Contacts of the helix formed by residues 493 - 513 (chain A) in PDB entry 1ORZ
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 493 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ARG* 1.4 70.5 + - - +
494A GLN* 1.3 78.0 + - + +
495A SER* 3.2 16.2 - - - +
496A SER* 2.6 34.6 + - - -
497A LEU* 3.1 7.8 + - - +
559A ARG* 3.1 10.5 - - - +
560A GLU* 2.7 28.8 + - - +
561A ASP* 2.9 27.1 - - - +
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Residues in contact with GLN 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A THR* 1.3 75.9 - - + +
495A SER* 1.3 76.0 + - - +
497A LEU* 3.3 4.6 + - - +
498A ASP* 3.0 24.1 + - - +
548A ALA* 5.7 1.7 - - + +
559A ARG* 3.0 27.4 + - - +
561A ASP* 3.3 18.9 + - - +
562A TYR* 3.8 19.5 - - - -
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Residues in contact with SER 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A THR* 3.2 9.3 - - - +
494A GLN* 1.3 89.7 + - - +
496A SER* 1.3 63.3 + - - +
498A ASP* 3.3 7.1 + - - +
499A GLU* 3.2 19.1 + - - +
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Residues in contact with SER 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A LYS* 4.8 10.8 - - - +
487A ASP* 2.9 46.0 + - - +
492A ARG* 4.5 0.7 - - - -
493A THR* 2.6 34.6 + - - -
495A SER* 1.3 79.8 - - - +
497A LEU* 1.3 66.7 + - - +
499A GLU* 2.9 15.9 + - - +
500A GLY 3.0 4.2 + - - -
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Residues in contact with LEU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A ASP* 3.3 35.0 - - + +
488A VAL* 4.5 6.7 - - + +
492A ARG* 4.5 11.4 - - + -
493A THR 3.1 10.3 + - - +
494A GLN 3.9 5.2 - - - +
496A SER* 1.3 79.3 + - - +
498A ASP* 1.3 53.3 + - - +
500A GLY* 4.4 0.7 - - - +
501A VAL* 2.7 38.9 + - + +
544A ALA* 5.0 9.3 - - + +
547A ALA* 3.2 22.9 - - + +
548A ALA* 3.0 50.7 - - + +
559A ARG* 3.9 14.8 - - - +
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Residues in contact with ASP 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A GLN 3.0 13.5 + - - +
495A SER* 3.6 10.8 - - - +
497A LEU* 1.3 77.4 - - - +
499A GLU* 1.3 61.6 + - - +
501A VAL* 2.7 29.4 - - - +
502A ARG* 3.2 25.6 + - - +
548A ALA* 5.4 1.5 - - - +
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Residues in contact with GLU 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A LYS* 5.6 6.1 - - - +
487A ASP* 4.7 4.3 - - - +
495A SER 3.2 8.5 + - - +
496A SER* 2.9 11.0 + - - +
498A ASP* 1.3 81.4 + - - +
500A GLY* 1.3 63.1 + - - +
502A ARG* 2.9 34.9 + - - +
503A ASN* 2.9 22.7 + - + +
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Residues in contact with GLY 500 (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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483A THR* 3.8 7.6 - - - -
487A ASP* 3.4 27.7 + - - -
496A SER 3.0 10.1 + - - -
497A LEU 3.7 1.6 - - - -
499A GLU* 1.3 73.9 - - - +
501A VAL* 1.3 66.7 + - - +
503A ASN* 2.9 6.2 + - - +
504A ILE* 2.8 30.2 + - - +
544A ALA* 5.6 1.6 - - - -
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Residues in contact with VAL 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A LEU* 2.7 20.7 + - + +
498A ASP* 2.7 36.3 - - - +
500A GLY* 1.3 73.1 - - - +
502A ARG* 1.3 64.6 + - + +
504A ILE* 3.3 16.8 + - + +
505A THR* 3.4 14.0 + - - +
544A ALA* 4.8 16.0 - - + +
545A VAL* 4.5 23.8 - - + +
548A ALA* 6.1 2.7 - - + -
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Residues in contact with ARG 502 (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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498A ASP* 3.9 20.1 + - - +
499A GLU* 2.9 40.3 + - - +
501A VAL* 1.3 81.4 - - + +
503A ASN* 1.3 67.8 + - - +
505A THR* 2.9 20.2 + - - -
506A ALA* 3.2 10.4 + - + +
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Residues in contact with ASN 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A ASN* 3.3 32.3 + - - +
483A THR* 4.1 16.0 + - - +
499A GLU* 2.9 15.3 + - + +
500A GLY* 2.9 14.7 + - - +
502A ARG* 1.3 75.9 - - - +
504A ILE* 1.3 65.4 + - - +
506A ALA* 2.9 18.9 + - - +
507A VAL* 2.9 11.8 + - - +
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Residues in contact with ILE 504 (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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480A MET* 5.2 5.2 - - + +
483A THR* 3.8 28.3 - - + -
484A MET* 5.1 3.6 - - - -
500A GLY 2.8 20.3 + - - +
501A VAL* 3.5 11.0 - - + +
502A ARG 3.1 0.2 - - - -
503A ASN* 1.3 73.7 - - - +
505A THR* 1.3 55.2 + - - +
507A VAL* 2.7 15.3 - - + +
508A GLU* 2.6 37.7 + - + +
537A LEU* 4.0 12.8 - - + -
540A ALA* 4.8 17.5 - - + +
541A SER* 3.2 35.4 - - - +
544A ALA* 5.1 7.9 - - + -
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Residues in contact with THR 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A VAL* 3.4 11.5 + - - +
502A ARG* 2.9 14.7 + - - -
504A ILE* 1.3 79.0 - - - +
506A ALA* 1.3 66.4 + - - +
508A GLU* 3.1 16.6 + - - +
509A LYS* 3.1 44.7 + - + +
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Residues in contact with ALA 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 ARG* 3.2 6.2 + - + +
503A ASN* 2.9 17.3 + - - +
505A THR* 1.3 81.1 - - - +
507A VAL* 1.3 55.0 + - - +
509A LYS* 3.3 14.6 + - - +
510A THR* 2.6 30.0 + - - +
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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
----------------------------------------------------------
476A ILE* 3.1 41.7 - - + +
479A ASN* 4.8 10.5 - - + +
480A MET* 4.1 13.2 - - + -
503A ASN* 2.9 15.3 + - - +
504A ILE* 2.7 43.1 - - + +
506A ALA* 1.3 74.3 - - - +
508A GLU* 1.3 53.9 + - - +
510A THR* 2.8 11.2 + - + -
511A PHE* 2.7 33.7 + - + +
537A LEU* 4.0 13.7 - - + -
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Residues in contact with GLU 508 (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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504A ILE* 2.6 24.2 + - + +
505A THR* 3.1 17.0 + - - +
507A VAL* 1.3 73.2 - - - +
509A LYS* 1.3 64.2 + - + +
511A PHE* 3.3 10.1 + - - +
512A ASP* 3.1 22.3 + - - +
537A LEU* 3.2 37.3 - - + +
541A SER* 5.2 4.0 + - - -
581A VAL* 4.8 4.3 - - - +
589A TYR* 4.0 22.4 + - - -
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Residues in contact with LYS 509 (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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505A THR* 3.1 33.7 + - + +
506A ALA* 3.6 12.0 - - - +
508A GLU* 1.3 78.6 - - + +
510A THR* 1.3 63.9 + - - +
512A ASP* 3.0 29.3 + - - +
513A ASP* 3.7 7.1 + - - +
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Residues in contact with THR 510 (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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471A ARG* 2.7 69.3 + - - +
476A ILE* 3.3 16.8 - - + -
506A ALA* 2.6 20.4 + - - +
507A VAL* 2.9 18.5 - - + -
509A LYS* 1.3 77.1 - - - +
511A PHE* 1.3 57.2 + - - +
513A ASP* 3.1 11.5 + - - +
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Residues in contact with PHE 511 (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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463A LYS* 4.6 16.7 + - - -
464A LEU* 5.3 7.2 - - + -
473A THR* 4.8 1.1 - - - -
476A ILE* 3.4 8.3 - - + +
507A VAL* 2.7 14.1 + - + +
508A GLU 3.6 8.7 - - - +
509A LYS 3.2 0.2 - - - -
510A THR* 1.3 70.8 - - - +
512A ASP* 1.3 77.1 + - - +
514A VAL* 2.8 47.8 + - + +
530A THR* 4.4 9.2 - - - -
531A LEU* 5.9 0.4 - - - -
533A LEU* 3.1 39.9 - - + -
534A GLN* 3.7 37.5 - - + -
537A LEU* 4.6 16.4 - - + -
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Residues in contact with ASP 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A LYS* 2.8 34.3 - - - +
470A SER* 5.2 0.2 + - - -
508A GLU* 3.1 21.9 - - - +
509A LYS* 3.0 18.0 + - - +
511A PHE* 1.3 87.0 - - - +
513A ASP* 1.3 61.5 + - - +
514A VAL 3.4 1.4 + - - +
537A LEU* 5.9 0.5 - - - +
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Residues in contact with ASP 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A SER* 2.7 31.1 + - - +
471A ARG* 2.7 26.3 + - + +
509A LYS 3.7 4.5 + - - +
510A THR* 3.1 11.4 + - - +
511A PHE 3.1 0.4 - - - -
512A ASP* 1.3 77.3 - - - +
514A VAL* 1.3 52.0 + - - -
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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
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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