Contacts of the helix formed by residues 563 - 579 (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 ARG 563 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536A ILE* 5.3 11.2 - - + -
537A PRO 4.5 7.0 - - - +
538A VAL* 3.7 21.8 - - + -
561A TYR 5.9 0.2 - - - +
562A ARG* 1.3 73.1 - - - +
564A TYR* 1.3 68.4 + - - +
565A LEU* 3.2 7.6 - - + +
566A GLU* 2.9 49.0 + - + +
567A PHE* 3.3 13.2 - - - -
640A PHE 5.1 0.4 - - - -
641A LEU* 4.5 22.0 - - - +
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Residues in contact with TYR 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A PRO 4.9 0.6 + - - -
539A PHE* 3.9 19.6 - + + -
562A ARG 3.9 1.2 + - - -
563A ARG* 1.3 73.8 - - - +
565A LEU* 1.3 74.2 + - + +
566A GLU 3.2 0.3 + - - -
567A PHE* 3.3 19.0 + - - +
568A TYR* 3.3 32.7 + + - -
588A SER 4.0 1.7 + - - -
589A LYS* 3.6 14.7 - - + -
590A ARG 3.2 23.2 + - - -
595A LYS* 4.0 27.4 - - + -
599A PHE* 3.6 30.4 - + - -
600A LEU* 4.3 26.4 - - + +
603A LYS* 4.6 4.4 - - + +
607A PHE* 3.5 33.4 - + - -
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Residues in contact with LEU 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A ARG* 3.2 6.7 - - + +
564A TYR* 1.3 93.6 - - + +
566A GLU* 1.3 63.9 + - + +
568A TYR* 3.1 17.9 + - + +
569A VAL* 3.2 17.7 + - + +
589A LYS* 3.8 31.9 - - + +
595A LYS* 4.7 19.3 - - + +
640A PHE 4.8 1.3 - - - +
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Residues in contact with GLU 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A TYR 4.3 2.4 - - - +
562A ARG* 2.7 39.8 + - - -
563A ARG* 2.9 61.8 + - + +
565A LEU* 1.3 78.4 - - + +
567A PHE* 1.3 55.8 + - - +
569A VAL* 3.3 3.5 + - - +
570A LEU* 3.0 27.7 + - - +
629A PHE* 3.6 13.0 - - + -
640A PHE* 3.5 38.4 + - + +
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Residues in contact with PHE 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A ILE* 4.2 4.9 - - + -
539A PHE* 3.4 33.9 - + + -
541A ILE* 4.2 18.6 - - + -
562A ARG* 3.7 18.2 - - + -
563A ARG 3.3 12.1 - - - -
564A TYR 3.5 9.4 - - - +
565A LEU 3.2 0.4 - - - -
566A GLU* 1.3 76.4 - - - +
568A TYR* 1.3 56.9 + - + +
570A LEU* 3.2 5.6 + - - +
571A GLU 3.0 23.7 + - - -
586A LEU* 3.4 20.8 - - + +
607A PHE* 3.6 36.3 - + + -
610A TYR* 4.6 11.9 - + + -
611A LEU* 3.8 28.5 - - + -
629A PHE* 4.0 15.3 - + - -
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Residues in contact with TYR 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A TYR* 3.3 55.2 + + - -
565A LEU* 3.1 10.0 + - - +
567A PHE* 1.3 74.3 - - + +
569A VAL* 1.3 62.1 + - + +
571A GLU* 3.4 12.7 + - - +
572A SER* 2.9 28.6 + - - -
586A LEU* 3.8 22.2 - - + -
587A PRO* 2.6 35.9 + - - +
588A SER* 3.6 3.3 + - - -
589A LYS* 3.8 41.7 - - + +
607A PHE* 4.0 16.5 - + - -
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Residues in contact with VAL 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A LEU* 3.2 13.4 + - + +
566A GLU 3.6 7.0 - - - +
568A TYR* 1.3 74.3 - - + +
570A LEU* 1.3 60.1 + - - +
572A SER* 3.3 5.8 + - - -
573A LYS* 2.9 54.8 + - + +
640A PHE* 3.5 41.1 - - + +
641A LEU 4.3 11.7 - - - +
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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
----------------------------------------------------------
566A GLU 3.0 14.6 + - - +
567A PHE* 3.2 8.3 + - + +
569A VAL* 1.3 76.7 - - - +
571A GLU* 1.3 57.1 + - - +
573A LYS* 3.7 1.2 - - - -
574A LEU* 2.8 64.0 + - + +
610A TYR* 4.5 7.0 - - + +
611A LEU* 4.0 15.9 - - + -
614A LEU* 4.4 4.5 - - + -
625A LEU* 4.1 20.0 - - + +
626A LEU* 4.2 9.0 - - + -
629A PHE* 3.8 39.9 - - + -
640A PHE* 3.8 24.0 - - + -
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Residues in contact with GLU 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A PHE 3.0 14.8 + - - +
568A TYR* 3.6 14.7 - - - +
569A VAL 3.3 0.2 - - - -
570A LEU* 1.3 77.5 - - - +
572A SER* 1.3 62.4 + - - +
574A LEU* 4.0 2.6 - - - +
575A THR* 3.0 42.8 + - + +
584A ALA 4.5 0.3 - - - +
585A GLN* 3.7 16.8 - - - +
586A LEU* 2.8 50.0 + - + +
610A TYR* 3.3 22.6 + - + +
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Residues in contact with SER 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A TYR 2.9 18.3 + - - -
569A VAL* 3.5 8.5 - - - -
571A GLU* 1.3 77.1 + - - +
573A LYS* 1.3 59.7 + - - +
575A THR* 3.0 8.1 + - - -
576A GLU* 3.0 32.8 + - - +
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Residues in contact with LYS 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A VAL* 2.9 35.0 + - + +
570A LEU* 3.9 3.4 - - - +
572A SER* 1.3 76.6 - - - +
574A LEU* 1.3 65.5 + - - +
576A GLU* 3.5 14.2 + - - +
577A PHE* 3.2 23.0 + - - +
625A LEU* 4.0 34.9 - - + +
639A GLN 2.7 28.6 + - - +
640A PHE* 4.8 3.6 - - + -
641A LEU 6.4 0.2 - - - -
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Residues in contact with LEU 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A LEU* 2.8 50.5 + - + +
571A GLU* 4.0 2.9 - - - +
573A LYS* 1.3 73.4 - - - +
575A THR* 1.3 53.3 + - + +
577A PHE 3.2 1.4 + - - -
578A HIS* 2.7 55.9 + - + +
581A PHE* 4.1 13.2 - - + -
610A TYR* 4.5 3.6 - - - +
614A LEU* 3.8 25.6 - - + -
620A LEU* 4.0 15.0 - - + -
623A SER* 3.7 22.9 - - - +
625A LEU* 4.0 15.9 - - + -
626A LEU* 4.7 4.9 - - + +
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Residues in contact with THR 575 (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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571A GLU* 3.0 36.2 + - + +
572A SER* 3.0 12.1 + - - -
574A LEU* 1.3 75.3 - - - +
576A GLU* 1.3 57.2 + - - +
579A GLY* 2.7 42.1 + - - +
580A ALA* 4.2 19.7 - - + -
581A PHE* 4.4 12.8 - - + +
585A GLN* 5.5 4.7 - - - +
610A TYR* 5.9 0.4 - - - +
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Residues in contact with GLU 576 (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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572A SER* 3.0 21.2 + - - +
573A LYS* 3.6 15.0 - - - +
574A LEU 3.2 0.2 - - - -
575A THR* 1.3 79.5 + - - +
577A PHE* 1.3 62.7 + - - +
579A GLY 4.5 0.7 + - - -
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Residues in contact with PHE 577 (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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573A LYS 3.2 11.8 + - - +
574A LEU 3.2 3.4 + - - +
576A GLU* 1.3 83.4 - - - +
578A HIS* 1.3 87.0 + + + +
625A LEU* 4.8 10.5 - - + -
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Residues in contact with HIS 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A LEU* 2.7 36.0 + - + +
577A PHE* 1.3 99.5 - + + +
579A GLY* 1.3 58.4 + - - +
581A PHE* 3.7 18.6 - - + -
619A GLU* 3.6 31.0 + - + +
620A LEU* 3.5 25.5 - - + +
623A SER* 4.4 10.9 + - - -
625A LEU* 5.4 2.8 - - + +
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Residues in contact with GLY 579 (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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575A THR* 2.7 35.8 + - - -
576A GLU 4.5 0.8 + - - -
577A PHE 3.6 1.2 - - - -
578A HIS* 1.3 76.6 - - - +
580A ALA* 1.3 66.7 + - - +
581A PHE* 3.6 12.0 - - - -
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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
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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