Contacts of the helix formed by residues 596 - 616 (chain A) in PDB entry 4BGJ
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 596 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537A PRO* 4.3 5.4 - - - -
594A PRO* 3.3 28.5 + - + +
595A LYS* 1.3 75.1 - - - +
597A TYR* 1.3 65.8 + - - +
598A GLU* 3.4 10.4 + - - +
599A PHE* 3.0 22.7 + - - +
600A LEU* 3.0 25.4 + - - +
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Residues in contact with TYR 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A TYR* 6.0 0.9 - - - +
519A VAL* 3.6 44.9 + - + +
521A PHE* 3.7 36.1 - + + -
537A PRO* 4.4 10.8 - - - +
596A ASN* 1.3 75.3 - - - +
598A GLU* 1.3 73.4 + - + +
600A LEU* 3.3 4.1 + - - +
601A LYS* 2.8 65.0 + - + +
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Residues in contact with GLU 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A ASN* 3.3 10.9 + - - +
597A TYR* 1.3 92.2 - - + +
599A PHE* 1.3 57.4 + - - +
601A LYS* 3.5 8.4 + - + +
602A SER* 3.1 26.0 + - - -
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Residues in contact with PHE 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A TYR* 3.6 39.9 - + - -
588A SER 5.8 1.1 - - - -
590A ARG* 3.4 55.6 - - + +
594A PRO 3.8 9.0 - - - +
595A LYS* 4.1 17.3 - - + -
596A ASN* 3.0 20.1 + - - +
598A GLU* 1.3 74.8 - - - +
600A LEU* 1.3 71.8 + - + +
602A SER* 2.6 26.7 + - - -
603A LYS* 3.3 39.6 + - + +
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Residues in contact with LEU 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A VAL* 4.0 13.5 - - + -
537A PRO* 3.6 35.7 - - + +
538A VAL* 3.9 10.1 - - - +
539A PHE* 3.4 42.1 - - + -
564A TYR* 4.3 21.3 - - + +
595A LYS* 3.5 24.7 - - + +
596A ASN 3.0 24.8 + - - +
597A TYR* 3.7 6.1 - - - +
599A PHE* 1.3 81.0 - - + +
601A LYS* 1.3 65.0 + - - +
603A LYS* 3.0 11.9 + - - -
604A ARG* 3.1 9.9 + - - -
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Residues in contact with LYS 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A VAL* 3.9 14.0 - - + +
597A TYR* 2.8 55.5 + - + +
598A GLU* 3.6 10.8 - - + +
600A LEU* 1.3 74.3 - - - +
602A SER* 1.3 60.2 + - - +
603A LYS 3.4 0.7 + - - -
604A ARG* 3.5 23.4 + - - +
605A GLU* 5.1 1.2 + - - +
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Residues in contact with SER 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A GLU 3.1 13.4 + - - -
599A PHE* 2.6 34.4 + - - -
601A LYS* 1.3 76.5 - - - +
603A LYS* 1.3 71.1 + - - +
604A ARG 3.5 0.2 - - - -
605A GLU* 5.0 4.0 + - - +
606A GLU* 4.3 6.1 + - - +
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Residues in contact with LYS 603 (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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539A PHE* 4.5 5.6 - - + -
564A TYR* 4.6 3.4 - - + +
587A PRO* 4.5 12.7 - - + +
599A PHE* 3.4 44.9 - - + +
600A LEU* 3.0 8.1 + - - +
602A SER* 1.3 93.1 - - - +
604A ARG* 1.3 65.4 + - - +
605A GLU 3.2 3.2 + - - -
606A GLU* 3.1 35.3 + - - +
607A PHE* 3.0 49.3 + - + -
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Residues in contact with ARG 604 (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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516A ILE* 2.6 54.1 + - + +
517A PRO* 4.1 10.7 + - - +
518A TYR* 4.0 22.2 - - - +
519A VAL* 4.7 5.2 - - + +
539A PHE* 3.9 14.1 - - + -
600A LEU 3.1 7.7 + - - +
601A LYS* 3.5 24.3 + - - +
602A SER 3.5 0.2 - - - -
603A LYS* 1.3 76.9 - - - +
605A GLU* 1.3 85.5 + - + +
607A PHE* 3.4 2.3 + - - +
608A GLN* 2.9 43.3 + - - +
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Residues in contact with GLU 605 (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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601A LYS 5.8 0.7 - - - +
602A SER 5.0 3.9 + - - +
603A LYS 3.3 0.4 - - - -
604A ARG* 1.3 102.4 + - + +
606A GLU* 1.3 65.9 + - + +
608A GLN* 3.3 13.4 + - - +
609A GLU* 3.0 24.8 + - - +
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Residues in contact with GLU 606 (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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587A PRO* 3.5 30.8 - - + +
602A SER 4.3 7.2 + - - +
603A LYS* 3.1 38.9 + - - +
605A GLU* 1.3 77.9 - - + +
607A PHE* 1.3 66.9 + - + +
609A GLU* 3.3 6.9 + - - +
610A TYR* 2.9 29.4 + - - +
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Residues in contact with PHE 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A ILE* 3.9 7.9 - - + -
539A PHE* 3.6 23.3 - + + -
564A TYR* 3.5 39.3 - + - -
567A PHE* 3.6 42.7 - + + -
568A TYR* 4.0 12.3 - + - -
586A LEU* 4.0 17.3 - - + -
587A PRO* 4.1 18.8 - - + -
603A LYS* 3.0 33.2 + - + +
604A ARG* 3.7 5.4 - - - +
606A GLU* 1.3 78.8 - - + +
608A GLN* 1.3 66.1 + - - +
610A TYR* 3.5 7.2 + - - +
611A LEU* 3.3 28.2 + - - +
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Residues in contact with GLN 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ILE* 4.0 2.6 - - + +
515A SER* 3.4 12.1 - - - -
516A ILE* 2.7 53.6 + - + +
517A PRO* 5.1 0.2 - - - +
604A ARG* 2.9 28.4 + - - +
605A GLU* 3.5 12.2 + - - +
607A PHE* 1.3 78.1 - - - +
609A GLU* 1.3 62.8 + - - +
611A LEU* 3.4 2.6 + - - +
612A GLN* 3.1 51.7 + - - +
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Residues in contact with GLU 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A GLU 3.0 18.2 + - - +
606A GLU* 3.6 7.2 - - - +
608A GLN* 1.3 74.9 - - - +
610A TYR* 1.3 65.8 + - - +
612A GLN* 3.3 12.7 + - + +
613A LYS* 3.0 58.9 + - + +
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Residues in contact with TYR 610 (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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567A PHE* 4.6 6.5 - + - -
570A LEU* 4.5 12.3 - - + -
571A GLU* 3.3 31.9 + - + +
574A LEU* 4.5 3.3 - - - +
575A THR* 5.9 0.2 - - - +
581A PHE* 5.7 2.1 - - - -
584A ALA* 3.3 40.1 - - + +
585A GLN 4.0 11.7 - - - +
586A LEU* 3.5 43.3 - - + -
606A GLU 2.9 17.0 + - - +
607A PHE 3.6 5.4 - - - +
608A GLN 3.3 0.2 - - - -
609A GLU* 1.3 78.0 - - - +
611A LEU* 1.3 73.9 + - + +
613A LYS* 3.3 8.2 + - - +
614A LEU* 3.1 52.3 + - + +
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Residues in contact with LEU 611 (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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514A ILE* 3.8 27.4 - - + -
516A ILE* 4.1 9.6 - - + -
541A ILE* 4.2 16.2 - - + -
567A PHE* 3.8 22.9 - - + -
570A LEU* 4.0 16.8 - - + -
607A PHE 3.3 12.1 + - - +
608A GLN 3.8 2.0 - - - +
610A TYR* 1.3 87.5 - - + +
612A GLN* 1.3 63.1 + - - +
614A LEU* 3.2 11.5 + - + +
615A LEU* 3.1 28.4 + - + +
626A LEU* 4.5 8.5 - - + +
629A PHE* 4.0 22.2 - - + -
630A LEU* 4.4 9.0 - - + -
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Residues in contact with GLN 612 (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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514A ILE* 2.9 36.6 + - + +
515A SER* 4.5 2.0 - - - +
608A GLN* 3.1 43.7 + - - +
609A GLU* 3.3 14.2 + - + +
611A LEU* 1.3 76.2 - - - +
613A LYS* 1.3 63.3 + - + +
615A LEU* 3.3 22.1 + - + +
616A GLN* 3.6 14.6 + - - +
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Residues in contact with LYS 613 (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 ASP* 2.9 40.3 + - - +
584A ALA* 4.1 12.3 - - + +
609A GLU* 3.0 49.8 + - + +
610A TYR* 3.5 8.1 - - - +
612A GLN* 1.3 74.9 - - + +
614A LEU* 1.3 65.3 + - - +
616A GLN* 3.1 16.9 + - - +
617A HIS* 3.5 16.2 + - - -
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Residues in contact with LEU 614 (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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570A LEU* 4.4 3.8 - - + -
574A LEU* 3.8 21.3 - - + -
581A PHE* 4.4 20.2 - - + -
584A ALA* 3.9 20.0 - - + -
610A TYR* 3.1 50.6 + - + +
611A LEU* 3.2 11.0 + - + +
613A LYS* 1.3 76.3 - - - +
615A LEU* 1.3 62.6 + - - +
616A GLN 3.1 1.4 + - - -
617A HIS* 3.1 14.4 + - + +
620A LEU* 3.4 36.9 - - + +
626A LEU* 4.1 20.2 - - + -
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Residues in contact with LEU 615 (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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509A LEU* 3.6 37.0 - - + +
510A ALA* 3.3 24.9 + - - +
512A TRP* 3.5 22.9 - - + +
514A ILE* 3.8 33.2 - - + +
611A LEU* 3.1 21.0 + - + +
612A GLN* 3.6 13.2 - - + +
613A LYS 3.2 0.6 - - - -
614A LEU* 1.3 75.6 - - - +
616A GLN* 1.3 67.2 + - - +
617A HIS 3.4 4.2 + - - +
620A LEU* 5.7 0.8 - - - -
621A SER* 5.4 1.2 - - - -
626A LEU* 4.0 10.5 - - + -
630A LEU* 3.8 25.4 - - + -
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Residues in contact with GLN 616 (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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510A ALA* 3.2 41.5 + - - +
512A TRP 4.9 3.0 + - - -
612A GLN 3.7 12.5 + - - +
613A LYS* 3.1 10.0 + - - +
614A LEU 3.1 1.2 - - - -
615A LEU* 1.3 83.8 + - - +
617A HIS* 1.3 64.5 + - - +
618A PRO* 3.3 9.5 - - - +
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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