Contacts of the helix formed by residues 589 - 601 (chain A) in PDB entry 3BWT
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 GLY 589 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584A GLN 4.1 0.9 - - - -
585A LEU 3.6 17.7 - - - +
586A ASP 5.3 0.2 - - - -
587A ILE 3.8 1.0 - - - -
588A LEU* 1.3 80.5 + - - +
590A SER* 1.3 57.1 + - - +
591A LYS 3.2 1.8 - - - -
592A ALA* 2.5 28.1 + - - +
593A ALA* 2.7 15.7 + - - -
623A GLU* 4.7 8.5 - - - -
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Residues in contact with SER 590 (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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588A LEU 5.4 0.9 - - - -
589A GLY* 1.3 76.3 - - - +
591A LYS* 1.3 60.5 + - - +
593A ALA* 3.2 7.7 + - - +
594A ASP* 2.9 42.5 + - - +
623A GLU* 5.3 4.5 - - - +
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Residues in contact with LYS 591 (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 LEU* 4.5 3.9 - - + +
588A LEU* 4.9 11.3 - - + +
589A GLY 3.0 2.8 + - - +
590A SER* 1.3 79.5 - - - +
592A ALA* 1.3 61.9 + - - +
594A ASP* 3.7 7.9 - - - +
595A ALA* 3.1 25.6 + - - +
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Residues in contact with ALA 592 (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 LEU* 3.7 16.1 - - + +
584A GLN* 3.4 33.9 - - + +
585A LEU* 3.9 9.4 - - + +
588A LEU* 3.6 14.7 - - + +
589A GLY 2.5 17.0 + - - +
591A LYS* 1.3 73.3 - - - +
593A ALA* 1.3 54.3 + - - +
595A ALA* 3.4 0.9 + - - +
596A ILE* 2.9 37.4 + - + +
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Residues in contact with ALA 593 (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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585A LEU* 3.6 17.4 - - + +
589A GLY 2.7 14.5 + - - +
590A SER* 3.6 10.3 - - - +
592A ALA* 1.3 73.0 - - - +
594A ASP* 1.3 60.3 + - - +
597A PHE* 2.8 34.4 + - - +
620A LEU* 4.0 4.7 - - + +
623A GLU* 3.8 29.4 - - + +
624A VAL* 4.2 11.7 - - + +
628A GLN* 4.5 2.0 - - - +
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Residues in contact with ASP 594 (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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590A SER* 2.9 29.9 + - - +
591A LYS* 3.7 8.7 - - - +
593A ALA* 1.3 75.8 - - - +
595A ALA* 1.3 61.0 + - - +
597A PHE* 3.2 0.7 + - - +
598A GLU* 2.8 39.6 + - + +
625A THR* 5.4 3.3 - - - +
628A GLN* 2.9 28.4 + - - +
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Residues in contact with ALA 595 (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 LEU* 4.4 9.0 - - + -
565A ILE* 3.8 29.6 - - + -
568A ILE* 3.8 9.0 - - + +
591A LYS 3.1 14.5 + - - +
592A ALA 3.8 3.1 - - - +
594A ASP* 1.3 79.7 - - - +
596A ILE* 1.3 63.0 + - - +
598A GLU* 3.5 4.3 + - - +
599A GLU* 3.2 30.0 + - - +
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Residues in contact with ILE 596 (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 LEU* 5.2 3.4 - - + -
568A ILE* 4.1 26.2 - - + -
581A LEU* 4.0 29.2 - - + +
584A GLN* 5.0 2.7 - - + -
585A LEU* 3.8 22.9 - - + -
592A ALA* 2.9 27.9 + - + +
595A ALA* 1.3 77.0 - - + +
597A PHE* 1.3 63.4 + - - +
600A THR* 3.0 45.0 + - + +
616A LEU* 4.8 15.7 - - + -
620A LEU* 3.6 24.5 - - + -
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Residues in contact with PHE 597 (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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593A ALA 2.8 24.8 + - - +
594A ASP 3.6 1.6 - - - +
596A ILE* 1.3 74.0 - - - +
598A GLU* 1.3 85.9 + - + +
600A THR* 4.4 0.2 - - - -
601A LYS* 3.0 48.9 + - + +
620A LEU* 4.2 10.2 - - + +
624A VAL* 4.1 9.4 - - + -
628A GLN* 3.4 58.6 - - + +
631A VAL* 3.8 27.1 - - + -
632A LEU* 3.7 28.5 - - + -
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Residues in contact with GLU 598 (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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594A ASP* 2.8 25.6 + - + +
595A ALA* 4.0 5.8 - - - +
597A PHE* 1.3 95.9 - - + +
599A GLU* 1.3 64.9 + - + +
601A LYS* 2.8 47.1 + - - +
602A ASP* 5.2 2.1 - - - +
628A GLN* 5.2 1.9 + - - -
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Residues in contact with GLU 599 (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 ILE* 3.5 6.4 - - - +
566A GLY* 2.5 33.8 + - - +
567A SER* 3.1 8.1 + - - -
568A ILE* 3.1 50.7 + - + +
569A HIS* 3.8 21.0 + - - +
595A ALA* 3.2 16.0 + - - +
597A PHE 3.3 0.2 - - - -
598A GLU* 1.3 81.0 - - + +
600A THR* 1.3 61.9 + - - +
602A ASP 5.4 0.4 - - - -
603A TYR* 4.0 11.8 - - - -
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Residues in contact with THR 600 (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 ILE* 4.2 7.4 - - + -
569A HIS* 4.9 2.5 - - - -
572A CYS* 4.0 26.7 - - - -
596A ILE* 3.0 32.3 + - + +
597A PHE 4.2 0.2 + - - -
599A GLU* 1.3 81.3 - - - +
601A LYS* 1.3 69.2 + - - +
602A ASP 3.2 2.9 - - - -
603A TYR* 2.9 19.7 + - - -
604A THR* 3.3 12.1 + - - +
607A LEU* 3.6 17.0 - - + -
616A LEU* 5.1 1.3 - - + -
617A ILE* 4.2 5.2 - - - +
620A LEU* 3.8 18.7 - - - +
632A LEU* 5.7 0.2 - - - +
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Residues in contact with LYS 601 (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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597A PHE* 3.0 41.1 + - + +
598A GLU* 2.8 39.4 + - - +
600A THR* 1.3 76.9 + - - +
602A ASP* 1.3 78.6 + - - +
604A THR* 2.7 28.7 + - - +
631A VAL* 5.0 6.2 - - + +
632A LEU* 4.0 15.7 - - + -
635A ILE* 3.3 21.6 - - + +
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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