Contacts of the helix formed by residues 563 - 575 (chain A) in PDB entry 5JG8
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 563 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559A ARG* 3.1 16.8 + - + +
560A MET* 3.2 13.0 - - - +
562A GLY* 1.3 73.3 - - - +
564A MET* 1.3 62.6 + - - +
565A GLN* 3.2 11.8 + - - +
566A LEU* 2.6 45.1 + - + +
567A PHE 3.3 12.3 + - - -
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Residues in contact with MET 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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562A GLY 3.7 4.4 + - - +
563A ASP* 1.3 70.7 + - - +
565A GLN* 1.3 61.3 + - - +
567A PHE* 3.3 6.8 + - - +
568A GLN* 2.9 48.9 + - + +
584A CYS 5.4 1.6 - - - +
585A GLY* 5.2 2.2 - - - -
586A THR* 4.4 21.5 - - + +
589A ARG* 3.1 55.2 - - + +
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Residues in contact with GLN 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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563A ASP* 3.2 10.5 + - - +
564A MET* 1.3 78.6 - - - +
566A LEU* 1.3 64.3 + - - +
568A GLN* 2.9 19.5 + - + +
569A THR* 3.0 17.1 + - - +
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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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542A THR 4.8 8.7 - - - +
543A TYR* 4.4 22.6 - - + +
556A LEU* 3.9 13.2 - - + -
559A ARG* 3.8 36.6 - - + +
560A MET* 3.9 20.6 - - + +
563A ASP* 2.6 29.5 + - + +
565A GLN* 1.3 73.8 - - - +
567A PHE* 1.3 63.6 + - - +
569A THR* 2.9 23.6 + - + +
570A PHE* 2.9 12.0 + - - +
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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
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560A MET* 3.7 16.7 - - + +
563A ASP 3.3 9.4 + - - +
564A MET* 3.3 8.0 + - - +
565A GLN 3.3 0.6 - - - -
566A LEU* 1.3 79.5 - - - +
568A GLN* 1.3 73.8 + - - +
570A PHE* 3.2 16.7 + + - -
571A TRP* 2.8 51.3 + + + +
584A CYS* 3.8 18.8 - - - -
589A ARG* 3.5 61.2 - - + -
592A THR* 4.1 12.1 - - + -
593A LEU* 3.8 23.3 - - + -
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Residues in contact with GLN 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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564A MET* 2.9 41.1 + - + +
565A GLN* 2.9 15.7 + - + +
567A PHE* 1.3 87.2 - - - +
569A THR* 1.3 54.0 + - - +
571A TRP* 3.3 17.3 + - - +
572A PHE* 2.9 28.8 + - - +
583A PRO 4.2 8.8 + - - +
584A CYS 4.2 12.9 + - - -
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Residues in contact with THR 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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542A THR* 3.9 28.9 - - + -
543A TYR* 4.4 4.5 - - + -
565A GLN* 3.0 15.6 + - - +
566A LEU* 2.9 17.6 + - + +
568A GLN* 1.3 76.3 - - - +
570A PHE* 1.3 63.1 + - - +
572A PHE* 3.0 11.0 + - + +
573A LEU* 2.9 32.1 + - + +
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Residues in contact with PHE 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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461A ASP* 4.1 12.1 - - - -
462A GLU* 4.4 0.9 - - + -
463A PHE* 3.8 24.9 - + - -
543A TYR* 3.4 30.9 + + + +
556A LEU* 5.5 0.4 - - + -
560A MET* 3.4 34.1 - - + -
566A LEU 2.9 6.7 + - - +
567A PHE* 3.7 18.6 - + - +
569A THR* 1.3 77.2 - - - +
571A TRP* 1.3 58.9 + + - +
573A LEU* 3.8 1.5 - - + +
574A TYR* 2.8 50.8 + + - +
592A THR* 3.8 17.9 - - + -
593A LEU* 5.3 1.1 - - + -
596A GLN* 3.6 28.5 - - + -
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Residues in contact with TRP 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 PHE* 2.8 40.3 + + + +
568A GLN* 3.6 19.5 - - - +
569A THR 3.1 0.2 - - - -
570A PHE* 1.3 78.4 - + - +
572A PHE* 1.3 64.8 + - - +
574A TYR* 3.1 31.2 - + - +
575A HIS* 3.1 55.7 + + - -
579A PRO* 4.1 12.9 - - + +
580A PRO* 4.1 18.6 + - + +
582A GLU 4.8 3.0 + - - -
583A PRO 4.7 2.1 + - - -
584A CYS* 3.5 29.0 - - + +
588A CYS* 3.5 16.8 - - - -
592A THR* 3.7 22.0 - - + -
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Residues in contact with PHE 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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536A LEU* 4.5 7.6 - - + -
568A GLN 2.9 14.2 + - - +
569A THR* 3.4 11.9 - - + +
571A TRP* 1.3 79.2 - - - +
573A LEU* 1.3 82.1 + - + +
575A HIS* 3.4 5.9 + - - +
577A GLY* 2.9 57.2 + - - -
579A PRO* 3.8 25.8 - - + -
1C NAG 3.9 25.6 - - + -
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Residues in contact with LEU 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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461A ASP* 3.6 15.0 - - - +
516A THR* 6.1 0.2 - - - +
536A LEU* 3.8 20.2 - - + +
537A TYR* 3.3 61.0 - - + -
542A THR* 4.1 13.5 - - + -
543A TYR* 3.6 18.8 - - - +
569A THR* 2.9 21.3 + - + +
570A PHE* 4.1 3.1 - - + +
572A PHE* 1.3 92.3 - - + +
574A TYR* 1.3 60.2 + - - +
576A LYS* 2.8 23.6 + - - +
577A GLY 4.5 1.1 - - - +
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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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460A VAL* 3.4 40.3 - - + +
461A ASP* 3.0 47.2 + - - +
462A GLU* 3.7 33.2 + - + -
570A PHE* 2.8 34.5 + + - +
571A TRP* 3.1 26.4 + + - +
573A LEU* 1.3 77.4 - - - +
575A HIS* 1.3 84.5 + + - +
576A LYS* 3.5 1.0 + - - +
592A THR* 4.2 10.6 - - + +
595A ALA* 6.1 0.7 - - - +
596A GLN* 4.0 8.1 - - - -
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Residues in contact with HIS 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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460A VAL* 4.8 4.7 - - + +
491A LEU* 3.2 31.6 - - + +
492A ASN 4.4 0.2 + - - -
571A TRP* 3.1 52.2 + + - +
572A PHE 3.4 1.8 + - - +
573A LEU 3.1 0.6 - - - -
574A TYR* 1.3 93.9 - + - +
576A LYS* 1.3 71.4 + - - +
577A GLY 3.2 0.8 + - - -
578A HIS* 3.4 25.6 + - - +
579A PRO* 3.5 16.2 - - + -
580A PRO* 3.2 33.3 - - + +
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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
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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