Contacts of the helix formed by residues 561 - 578 (chain A) in PDB entry 4BI2
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 ASP 561 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559A GLU 4.3 0.8 + - - -
560A ALA* 1.4 76.5 - - - +
562A ASN* 1.3 60.8 + - - +
563A GLN* 3.5 15.2 - - + +
564A THR* 2.1 61.0 + - - -
565A LEU* 3.0 18.9 + - - +
669A ASN* 4.6 3.3 + - - -
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Residues in contact with ASN 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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560A ALA 5.2 0.7 - - - -
561A ASP* 1.3 78.0 - - - +
563A GLN* 1.4 57.2 + - - +
565A LEU* 3.8 21.5 - - + +
566A ASP* 3.1 25.8 + - - +
569A ARG* 5.2 1.7 + - - +
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Residues in contact with GLN 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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561A ASP* 3.1 13.6 + - + +
562A ASN* 1.4 75.3 - - - +
564A THR* 1.4 53.9 + - - +
566A ASP* 3.1 7.4 + - - +
567A SER* 2.9 31.8 + - - -
669A ASN* 5.0 4.0 - - - +
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Residues in contact with THR 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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560A ALA* 4.6 9.2 - - + -
561A ASP* 2.1 51.4 + - - -
563A GLN* 1.4 61.4 - - - +
565A LEU* 1.4 63.4 + - - +
567A SER* 2.7 23.7 + - - +
568A TYR* 3.0 53.4 + - + +
669A ASN* 3.4 22.1 + - + +
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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
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557A LEU* 3.7 41.3 - - + -
560A ALA* 3.8 18.8 - - + +
561A ASP 3.0 24.2 + - - +
562A ASN* 3.8 22.7 - - + +
563A GLN 3.3 0.2 - - - -
564A THR* 1.4 75.2 - - - +
566A ASP* 1.3 61.0 + - - +
568A TYR* 3.3 6.6 + - + +
569A ARG* 3.0 58.0 + - + +
595A ASP* 5.8 2.5 - - - +
598A ILE* 6.0 0.4 - - + -
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Residues in contact with ASP 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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562A ASN 3.1 14.8 + - - +
563A GLN* 3.1 8.9 + - - +
565A LEU* 1.3 79.1 - - - +
567A SER* 1.3 56.9 + - - +
569A ARG* 3.3 21.7 + - - +
570A ASN* 2.8 38.0 + - - +
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Residues in contact with SER 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A GLN 2.9 12.1 + - - -
564A THR* 2.7 20.8 + - - -
566A ASP* 1.3 75.0 + - - +
568A TYR* 1.4 53.8 + - - +
570A ASN* 3.4 6.2 + - - +
571A GLU* 2.9 36.2 + - - +
667A ILE* 3.6 21.3 - - - +
668A ALA* 3.9 2.9 - - - -
669A ASN* 3.2 36.7 + - - -
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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
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536A SER* 4.4 12.1 + - - -
555A VAL* 3.9 16.2 - - + -
556A ASN 5.4 2.5 - - - -
557A LEU* 3.9 23.6 - - + -
560A ALA* 5.1 3.6 - - + -
564A THR* 3.0 40.9 + - + +
565A LEU* 3.4 10.5 - - + +
567A SER* 1.4 86.8 + - - +
569A ARG* 1.4 56.8 + - + +
571A GLU* 3.4 1.9 + - - +
572A ILE* 3.0 35.8 + - - +
598A ILE* 4.0 18.8 - - + -
668A ALA* 3.7 15.7 - - + -
669A ASN* 4.1 12.8 + - - +
1796A 7PE 3.6 33.2 + - - +
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Residues in contact with ARG 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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562A ASN* 5.2 1.4 + - - +
565A LEU* 3.0 49.2 + - + +
566A ASP* 3.8 29.0 + - - +
568A TYR* 1.4 71.9 - - + +
570A ASN* 1.3 65.3 + - - +
572A ILE* 3.6 8.9 + - - +
573A ALA* 3.1 25.1 + - - +
593A ILE* 4.9 19.4 - - + +
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Residues in contact with ASN 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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566A ASP* 2.8 26.8 + - - +
567A SER* 3.6 5.2 - - - +
569A ARG* 1.3 76.2 - - - +
571A GLU* 1.4 64.3 + - - +
573A ALA* 3.2 4.7 + - - +
574A TYR* 3.0 58.2 + - - -
667A ILE* 3.5 21.9 - - + +
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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
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567A SER 2.9 19.9 + - - +
568A TYR 3.7 4.0 - - - +
570A ASN* 1.4 71.3 - - - +
572A ILE* 1.4 55.2 + - - +
574A TYR* 3.6 2.8 + - - +
575A LEU* 3.0 29.4 + - + +
664A ASP* 3.7 13.5 - - - +
665A PHE* 2.7 42.2 + - - +
666A GLY* 3.7 5.0 + - - -
667A ILE* 3.1 23.2 + - + +
668A ALA* 2.9 38.1 + - + +
1796A 7PE 3.7 26.4 + - - +
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Residues in contact with ILE 572 (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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568A TYR 3.0 23.9 + - - +
569A ARG* 3.8 8.1 - - - +
571A GLU* 1.4 71.5 - - - +
573A ALA* 1.3 55.6 + - - +
575A LEU* 3.0 7.8 + - - +
576A ASN* 2.8 33.6 + - - +
588A LEU* 4.3 1.4 - - + +
591A TYR* 3.9 41.5 - - + -
593A ILE* 4.9 7.0 - - + -
598A ILE* 3.9 40.8 - - + -
600A MET* 3.6 25.1 - - + -
1796A 7PE 3.9 9.0 - - - -
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Residues in contact with ALA 573 (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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569A ARG 3.1 18.1 + - - +
570A ASN* 3.7 6.3 - - - +
572A ILE* 1.3 76.2 - - - +
574A TYR* 1.4 51.8 + - + +
576A ASN* 3.2 13.4 + - - +
577A LYS* 2.7 36.4 + - - +
591A TYR* 5.8 1.3 - - - -
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Residues in contact with TYR 574 (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 ASN* 3.0 49.3 + - - +
571A GLU 3.7 2.7 - - - +
573A ALA* 1.4 76.9 - - + +
575A LEU* 1.4 51.7 + - - +
577A LYS* 3.1 7.5 + - + -
578A LEU* 2.8 51.3 + - + +
641A HIS* 4.0 22.8 + + + -
643A ILE* 3.5 29.6 - - + -
665A PHE* 3.4 19.3 - - + -
667A ILE* 3.7 11.0 - - + -
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Residues in contact with LEU 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 19.7 + - + +
572A ILE 3.0 2.7 + - - +
574A TYR* 1.4 73.4 - - - +
576A ASN* 1.3 60.2 + - - +
578A LEU 3.9 1.0 + - - -
579A GLN* 3.3 26.0 + - - +
585A ILE* 4.2 11.0 - - + +
586A ILE* 3.5 37.9 - - + +
588A LEU* 3.8 20.9 - - + -
600A MET* 3.7 29.4 - - + -
602A MET* 4.7 6.3 - - - -
662A LEU 5.3 0.2 - - - +
663A ILE 4.6 5.4 - - - +
665A PHE* 3.3 18.7 - - + -
1796A 7PE 4.0 16.4 - - - +
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Residues in contact with ASN 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 ILE 2.8 12.9 + - - +
573A ALA* 3.3 14.6 + - - +
575A LEU* 1.3 77.1 - - - +
577A LYS* 1.4 62.8 + - - +
579A GLN* 3.1 26.5 - - - +
580A GLN* 4.7 1.0 + - - +
588A LEU* 4.1 14.8 - - + +
591A TYR* 3.9 25.3 + - + -
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Residues in contact with LYS 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 ALA 2.7 20.4 + - - +
574A TYR* 3.1 13.0 + - + +
576A ASN* 1.4 73.3 - - - +
578A LEU* 1.3 69.6 + - + +
579A GLN 3.3 0.4 - - - -
580A GLN* 3.4 26.5 - - - +
581A HIS* 3.7 8.0 + - + -
641A HIS* 4.7 11.9 - - + +
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Residues in contact with LEU 578 (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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574A TYR* 2.8 28.1 + - + +
575A LEU 4.2 1.1 - - - +
577A LYS* 1.3 78.9 - - + +
579A GLN* 1.4 64.3 + - - +
580A GLN 3.3 1.3 - - - -
581A HIS* 3.3 16.2 + - + +
582A SER 3.4 12.8 + - - +
585A ILE* 4.0 21.1 - - + +
637A THR* 4.3 2.2 - - - +
638A ILE* 3.6 44.0 - - + +
641A HIS* 3.6 40.4 - - + +
643A ILE* 4.1 8.3 - - + -
665A PHE* 4.0 14.8 - - + -
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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