Contacts of the helix formed by residues 598 - 611 (chain C) in PDB entry 1DQ8
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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709B GLU* 3.5 20.9 - - - +
792B TYR* 4.6 1.8 - - + -
596C LEU* 3.9 1.0 - - - +
597C PRO* 1.3 89.6 - - + +
599C ALA* 1.3 65.9 + - - +
600C CYS* 4.0 8.1 - - + +
601C ASP* 3.0 32.6 + - - +
602C SER* 3.1 14.0 + - - -
641C ARG* 3.6 8.3 - - - -
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Residues in contact with ALA 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707B VAL* 3.7 26.8 - - + +
708B CYS 5.2 0.2 - - - -
709B GLU* 2.7 27.8 + - + +
792B TYR* 4.0 3.4 - - - +
598C ARG* 1.3 72.3 - - - +
600C CYS* 1.3 57.7 + - - +
602C SER* 3.1 2.7 + - - -
603C ALA* 2.8 30.9 + - - +
638C ILE* 5.4 0.5 - - - +
640C GLY* 3.5 32.0 - - - +
641C ARG* 3.7 4.9 - - - +
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Residues in contact with CYS 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B SER* 3.6 22.4 - - - -
582B ARG* 3.4 57.8 + - - +
707B VAL* 6.5 0.2 - - - -
709B GLU* 3.1 24.2 + - - +
598C ARG* 3.1 7.2 - - + -
599C ALA* 1.3 77.6 - - - +
601C ASP* 1.3 64.9 + - - +
603C ALA* 3.6 3.5 + - - +
604C GLU* 3.2 20.3 + - - +
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Residues in contact with ASP 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C LEU* 3.7 23.3 - - + -
597C PRO* 3.7 12.2 - - - +
598C ARG* 3.0 41.1 + - - +
600C CYS* 1.3 80.1 - - - +
602C SER* 1.3 64.5 + - - +
604C GLU* 3.0 18.9 + - - +
605C VAL* 2.9 24.9 + - - +
675C PHE* 6.4 0.4 - - + -
677C GLU* 4.6 8.0 - - - +
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Residues in contact with SER 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C LEU* 3.6 18.1 - - - +
598C ARG 3.1 5.7 + - - -
599C ALA 3.1 7.2 + - - -
601C ASP* 1.3 75.1 - - - +
603C ALA* 1.3 57.8 + - - +
605C VAL* 3.1 4.6 + - - +
606C LYS* 2.9 28.6 + - - +
638C ILE* 3.4 25.7 - - - +
640C GLY 3.8 7.6 - - - -
641C ARG* 2.5 36.4 + - - -
642C ASN 4.3 1.1 - - - -
643C LEU* 4.3 3.2 - - - +
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Residues in contact with ALA 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B ARG* 3.9 22.2 - - + -
584B LEU* 3.6 31.2 - - + +
707B VAL* 4.8 1.6 - - + -
599C ALA 2.8 16.3 + - - +
600C CYS 3.7 5.4 - - - +
601C ASP 3.2 0.2 - - - -
602C SER* 1.3 75.9 - - - +
604C GLU* 1.3 57.1 + - - +
606C LYS* 3.3 5.4 + - - +
607C ALA* 2.9 28.6 + - - +
638C ILE* 4.2 2.4 - - + +
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Residues in contact with GLU 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600C CYS 3.2 11.0 + - - +
601C ASP* 3.0 21.6 + - - +
603C ALA* 1.3 76.6 - - - +
605C VAL* 1.3 60.2 + - - +
607C ALA* 3.2 8.1 + - + +
608C TRP* 2.9 28.8 + - + +
675C PHE* 4.0 24.8 - - + -
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Residues in contact with VAL 605 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C LEU* 3.6 23.1 - - + -
601C ASP 2.9 18.2 + - - +
602C SER 3.1 6.2 + - - +
604C GLU* 1.3 74.7 - - - +
606C LYS* 1.3 56.8 + - - +
608C TRP* 3.3 1.6 + - - +
609C LEU* 2.9 30.7 + - + +
643C LEU* 3.5 23.6 - - + -
671C LEU* 4.0 33.4 - - + -
675C PHE* 3.6 37.7 - - + -
678C MET* 5.1 2.2 - - - -
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Residues in contact with LYS 606 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B LEU* 3.9 38.8 - - + +
585B ALA* 5.5 3.6 - - - +
602C SER 2.9 13.2 + - - +
603C ALA* 3.6 9.4 - - - +
605C VAL* 1.3 77.9 - - - +
607C ALA* 1.3 63.8 + - - +
609C LEU* 3.2 11.4 + - - +
610C GLU* 2.9 44.7 + - - +
636C THR* 2.8 50.2 + - - +
637C SER* 5.7 0.2 - - - +
638C ILE* 3.8 24.0 - - + +
643C LEU* 4.4 10.0 - - + +
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Residues in contact with ALA 607 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603C ALA 2.9 18.0 + - - +
604C GLU* 3.6 7.6 - - + +
606C LYS* 1.3 74.7 - - - +
608C TRP* 1.3 63.2 + - - +
610C GLU* 3.0 22.2 + - - +
611C THR* 3.3 17.4 + - - +
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Residues in contact with TRP 608 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604C GLU* 2.9 17.2 + - + +
605C VAL 3.5 3.6 - - - +
607C ALA* 1.3 75.5 - - - +
609C LEU* 1.3 68.5 + - + +
611C THR* 2.7 34.9 + - + -
613C GLU* 5.2 3.3 - - + +
614C GLY* 3.6 19.9 - - - +
617C VAL* 3.1 33.9 - - + -
618C ILE* 3.6 17.0 - - + -
671C LEU* 3.4 33.2 - - + -
674C TYR* 3.6 41.8 - + - -
675C PHE* 3.9 22.9 - + + -
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Residues in contact with LEU 609 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605C VAL* 2.9 33.5 + - + +
606C LYS* 3.2 5.6 + - - +
608C TRP* 1.3 99.5 - - + +
610C GLU* 1.3 60.6 + - + +
611C THR 3.6 0.6 + - - -
614C GLY 4.9 1.3 - - - +
615C PHE* 3.7 28.3 - - - +
618C ILE* 4.1 16.6 - - + -
634C LEU* 3.8 28.0 - - + +
636C THR* 4.3 15.5 - - + -
643C LEU* 4.5 2.7 - - + -
645C ILE* 3.9 33.4 - - + -
647C PHE* 6.3 0.9 - - + -
671C LEU* 4.2 7.4 - - + -
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Residues in contact with GLU 610 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B LEU 4.7 5.5 - - - +
606C LYS* 2.9 53.1 + - + +
607C ALA* 3.0 13.6 + - - +
609C LEU* 1.3 76.7 - - + +
611C THR* 1.3 64.0 + - - +
612C SER 4.0 0.2 + - - -
615C PHE* 5.4 0.4 - - - -
636C THR* 3.6 9.4 + - + +
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Residues in contact with THR 611 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607C ALA* 3.3 16.8 - - + +
608C TRP* 2.7 25.0 + - + +
610C GLU* 1.3 82.1 - - - +
612C SER* 1.3 62.9 + - - +
613C GLU* 3.6 15.1 + - - +
614C GLY* 3.0 15.8 + - - -
615C PHE* 3.2 22.5 + - - +
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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