Contacts of the helix formed by residues 601 - 606 (chain A) in PDB entry 1DDJ
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 ALA 601 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600A THR* 1.3 87.3 + - - +
602A ALA* 1.3 65.0 + - - +
603A HIS* 4.1 4.0 - - + +
604A CYS* 3.1 24.9 + - - +
605A LEU* 4.1 2.8 + - - +
646A ASP* 3.5 29.4 - - - +
648A ALA* 4.2 2.2 - - - -
741A ALA* 5.1 0.9 - - + -
742A GLY* 3.4 26.8 - - - +
758A VAL* 4.2 1.1 - - + -
759A THR 3.9 6.1 - - - +
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Residues in contact with ALA 602 (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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601A ALA* 1.3 71.2 - - - +
603A HIS* 1.3 62.6 + - - +
605A LEU* 2.9 19.6 + - - +
606A GLU* 3.7 8.5 + - - +
640A LEU* 3.9 21.7 - - + +
645A LYS 3.8 20.2 - - - +
646A ASP* 3.0 10.0 + - - +
647A ILE 3.4 16.7 - - - +
648A ALA* 3.8 10.8 - - - -
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Residues in contact with HIS 603 (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 CYS* 5.4 1.3 - - - -
601A ALA* 3.1 4.2 - - + -
602A ALA* 1.3 73.1 - - - +
604A CYS* 1.3 62.3 + - - +
605A LEU 3.3 0.7 + - - -
606A GLU* 3.1 54.2 + - - +
646A ASP* 2.7 30.4 + - - +
741A ALA* 4.3 21.1 - - + -
761A TRP* 6.0 3.3 - + - -
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Residues in contact with CYS 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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579A LEU* 4.0 13.9 - - + -
587A PHE* 3.1 24.1 - - - -
588A CYS* 2.0 53.8 - - + -
600A THR* 3.9 9.9 - - - +
601A ALA* 3.1 15.9 + - - +
602A ALA 3.1 0.4 + - - -
603A HIS* 1.3 77.3 - - - +
605A LEU* 1.3 59.7 + - + +
606A GLU 3.3 1.7 + - - -
607A LYS* 4.9 2.9 + - - +
614A TYR* 3.8 3.5 - - - -
741A ALA* 3.4 23.6 - - - -
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Residues in contact with LEU 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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579A LEU* 4.1 10.3 - - + -
600A THR* 4.7 1.6 - - + -
601A ALA 4.2 5.2 - - - +
602A ALA 2.9 10.0 + - - +
604A CYS* 1.3 79.6 - - - +
606A GLU* 1.3 62.8 + - - +
607A LYS 3.2 3.4 - - - -
608A SER 3.2 19.6 + - - +
609A PRO* 5.2 0.3 - - - +
614A TYR* 3.4 38.6 - - + +
638A LEU* 4.4 17.5 - - + -
639A PHE 5.3 0.4 - - - +
640A LEU* 3.9 16.6 - - + +
648A ALA* 3.7 26.2 - - + -
649A LEU 5.1 0.2 - - - +
650A LEU* 3.6 35.0 - - + -
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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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602A ALA 4.4 3.0 - - - +
603A HIS* 3.1 56.5 + - - +
604A CYS 3.3 0.8 - - - -
605A LEU* 1.3 78.8 - - - +
607A LYS* 1.3 66.7 + - + +
608A SER 3.5 0.2 - - - -
644A ARG* 6.0 0.3 + - - -
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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