Contacts of the helix formed by residues 564 - 571 (chain A) in PDB entry 2RD0
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 ILE 564 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A LYS* 4.6 8.7 - - + -
534A ILE* 5.8 0.7 - - + +
535A SER* 2.8 36.1 - - - +
551A LEU* 5.5 7.6 - - + -
558A CYS* 3.4 38.6 - - + -
561A ILE* 3.2 30.3 - - + +
562A PRO 2.9 1.4 + - - +
563A GLU* 1.3 76.4 - - - +
565A LEU* 1.3 68.1 + - - +
566A PRO* 3.3 3.6 - - - -
567A LYS* 2.8 26.5 + - + +
568A LEU* 3.0 30.9 + - + +
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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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562A PRO 3.0 15.4 + - - +
564A ILE* 1.3 76.8 - - - +
566A PRO* 1.4 57.4 - - + +
568A LEU* 3.0 16.9 + - + +
569A LEU* 2.7 56.6 + - + +
583A MET* 5.0 1.1 - - - -
587A VAL* 4.7 15.9 - - + -
590A TRP* 3.5 42.8 - - + +
593A ILE* 4.4 2.2 - - + -
601A LEU* 4.3 10.8 - - + -
614A PHE* 3.4 38.1 - - + -
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Residues in contact with PRO 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 PRO 4.7 0.2 - - - +
563A GLU 3.6 18.4 - - - +
564A ILE* 3.3 1.8 - - - +
565A LEU* 1.4 91.6 - - + +
567A LYS* 1.3 73.1 + - + +
569A LEU* 3.1 6.0 + - + +
570A LEU* 3.0 20.0 + - + +
593A ILE* 4.9 5.8 - - + -
597A GLN* 5.9 5.6 - - + +
600A GLU* 3.5 28.9 - - - +
601A LEU* 4.1 21.1 - - + -
606A TYR* 3.5 24.1 + - + +
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Residues in contact with LYS 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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534A ILE* 3.4 23.6 - - + +
535A SER* 3.5 14.7 + - - +
537A ARG* 2.7 39.2 + - - +
538A ASP 4.6 7.5 - - - -
539A PRO* 4.9 8.5 - - + +
541A SER* 5.4 1.6 - - - -
543A ILE* 4.3 18.3 - - + +
551A LEU* 4.0 17.6 - - + +
563A GLU 5.7 1.2 + - - -
564A ILE* 2.8 23.1 + - + +
566A PRO* 1.3 85.6 - - + +
568A LEU* 1.3 56.8 + - - +
570A LEU* 3.1 30.1 + - + +
571A SER* 2.6 24.3 + - - -
600A GLU* 5.7 2.4 + - - +
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Residues in contact with LEU 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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551A LEU* 3.9 21.1 - - + +
552A TRP* 4.3 6.9 - - + -
555A ARG* 3.8 33.2 - - + +
564A ILE* 3.0 25.1 + - + +
565A LEU* 3.0 15.3 + - + +
567A LYS* 1.3 77.1 - - - +
569A LEU* 1.3 57.3 + - - +
571A SER* 3.0 26.5 + - - -
572A VAL* 3.6 9.0 + - - +
583A MET* 3.6 25.1 - - + -
586A LEU* 4.9 4.5 - - + -
590A TRP* 3.9 32.8 - - + -
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Residues in contact with LEU 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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565A LEU* 2.7 43.5 + - + +
566A PRO 3.1 6.0 + - - +
568A LEU* 1.3 73.3 - - - +
570A LEU* 1.3 59.7 + - - +
571A SER 3.3 0.7 + - - -
572A VAL* 3.6 5.5 + - - -
574A TRP* 3.0 40.7 + - + -
583A MET* 3.9 31.4 - - + -
587A VAL* 4.6 6.3 - - + -
601A LEU* 3.8 24.9 - - + -
606A TYR* 4.0 12.1 - - + -
611A VAL* 3.8 35.9 - - + -
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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
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539A PRO 4.9 12.3 - - - +
543A ILE* 4.4 20.2 - - + -
548A LYS* 3.9 19.6 + - - +
566A PRO 3.0 18.7 + - - +
567A LYS* 3.1 24.4 + - + +
569A LEU* 1.3 75.8 - - - +
571A SER* 1.3 60.1 + - - +
572A VAL 3.3 6.2 + - - +
574A TRP* 4.8 3.2 + - - +
600A GLU* 5.6 1.6 - - - +
605A ASN* 5.4 14.4 - - + +
606A TYR* 3.9 19.0 - - + +
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Residues in contact with SER 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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543A ILE* 4.8 0.5 - - - +
548A LYS* 3.4 49.8 - - - +
551A LEU* 3.4 17.9 - - - +
552A TRP* 4.4 13.7 - - - +
567A LYS 2.6 22.3 + - - -
568A LEU* 3.0 16.8 + - - -
570A LEU* 1.3 74.5 - - - +
572A VAL* 1.3 64.2 + - - +
573A LYS 3.5 1.9 + - - -
579A GLU* 5.4 0.9 - - - +
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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