Contacts of the helix formed by residues 550 - 571 (chain A) in PDB entry 1Q9X
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 VAL 550 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A GLN* 4.1 28.9 - - + +
342A ASN* 5.8 2.9 - - - +
546A GLN* 3.3 33.0 + - + +
547A ARG* 4.8 7.6 - - + +
548A THR 3.1 0.6 - - - +
549A GLU* 1.3 77.7 - - + +
551A ALA* 1.3 55.2 + - + +
553A MET* 3.1 6.6 + - - +
554A THR* 2.4 51.4 + - - +
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Residues in contact with ALA 551 (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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346A ASP* 4.4 4.5 - - - +
547A ARG 3.5 18.9 + - - +
548A THR* 3.5 6.7 + - + +
550A VAL* 1.3 79.6 - - - +
552A GLY* 1.3 54.0 - - - +
554A THR* 3.9 5.8 - - - -
555A ALA* 2.8 39.0 + - - +
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Residues in contact with GLY 552 (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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485A HIS* 4.2 13.1 - - - +
488A TYR* 4.8 3.4 - - - -
489A MET* 3.5 22.3 - - - +
548A THR 2.5 22.5 + - - -
551A ALA* 1.3 70.0 - - - +
553A MET* 1.3 62.0 + - - +
555A ALA* 4.8 2.5 - - - -
556A GLN* 3.1 26.2 + - - +
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Residues in contact with MET 553 (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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489A MET* 3.3 34.0 - - + +
549A GLU* 3.1 31.9 + - - +
550A VAL* 3.1 7.9 + - - +
552A GLY* 1.3 76.3 - - - +
554A THR* 1.3 58.4 + - - +
555A ALA 3.3 0.2 + - - -
556A GLN* 3.3 4.5 + - - +
557A ILE* 2.8 55.1 + - + +
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Residues in contact with THR 554 (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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339A GLN* 4.0 15.1 + - + +
342A ASN* 4.0 11.1 + - + +
343A LEU* 3.6 43.6 - - + +
346A ASP* 4.5 7.6 - - - -
550A VAL* 2.4 48.4 + - - +
551A ALA* 3.9 5.4 + - - -
553A MET* 1.3 72.7 - - - +
555A ALA* 1.3 57.6 + - - +
557A ILE* 4.1 5.7 - - - +
558A ASN* 3.1 27.4 + - - +
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Residues in contact with ALA 555 (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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346A ASP* 3.6 19.4 + - - +
485A HIS* 4.1 22.4 - - + +
551A ALA 2.8 23.5 + - - +
552A GLY 4.5 0.7 - - - +
554A THR* 1.3 71.4 - - - +
556A GLN* 1.3 60.1 + - - +
558A ASN* 3.0 25.1 + - - +
559A ARG* 3.0 25.9 + - - +
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Residues in contact with GLN 556 (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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482A ARG* 3.8 42.1 + - - +
485A HIS* 4.3 14.9 - - + +
486A LYS* 3.4 37.2 - - + +
489A MET* 4.4 16.1 - - - +
552A GLY 3.1 19.3 + - - +
553A MET* 4.5 2.0 - - - +
555A ALA* 1.3 75.3 - - - +
557A ILE* 1.3 70.8 + - - +
558A ASN 3.0 1.3 - - - -
559A ARG* 2.7 31.0 + - - +
560A LYS* 2.7 17.3 + - - +
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Residues in contact with ILE 557 (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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343A LEU* 4.5 10.5 - - + -
553A MET* 2.8 49.2 + - + +
554A THR* 4.1 4.5 - - - +
556A GLN* 1.3 83.5 - - - +
558A ASN* 1.3 58.3 + - - +
560A LYS* 3.2 25.3 + - - +
561A LEU* 2.7 53.0 + - + +
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Residues in contact with ASN 558 (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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343A LEU* 3.5 18.4 - - + +
346A ASP* 2.8 33.4 + - - +
347A MET* 3.1 31.4 - - + +
350A TYR* 5.0 1.6 - - - +
554A THR 3.1 14.9 + - - +
555A ALA* 3.0 16.9 + - - +
556A GLN 3.0 0.8 - - - -
557A ILE* 1.3 75.4 - - - +
559A ARG* 1.3 64.9 + - - +
561A LEU* 3.7 9.5 - - - +
562A LEU* 2.7 42.6 + - - +
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Residues in contact with ARG 559 (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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346A ASP* 4.4 4.4 + - - -
350A TYR* 3.2 39.4 - - - +
478A VAL* 3.8 13.5 - - + -
481A GLN* 3.0 37.8 - - - +
482A ARG* 3.8 21.3 - - + -
485A HIS* 3.1 41.2 + - - -
555A ALA* 3.0 21.6 + - - +
556A GLN* 2.7 17.9 + - - +
558A ASN* 1.3 82.2 + - - +
560A LYS* 1.3 54.5 + - - +
561A LEU 3.1 1.3 - - - -
562A LEU* 3.0 7.3 + - - +
563A ILE* 2.7 40.3 + - - +
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Residues in contact with LYS 560 (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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482A ARG* 3.4 39.3 - - - +
556A GLN* 2.7 16.4 + - - +
557A ILE* 3.5 30.5 - - + +
559A ARG* 1.3 71.9 - - - +
561A LEU* 1.3 65.2 - - + +
563A ILE* 3.4 5.3 + - - +
564A ASN* 2.8 48.1 + - - +
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Residues in contact with LEU 561 (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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280A PHE* 4.3 18.6 - - + -
282A PHE* 4.5 20.4 - - + -
343A LEU* 3.6 38.1 - - + -
347A MET* 4.2 12.8 - - + -
557A ILE* 2.7 40.9 + - + +
558A ASN* 3.7 4.5 - - - +
560A LYS* 1.3 77.3 - - + +
562A LEU* 1.3 66.7 + - - +
564A ASN* 3.4 4.8 + - - +
565A SER* 3.0 27.1 + - - -
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Residues in contact with LEU 562 (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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347A MET* 3.1 30.1 - - + -
350A TYR* 3.8 22.9 - - + -
364A THR* 4.0 18.8 - - + -
365A TRP* 2.9 42.1 + - + +
368A ILE* 3.5 27.4 - - + -
478A VAL* 4.4 12.6 - - + -
558A ASN* 2.7 28.0 + - - +
559A ARG* 3.0 9.6 + - - +
561A LEU* 1.3 72.8 - - - +
563A ILE* 1.3 63.2 + - - +
565A SER* 2.9 11.2 + - - +
566A LEU 3.3 0.3 + - - -
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Residues in contact with ILE 563 (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 TRP* 4.6 3.6 - - + -
414A SER* 4.6 7.2 - - - +
417A PRO* 3.6 33.6 - - + +
475A ILE* 4.3 18.7 - - + +
478A VAL* 3.7 23.6 - - + -
479A PHE* 4.0 35.4 - - + +
482A ARG* 4.2 17.3 - - + -
559A ARG 2.7 27.6 + - - +
560A LYS* 3.7 4.5 - - - +
562A LEU* 1.3 76.6 - - - +
564A ASN* 1.3 73.5 + - - +
565A SER 3.3 0.5 + - - -
566A LEU* 3.6 12.1 + - - +
567A TYR 4.6 1.2 + - - -
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Residues in contact with ASN 564 (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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414A SER* 4.9 9.7 + - - -
417A PRO* 5.0 5.0 - - - +
560A LYS* 2.8 39.0 + - - +
561A LEU* 3.8 4.2 - - - +
563A ILE* 1.3 84.9 - - - +
565A SER* 1.3 62.1 + - - +
566A LEU 3.4 0.4 - - - -
567A TYR* 4.5 7.0 + - - +
568A GLY 4.8 2.4 + - - -
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Residues in contact with SER 565 (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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361A PRO* 3.8 29.7 - - - +
365A TRP* 3.2 13.6 + - - -
561A LEU 3.0 15.6 + - - -
562A LEU* 2.9 22.3 + - - +
563A ILE 3.2 0.2 - - - -
564A ASN* 1.3 78.9 - - - +
566A LEU* 1.3 65.7 + - - +
568A GLY* 3.1 13.7 + - - -
569A ALA 3.2 8.0 + - - -
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Residues in contact with LEU 566 (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 TRP* 3.6 42.3 - - + +
369A ILE* 5.3 2.0 - - + -
417A PRO* 5.8 1.3 - - + -
420A ILE* 4.5 2.0 - - + -
471A VAL* 3.9 15.5 - - + -
475A ILE* 3.5 42.0 - - + -
562A LEU 3.3 1.4 + - - -
563A ILE* 3.8 11.9 - - - +
564A ASN 3.4 0.4 - - - -
565A SER* 1.3 76.9 + - - +
567A TYR* 1.3 70.7 + - - +
569A ALA* 2.6 26.9 + - + +
570A LEU* 2.8 31.5 + - + -
575A PHE* 4.3 9.9 - - + -
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Residues in contact with TYR 567 (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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391A TYR* 2.9 26.9 + + - -
416A TYR* 3.5 49.1 - + + -
417A PRO* 5.8 2.6 - - + +
420A ILE* 5.4 4.6 - - + +
563A ILE 4.6 2.4 + - - -
564A ASN 4.5 6.1 + - - +
565A SER 3.4 1.2 + - - -
566A LEU* 1.3 77.0 - - - +
568A GLY* 1.3 59.8 + - - +
570A LEU* 3.0 12.6 + - + +
571A GLY* 2.9 27.5 + - - -
583A ALA* 4.6 6.1 - - + -
586A ILE* 4.1 35.0 - - + -
587A THR* 3.1 23.3 - - + +
913E G 3.9 35.1 + + - +
914E G 5.1 1.2 + - - -
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Residues in contact with GLY 568 (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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361A PRO* 5.8 0.9 - - - -
362A ILE* 4.6 0.8 - - - +
564A ASN 4.8 2.0 + - - -
565A SER 3.1 9.1 + - - -
566A LEU 2.8 1.6 + - - -
567A TYR* 1.3 81.1 - - - +
569A ALA* 1.3 65.3 + - - +
571A GLY* 3.5 5.4 + - - -
572A ASN* 3.3 16.3 + - - +
913E G 4.2 22.8 - - - +
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Residues in contact with ALA 569 (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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361A PRO* 4.1 22.6 - - - +
362A ILE* 3.9 16.2 - - + +
365A TRP* 4.6 0.9 - - + -
565A SER 3.2 5.8 + - - +
566A LEU* 2.6 24.4 + - + +
568A GLY* 1.3 69.8 - - - +
570A LEU* 1.3 64.1 + - - +
572A ASN* 3.0 18.7 + - - +
575A PHE* 3.3 38.4 - - + +
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Residues in contact with LEU 570 (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 ILE* 3.7 35.0 - - + -
425A ILE* 5.7 4.0 - - + -
427A PRO* 5.9 1.3 - - + -
471A VAL* 4.1 26.0 - - + -
566A LEU* 2.8 29.5 + - + +
567A TYR* 3.4 11.9 - - + +
569A ALA* 1.3 71.6 - - - +
571A GLY* 1.3 55.9 + - - +
572A ASN 3.3 0.4 - - - -
575A PHE* 3.9 21.3 - - + -
577A TYR 4.4 13.7 - - - +
578A TYR* 3.2 27.6 - - - -
579A ASP 4.3 1.6 + - - -
582A ASN* 6.3 2.0 - - + +
583A ALA* 4.5 7.0 - - + +
586A ILE* 4.1 17.3 - - + -
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Residues in contact with GLY 571 (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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391A TYR* 3.6 29.0 - - - -
567A TYR* 2.9 13.5 + - - -
568A GLY 3.5 3.8 + - - -
569A ALA 3.1 0.8 + - - -
570A LEU* 1.3 75.9 - - - +
572A ASN* 1.3 58.5 + - - +
573A VAL* 4.1 1.9 + - - +
578A TYR* 3.7 16.2 - - - -
583A ALA* 4.5 4.0 - - - -
913E G 3.6 21.7 - - - +
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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