Contacts of the helix formed by residues 575 - 592 (chain A) in PDB entry 4IDT
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 ALA 575 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A HIS* 3.4 52.3 - - + +
512A LEU* 3.5 12.9 - - + +
541A LEU* 4.3 14.4 - - + +
574A ASP* 1.3 76.3 - - - +
576A LYS* 1.3 64.4 + - + +
577A VAL 3.0 0.2 - - - -
578A ASP* 2.9 15.5 + - - +
579A VAL* 3.8 0.7 + - - -
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Residues in contact with LYS 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A ASP* 3.0 23.6 + - - +
575A ALA* 1.3 77.8 - - + +
577A VAL* 1.3 62.9 + - - +
579A VAL* 3.0 19.5 + - + +
580A TRP 3.2 4.7 + - - -
638A PRO* 2.7 29.7 + - + +
639A ILE* 3.8 10.1 + - - +
641A ARG* 2.6 54.7 + - + +
642A VAL 3.4 26.0 - - - +
643A SER* 4.0 13.7 - - - +
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Residues in contact with VAL 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A LEU* 4.5 6.5 - - + -
514A GLY* 5.1 1.3 - - - -
555A TYR* 4.3 20.9 - - + +
563A MET* 5.8 1.6 - - - -
564A ALA* 4.4 7.4 - - + +
566A GLU* 3.5 17.9 - - + +
567A VAL* 3.7 31.0 - - + -
573A CYS* 3.9 17.7 - - + -
574A ASP 3.1 17.5 + - - +
576A LYS* 1.3 78.7 - - - +
578A ASP* 1.3 69.7 + - - +
580A TRP* 3.5 3.8 + - - +
581A SER* 3.1 29.9 + - - +
641A ARG* 3.7 5.8 - - - +
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Residues in contact with ASP 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A LEU* 4.0 13.2 - - + +
507A HIS* 3.0 26.3 + - + +
512A LEU* 3.0 11.4 - - - +
513A HIS* 2.8 26.7 + - - +
514A GLY* 2.9 26.4 + - - -
516A VAL* 3.7 16.1 - - + +
575A ALA 2.9 10.6 + - - +
577A VAL* 1.3 75.8 - - - +
579A VAL* 1.3 59.9 + - - +
581A SER* 3.6 7.0 + - - -
582A SER* 2.8 31.1 + - - -
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Residues in contact with VAL 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A LEU* 5.2 2.0 - - + -
503A LEU* 5.5 0.4 - - + -
507A HIS* 4.7 2.9 - - + -
575A ALA 4.2 3.6 - - - +
576A LYS* 3.0 21.7 + - + +
578A ASP* 1.3 75.9 - - - +
580A TRP* 1.3 61.9 + - - +
582A SER* 2.5 24.9 + - - -
583A CYS* 3.1 9.7 + - - -
633A GLY* 4.0 16.4 - - - +
641A ARG* 4.2 3.4 - - - -
642A VAL* 3.5 28.7 - - + +
643A SER* 4.4 1.3 - - - -
644A ALA* 3.8 27.6 - - + +
647A LEU* 3.6 25.1 - - + -
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Residues in contact with TRP 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A THR 4.9 0.4 + - - -
562A HIS 3.5 18.6 - - - -
563A MET 3.1 15.6 + - - -
564A ALA* 3.6 11.0 - - + -
565A PRO* 3.6 33.7 - - + -
576A LYS 3.2 1.8 + - - -
577A VAL 3.6 8.1 - - - +
579A VAL* 1.3 77.6 - - - +
581A SER* 1.3 63.7 + - - +
583A CYS* 3.0 4.5 + - - +
584A CYS* 2.9 34.0 + - - -
596A TRP* 4.5 11.8 - + - +
608A ILE* 4.7 2.7 - - + -
613A PRO* 4.2 1.3 - - + -
614A PRO* 4.2 27.6 - - + -
633A GLY 3.7 9.1 + - - -
634A LEU* 3.4 47.2 - - + +
635A ARG 3.8 9.2 - - - -
636A LYS* 4.0 8.3 - - + -
641A ARG* 3.8 29.4 - - - +
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Residues in contact with SER 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A GLY 5.6 1.6 - - - -
515A ASP* 5.6 1.4 + - - -
516A VAL* 3.3 32.1 + - - -
555A TYR* 5.6 1.2 + - - -
562A HIS* 2.9 32.3 + - - +
563A MET* 5.5 2.4 - - - -
577A VAL* 3.1 19.4 + - - +
578A ASP* 3.6 10.1 + - - -
580A TRP* 1.3 77.3 - - - +
582A SER* 1.3 58.3 + - - +
584A CYS* 3.0 6.4 + - - +
585A MET* 2.8 26.2 + - - +
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Residues in contact with SER 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A LEU* 3.9 21.7 - - - +
499A ALA* 5.9 0.7 - - - -
500A LEU* 3.7 20.3 - - - +
503A LEU* 4.2 10.1 - - - -
516A VAL* 3.9 12.1 - - - +
578A ASP 2.8 14.6 + - - -
579A VAL* 2.5 23.9 + - - -
581A SER* 1.3 77.9 - - - +
583A CYS* 1.3 55.6 + - - +
585A MET* 3.2 9.2 + - - +
586A MET* 2.9 25.1 + - - +
647A LEU* 3.7 6.6 - - - +
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Residues in contact with CYS 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A LEU* 5.4 4.9 - - - -
579A VAL 3.1 8.7 + - - +
580A TRP 3.0 6.5 + - - +
582A SER* 1.3 77.5 + - - +
584A CYS* 1.3 60.9 + - - +
585A MET 3.2 0.2 - - - -
586A MET* 3.3 8.3 + - - +
587A LEU* 3.0 32.2 + - - +
630A ILE* 4.1 22.0 - - + +
633A GLY* 3.6 28.5 - - - -
634A LEU* 3.6 26.5 - - + -
647A LEU* 3.7 17.9 - - - -
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Residues in contact with CYS 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A THR 3.4 18.4 - - - -
562A HIS* 3.7 21.0 + - + -
580A TRP* 2.9 44.6 + - - +
581A SER 3.3 8.7 - - - +
583A CYS* 1.3 77.3 - - - +
585A MET* 1.3 62.1 + - - +
587A LEU* 3.4 7.6 + - - +
588A HIS* 3.1 21.0 + - - +
595A PRO* 3.6 24.2 - - + +
596A TRP* 5.0 2.0 - - - -
614A PRO* 5.4 1.8 - - - -
634A LEU* 4.3 6.3 - - - -
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Residues in contact with MET 585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A LEU* 4.1 6.1 - - + -
495A TYR 5.3 0.2 - - - +
496A LEU* 4.7 7.6 - - + +
499A ALA* 4.2 24.9 - - + -
516A VAL* 4.4 10.1 - - + -
517A LYS* 3.3 32.8 - - - +
518A ALA* 3.3 24.9 - - + +
521A VAL* 3.7 12.8 - - + -
562A HIS* 3.5 12.7 + - - +
581A SER 2.8 11.7 + - - +
582A SER* 3.3 14.1 - - - +
583A CYS 3.2 0.2 - - - -
584A CYS* 1.3 75.2 - - - +
586A MET* 1.3 59.7 + - - +
588A HIS* 3.0 7.0 + - - +
589A MET* 2.9 46.4 + - + +
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Residues in contact with MET 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A GLU 4.4 0.7 - - - +
492A ALA* 3.7 42.8 - - + +
493A LEU* 3.8 32.1 - - + +
496A LEU* 3.9 23.3 - - + -
582A SER 2.9 13.4 + - - +
583A CYS* 3.4 13.2 - - - +
585A MET* 1.3 74.0 - - - +
587A LEU* 1.3 65.6 + - - +
589A MET* 3.1 11.4 + - - +
590A LEU* 2.9 41.2 + - + +
626A THR* 4.2 9.6 - - + -
630A ILE* 3.8 21.8 - - + -
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Residues in contact with LEU 587 (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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583A CYS 3.0 15.6 + - - +
584A CYS* 3.6 9.0 - - - +
585A MET 3.3 0.2 - - - -
586A MET* 1.3 75.5 - - - +
588A HIS* 1.3 57.1 + - - +
590A LEU* 3.2 3.3 + - + -
591A ASN* 2.8 41.0 + - - +
593A CYS 4.2 2.5 - - - +
595A PRO* 4.1 28.7 - - + -
614A PRO* 3.8 20.6 - - + +
617A GLU* 3.8 32.5 - - + +
618A ILE* 3.9 18.6 - - + +
619A PRO* 4.8 2.5 - - + -
630A ILE* 4.6 12.3 - - + -
634A LEU* 4.0 19.1 - - + -
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Residues in contact with HIS 588 (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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478A GLY* 5.3 5.4 - - - -
481A VAL* 3.6 23.6 - - + +
518A ALA* 4.1 25.8 + - + +
519A ASP* 5.8 1.8 - - - -
562A HIS* 4.9 1.6 + - - -
584A CYS 3.1 12.5 + - - +
585A MET* 3.0 11.4 + - - +
587A LEU* 1.3 76.9 - - - +
589A MET* 1.3 57.9 + - - +
592A GLY* 2.8 29.9 + - - -
593A CYS* 3.4 24.6 - - - +
594A HIS* 2.9 44.3 + + + +
595A PRO* 4.7 0.2 - - - +
373B LYS* 4.8 2.8 + - - -
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Residues in contact with MET 589 (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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477A LEU* 3.8 23.1 - - + -
481A VAL* 3.9 18.4 - - + -
486A CYS* 3.3 5.4 - - - +
487A LEU* 2.8 58.5 + - + -
492A ALA* 3.5 35.2 - - + +
495A TYR* 4.2 3.4 - - - -
496A LEU* 4.2 12.6 - - + +
518A ALA* 5.3 1.1 - - + -
585A MET* 2.9 28.3 + - + +
586A MET* 3.5 28.9 - - - +
588A HIS* 1.3 76.3 - - + +
590A LEU* 1.3 60.5 + - - +
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Residues in contact with LEU 590 (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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486A CYS* 3.3 18.2 - - - +
487A LEU 4.2 6.4 - - - +
489A GLU* 3.8 31.9 - - + +
492A ALA* 3.9 9.9 - - + -
586A MET* 2.9 46.5 + - + +
587A LEU* 3.8 5.8 - - + +
589A MET* 1.3 79.8 - - - +
591A ASN* 1.3 60.2 + - - +
619A PRO* 4.0 33.7 - - + +
622A CYS* 4.0 19.1 - - - -
630A ILE* 4.1 10.3 - - + -
670A LYS* 5.2 5.0 + - - -
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Residues in contact with ASN 591 (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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486A CYS* 3.9 5.4 - - - -
587A LEU* 2.8 31.7 + - - +
590A LEU* 1.3 78.0 - - - +
592A GLY* 1.3 61.6 + - - +
593A CYS* 3.4 19.6 + - - +
617A GLU* 2.8 28.4 + - - +
619A PRO* 3.7 22.1 - - - +
672A PRO* 3.4 1.0 - - - +
673A ARG* 3.0 59.2 + - + +
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Residues in contact with GLY 592 (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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481A VAL* 4.3 4.0 - - - +
485A GLY 3.0 29.2 - - - +
486A CYS* 4.0 1.4 - - - +
588A HIS* 2.8 27.6 + - - -
590A LEU 3.6 1.4 - - - -
591A ASN* 1.3 73.2 - - - +
593A CYS* 1.3 59.6 + - - +
672A PRO* 3.9 13.3 - - - +
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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