Contacts of the helix formed by residues 598 - 610 (chain A) in PDB entry 1DQA
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 ARG 598 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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596A LEU* 3.7 4.5 - - - +
597A PRO* 1.3 90.3 + - + +
599A ALA* 1.3 59.8 + - - +
600A CYS* 3.2 5.4 - - + +
601A ASP* 3.0 30.2 + - - +
602A SER* 3.1 10.2 + - - -
641A ARG* 3.6 10.2 - - - +
709D GLU* 3.5 28.4 + - - +
710D ALA* 5.9 1.8 - - - +
711D VAL* 3.7 30.2 - - - +
784D SER* 5.4 3.4 + - - -
792D TYR* 4.0 12.2 - - - -
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Residues in contact with ALA 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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598A ARG* 1.3 68.1 - - - +
600A CYS* 1.3 62.2 + - - +
602A SER* 3.0 11.5 + - - -
603A ALA* 2.9 31.0 + - - +
638A ILE* 4.3 1.2 - - - +
640A GLY* 3.5 25.6 - - - +
641A ARG* 3.7 4.1 - - - +
707D VAL* 3.8 25.9 - - + +
708D CYS 5.4 0.4 - - - -
709D GLU* 2.8 26.4 + - + +
792D TYR* 4.1 2.0 - - - +
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Residues in contact with CYS 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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598A ARG* 3.2 3.6 - - + -
599A ALA* 1.3 76.8 - - - +
601A ASP* 1.3 65.4 + - - +
603A ALA* 3.7 3.5 - - - +
604A GLU* 3.4 18.2 + - - +
580D SER* 3.6 24.2 - - - -
582D ARG* 3.5 56.7 + - - +
707D VAL* 6.4 0.2 - - - -
709D GLU* 3.1 23.9 + - - +
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Residues in contact with ASP 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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596A LEU* 3.6 20.2 - - + -
597A PRO* 3.5 16.3 - - + +
598A ARG* 3.0 32.7 + - - +
600A CYS* 1.3 79.4 - - - +
602A SER* 1.3 64.3 + - - +
603A ALA 3.2 1.3 - - - -
604A GLU* 3.0 27.5 + - - +
605A VAL* 3.0 15.6 + - - +
677A GLU* 4.9 4.4 - - - +
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Residues in contact with SER 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A LEU* 3.7 17.6 - - - +
598A ARG 3.1 6.3 + - - -
599A ALA* 3.0 13.2 + - - -
601A ASP* 1.3 76.9 - - - +
603A ALA* 1.3 55.7 + - - +
605A VAL* 3.2 3.9 + - - +
606A LYS* 2.9 29.6 + - - +
638A ILE* 3.2 12.5 - - - +
640A GLY 2.9 23.9 + - - -
641A ARG 3.6 22.7 - - - -
642A ASN 4.4 4.7 - - - -
643A LEU* 4.1 8.5 - - - +
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Residues in contact with ALA 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A ALA 2.9 18.6 + - - +
600A CYS 3.7 6.7 - - - +
601A ASP 3.2 0.2 - - - -
602A SER* 1.3 78.2 + - - +
604A GLU* 1.3 60.5 + - - +
606A LYS* 3.4 4.5 + - - +
607A ALA* 3.1 22.9 + - - +
638A ILE* 3.5 9.6 - - + -
582D ARG* 4.0 20.9 - - + -
584D LEU* 3.7 25.3 - - + +
707D VAL* 4.9 0.4 - - + -
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Residues in contact with GLU 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 CYS 3.4 10.2 + - - +
601A ASP* 3.0 22.1 + - - +
603A ALA* 1.3 78.0 - - - +
605A VAL* 1.3 60.5 + - - +
607A ALA* 3.2 8.2 + - - +
608A TRP* 2.9 27.7 + - + +
675A PHE* 4.1 23.6 - - + -
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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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596A LEU* 4.0 22.9 - - + -
601A ASP 3.0 13.6 + - - +
602A SER* 3.2 7.6 + - - +
604A GLU* 1.3 77.3 - - - +
606A LYS* 1.3 61.3 + - - +
608A TRP* 3.2 2.1 + - - +
609A LEU* 2.9 33.8 + - + +
643A LEU* 3.5 21.1 - - + -
671A LEU* 4.4 22.4 - - + -
675A PHE* 3.7 38.1 - - + -
678A MET* 5.2 3.1 - - - -
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Residues in contact with LYS 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 SER 2.9 13.4 + - - +
603A ALA* 3.5 9.6 - - - +
604A GLU 3.3 0.2 - - - -
605A VAL* 1.3 76.9 - - - +
607A ALA* 1.3 62.6 + - - +
609A LEU* 3.3 4.4 + - - +
610A GLU* 2.7 60.5 + - - +
635A HIS* 5.9 0.6 - - - -
636A THR* 3.1 51.0 + - + +
637A SER* 4.3 7.0 - - - +
638A ILE* 4.2 16.4 - - + +
643A LEU* 4.1 4.4 - - + +
584D LEU* 4.4 36.1 + - + +
585D ALA* 5.6 4.0 - - - +
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Residues in contact with ALA 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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603A ALA 3.1 13.2 + - - +
604A GLU* 3.2 12.3 + - + +
606A LYS* 1.3 77.3 - - - +
608A TRP* 1.3 62.4 + - - +
610A GLU* 3.0 21.5 + - - +
611A THR* 3.4 16.1 + - - +
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Residues in contact with TRP 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 GLU* 2.9 14.3 + - + +
605A VAL 3.5 7.6 - - - +
607A ALA* 1.3 76.5 - - - +
609A LEU* 1.3 78.0 - - + +
611A THR* 2.7 32.8 + - + -
614A GLY* 3.6 22.9 - - - -
617A VAL* 3.1 32.1 - - + -
618A ILE* 3.9 5.4 - - + -
671A LEU* 3.7 23.8 - - + -
674A TYR* 3.7 41.2 - + - -
675A PHE* 3.8 26.1 - + + -
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Residues in contact with LEU 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* 2.9 33.3 + - + +
606A LYS 3.7 4.7 - - - +
608A TRP* 1.3 89.7 - - + +
610A GLU* 1.3 59.3 + - + +
611A THR 3.3 7.2 + - - +
614A GLY 4.9 2.0 - - - -
615A PHE* 4.1 13.0 - - - +
618A ILE* 3.8 29.8 - - + -
634A LEU* 4.2 24.3 - - + +
636A THR* 3.9 19.7 - - + +
643A LEU* 4.1 6.7 - - + -
645A ILE* 3.8 30.5 - - + -
647A PHE* 6.3 1.3 - - + -
671A LEU* 4.0 11.7 - - + -
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Residues in contact with GLU 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A LYS* 2.7 54.2 + - - +
607A ALA* 3.0 15.3 + - - +
609A LEU* 1.3 79.6 - - + +
611A THR* 1.3 59.6 + - - +
612A SER 4.1 0.5 + - - -
615A PHE* 5.8 0.2 - - - -
636A THR* 4.5 9.5 + - - +
584D LEU 4.7 8.3 - - - +
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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