Contacts of the helix formed by residues 559 - 568 (chain A) in PDB entry 1B3U
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 VAL 559 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521A LEU* 4.4 15.7 - - + -
525A LEU* 4.4 5.2 - - - -
543A LEU* 4.3 20.0 - - + +
547A GLY* 5.8 0.2 - - - -
550A LEU* 3.9 25.4 - - + -
554A THR 3.4 3.1 + - - +
555A LEU* 3.2 34.8 + - + +
558A GLU* 1.3 75.3 - - - +
560A LYS* 1.3 68.1 + - - +
562A ILE* 3.2 4.5 + - - +
563A LEU* 2.9 44.9 + - + +
585A LEU* 4.4 5.8 - - + -
587A LEU* 4.6 1.8 - - + -
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Residues in contact with LYS 560 (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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555A LEU 2.8 14.3 + - - +
556A GLN* 3.5 35.1 + - + +
559A VAL* 1.3 73.1 - - - +
561A PRO* 1.3 69.1 - - + +
563A LEU* 3.1 5.5 + - - +
564A GLU* 2.8 57.1 + - + +
582A LEU* 4.6 8.3 - - + -
587A LEU* 4.2 33.7 + - + +
588A ALA* 5.2 3.0 + - - -
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Residues in contact with PRO 561 (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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556A GLN 3.5 12.3 - - - +
557A SER* 3.6 17.0 - - - +
558A GLU* 3.7 11.4 - - - +
559A VAL 3.6 3.1 - - - -
560A LYS* 1.3 94.8 - - + +
562A ILE* 1.3 64.0 + - + +
564A GLU* 3.3 14.0 + - + +
565A LYS* 3.1 23.3 + - - +
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Residues in contact with ILE 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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525A LEU* 3.8 30.7 - - + +
528A ALA* 3.8 22.9 - - + -
543A LEU* 4.1 20.0 - - + -
558A GLU 3.4 16.4 - - - +
559A VAL 3.2 7.5 + - - +
560A LYS 3.2 0.4 - - - -
561A PRO* 1.3 80.5 - - + +
563A LEU* 1.3 63.6 + - - +
565A LYS* 3.3 33.5 + - + +
566A LEU* 3.2 23.6 + - + +
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Residues in contact with LEU 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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540A ALA* 4.2 17.0 - - + -
543A LEU* 3.7 22.9 - - + -
559A VAL* 2.9 37.6 + - + +
560A LYS 3.7 0.4 - - - +
562A ILE* 1.3 76.8 - - - +
564A GLU* 1.3 63.1 + - - +
566A LEU* 3.2 16.7 + - + +
567A THR* 3.1 20.3 + - - +
578A ALA* 3.8 6.6 - - - +
581A ALA* 3.8 32.3 - - + -
582A LEU* 3.6 31.2 - - + +
585A LEU* 4.1 12.6 - - + -
587A LEU* 4.5 1.1 - - + -
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Residues in contact with GLU 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 LYS* 2.8 54.2 + - + +
561A PRO* 3.6 12.6 - - - +
562A ILE 3.2 0.4 - - - -
563A LEU* 1.3 77.1 - - - +
565A LYS* 1.3 60.4 + - - +
567A THR* 2.4 33.4 + - - +
568A GLN* 3.8 6.4 + - - +
582A LEU* 4.2 14.6 - - + -
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Residues in contact with LYS 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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525A LEU 5.4 0.4 + - - -
528A ALA* 4.2 26.2 - - - +
529A GLY* 5.1 5.0 - - - +
561A PRO 3.1 11.9 + - - +
562A ILE* 3.3 37.5 + - + +
564A GLU* 1.3 77.5 - - - +
566A LEU* 1.3 65.6 + - + +
568A GLN* 3.0 32.2 + - - +
569A ASP* 3.8 1.0 + - - +
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Residues in contact with LEU 566 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528A ALA* 4.1 27.1 - - + +
536A ARG* 4.5 14.8 - - + +
539A VAL* 4.4 13.2 - - + -
540A ALA* 4.6 6.5 - - + -
562A ILE* 3.2 31.7 + - + +
563A LEU* 3.6 20.6 - - + +
564A GLU 3.2 0.8 - - - -
565A LYS* 1.3 80.2 - - + +
567A THR* 1.3 60.9 + - - +
568A GLN 3.0 5.8 - - - -
569A ASP* 3.2 28.1 - - - +
574A VAL* 3.8 21.4 - - + +
575A LYS* 3.7 10.4 - - - -
578A ALA* 3.7 11.9 - - + -
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Residues in contact with THR 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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563A LEU 3.1 16.8 - - - +
564A GLU* 2.4 25.4 + - - +
566A LEU* 1.3 77.5 - - - +
568A GLN* 1.3 73.9 + - - +
569A ASP 3.3 4.0 + - - +
575A LYS* 3.9 19.5 - - - +
578A ALA* 3.8 15.3 - - + -
579A GLN* 4.1 16.8 - - - +
582A LEU* 3.8 22.9 - - + -
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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 GLU 3.8 10.5 + - - +
565A LYS* 3.0 17.5 + - - +
567A THR* 1.3 101.3 + - - +
569A ASP* 1.3 61.4 + - - +
570A GLN 4.0 0.2 + - - -
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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