Contacts of the helix formed by residues 603 - 609 (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 TYR 603 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569A HIS* 3.8 44.2 - + + +
599A GLU 4.0 18.2 - - - -
600A THR 2.9 8.5 + - - +
602A ASP* 1.3 103.8 + - + +
604A THR* 1.3 64.0 + - - +
605A VAL 3.2 2.7 - - - -
606A GLU* 3.1 21.3 + - + +
607A LEU* 2.9 27.8 + - + +
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Residues in contact with THR 604 (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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600A THR* 3.3 5.1 + - - +
601A LYS* 2.7 37.6 + - - +
602A ASP 3.6 1.4 + - - -
603A TYR* 1.3 75.6 - - - +
605A VAL* 1.3 54.4 + - - +
607A LEU* 3.2 5.8 + - - +
608A MET* 2.7 47.5 + - - +
617A ILE* 4.6 12.9 - - + +
632A LEU* 3.5 31.3 + - + -
635A ILE* 4.0 11.5 - - + +
636A SER* 3.7 22.3 - - - -
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Residues in contact with VAL 605 (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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603A TYR 3.2 0.6 - - - -
604A THR* 1.3 78.4 + - - +
606A GLU* 1.3 61.0 + - - +
608A MET* 3.3 7.3 + - - +
609A THR* 3.0 27.8 + - + +
635A ILE* 4.4 7.6 - - + +
636A SER* 4.1 18.2 - - - -
639A HIS* 3.7 45.8 - - + +
642A GLU* 3.9 21.3 - - - +
643A ILE* 3.9 16.2 - - + -
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Residues in contact with GLU 606 (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 HIS* 6.0 3.8 - - - -
603A TYR* 3.1 24.6 + - + +
605A VAL* 1.3 80.6 - - + +
607A LEU* 1.3 65.8 + - + +
609A THR* 3.7 7.9 + - - +
610A ASP* 3.4 19.1 + - - +
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Residues in contact with LEU 607 (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 HIS* 4.6 15.7 - - + +
572A CYS* 3.9 37.7 - - + +
600A THR* 3.6 36.1 - - + +
603A TYR* 2.9 25.6 + - + +
604A THR 3.8 1.1 - - - +
606A GLU* 1.3 82.1 - - + +
608A MET* 1.3 57.3 + - - +
610A ASP* 3.4 8.3 + - + -
613A GLY* 2.8 9.4 - - - +
614A ASN 2.7 32.4 + - - -
616A LEU* 5.0 2.2 - - + -
617A ILE* 3.8 24.0 - - + -
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Residues in contact with MET 608 (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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604A THR* 2.7 25.0 + - - +
605A VAL* 3.3 6.0 + - - +
607A LEU* 1.3 79.1 - - - +
609A THR* 1.3 57.5 + - - +
610A ASP 3.2 0.7 - - - -
614A ASN* 3.1 22.5 - - - +
617A ILE* 4.0 26.2 - - + -
621A LEU* 4.5 2.2 - - + -
632A LEU* 5.5 2.9 - - + +
636A SER* 4.1 14.4 - - - +
640A PHE* 5.8 0.4 - - - -
643A ILE* 3.7 38.4 - - + -
649A GLY* 3.0 19.3 + - - -
652A ALA* 3.8 26.9 - - + +
653A LEU* 5.0 3.4 - - + +
656A LEU* 3.8 29.2 - - + -
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Residues in contact with THR 609 (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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605A VAL 3.0 17.2 + - - +
606A GLU* 3.7 9.8 + - - +
608A MET* 1.3 77.8 - - - +
610A ASP* 1.3 59.2 + - - +
642A GLU* 4.4 16.6 + - + +
643A ILE* 3.9 26.7 - - + +
646A ASN* 3.1 50.8 + - + +
648A HIS* 3.7 4.0 - - - -
649A GLY* 4.1 1.3 - - - -
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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