 - - - +
543A SER* 2.8 39.5 + - - +
546A LYS* 3.8 42.1 - - + +
547A ILE* 4.4 4.5 - - - +
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Residues in contact with VAL 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A THR* 3.4 34.3 - - - +
464A SER* 5.2 6.7 - - - -
466A LEU* 5.4 0.4 - - + -
467A LYS* 4.0 25.6 - - + +
503A PHE 3.3 11.6 + - - +
504A CYS* 3.2 12.5 + - - +
506A ASN* 1.3 79.7 - - + +
508A LEU* 1.3 74.0 + - + +
510A GLU* 3.3 28.6 + - - +
511A VAL* 3.8 7.6 - - - +
546A LYS* 6.1 0.2 - - - -
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Residues in contact with LEU 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A LEU* 4.2 23.3 - - + -
467A LYS* 4.5 3.4 - - - +
470A VAL* 3.7 29.8 - - + -
478A ALA* 5.3 0.7 - - + -
482A ILE* 4.4 11.0 - - + -
483A ILE* 4.5 4.5 - - + -
486A VAL* 4.3 22.4 - - + -
504A CYS* 2.8 26.2 + - + +
505A ILE 4.1 0.2 - - - +
507A VAL* 1.3 81.2 - - + +
509A SER* 1.3 56.9 + - - +
511A VAL* 3.0 8.2 + - + +
512A CYS* 2.9 37.6 + - - +
521A MET* 3.4 34.3 - - + -
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Residues in contact with SER 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A ILE* 3.0 11.2 + - - -
506A ASN 3.2 15.4 + - - -
508A LEU* 1.3 76.6 - - - +
510A GLU* 1.3 61.8 + - - +
511A VAL 3.1 0.6 + - - -
512A CYS* 4.3 1.6 - - - +
513A GLY* 4.2 5.0 + - - -
517A THR* 3.6 37.3 + - - -
521A MET* 4.6 4.4 - - - -
546A LYS* 5.4 0.7 - - - +
547A ILE* 3.3 25.4 - - - +
550A ILE* 3.7 28.5 - - - +
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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
------------------------------------------------------------
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