Contacts of the helix formed by residues 598 - 610 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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709A GLU* 3.6 21.3 - - - +
792A TYR* 5.2 2.5 - - + -
596D LEU* 3.2 5.2 - - - +
597D PRO* 1.3 87.6 - - + +
599D ALA* 1.3 63.8 - - - +
600D CYS* 3.2 7.6 - - + +
601D ASP* 3.1 22.7 + - - +
602D SER* 3.1 18.4 + - - -
641D ARG* 3.6 8.8 - - - +
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Residues in contact with ALA 599 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707A VAL* 3.8 25.6 - - + +
708A CYS 4.8 0.9 - - - +
709A GLU* 2.7 30.7 + - + +
792A TYR* 3.9 2.7 - - - +
598D ARG* 1.3 69.0 - - - +
600D CYS* 1.3 57.8 - - - +
602D SER* 2.7 24.1 + - - -
603D ALA* 2.9 19.3 + - - +
640D GLY* 3.5 24.0 - - - +
641D ARG* 3.7 3.0 - - - +
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Residues in contact with CYS 600 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580A SER* 3.8 23.1 - - - -
581A SER* 5.3 0.2 - - - -
582A ARG* 3.5 56.7 + - - +
709A GLU* 3.0 20.6 + - - +
598D ARG* 3.2 6.7 - - + -
599D ALA* 1.3 77.9 - - - +
601D ASP* 1.3 64.8 + - - +
603D ALA* 3.5 4.0 + - - +
604D GLU* 3.2 19.8 + - - +
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Residues in contact with ASP 601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596D LEU* 3.6 19.7 - - + -
597D PRO* 3.5 15.3 - - - +
598D ARG* 3.1 39.2 + - - +
600D CYS* 1.3 79.2 - - - +
602D SER* 1.3 66.0 + - - +
604D GLU* 3.1 14.9 + - - +
605D VAL* 3.0 24.6 + - - +
675D PHE* 5.0 2.0 - - + -
677D GLU* 5.1 2.1 - - - +
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Residues in contact with SER 602 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596D LEU* 3.9 15.2 - - - +
598D ARG 3.1 5.9 + - - -
599D ALA* 2.7 21.1 + - - -
601D ASP* 1.3 75.8 - - - +
603D ALA* 1.3 61.2 + - - +
605D VAL* 3.2 5.3 + - - +
606D LYS* 3.0 18.5 + - - +
638D ILE* 3.6 23.2 - - - +
640D GLY 2.8 20.6 + - - -
641D ARG 3.7 22.4 - - - -
642D ASN 4.1 2.5 - - - -
643D LEU* 4.3 5.1 - - - +
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Residues in contact with ALA 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582A ARG* 3.9 23.6 - - + -
584A LEU* 3.6 31.7 - - + +
707A VAL* 4.8 0.9 - - + -
599D ALA 2.9 16.3 + - - +
600D CYS 3.6 6.7 - - - +
601D ASP 3.2 0.2 - - - -
602D SER* 1.3 77.8 + - - +
604D GLU* 1.3 55.6 + - - +
606D LYS* 3.3 4.5 + - - +
607D ALA* 2.9 29.3 + - - +
638D ILE* 4.0 2.4 - - - +
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Residues in contact with GLU 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600D CYS 3.2 11.5 + - - +
601D ASP* 3.1 16.9 + - - +
603D ALA* 1.3 76.7 - - - +
605D VAL* 1.3 66.4 + - - +
607D ALA* 3.3 7.1 + - + +
608D TRP* 3.0 22.9 + - + +
675D PHE* 3.5 24.8 - - + -
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Residues in contact with VAL 605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596D LEU* 3.9 21.5 - - + -
601D ASP 3.0 15.6 + - - +
602D SER 3.2 6.0 + - - +
604D GLU* 1.3 75.0 - - - +
606D LYS* 1.3 58.2 + - - +
608D TRP* 3.1 2.9 + - - +
609D LEU* 2.9 39.5 + - + +
643D LEU* 3.5 22.2 - - + -
671D LEU* 3.9 26.9 - - + -
675D PHE* 3.8 35.0 - - + -
678D MET* 5.2 2.9 - - - -
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Residues in contact with LYS 606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584A LEU* 3.8 37.9 - - + +
585A ALA* 5.4 3.6 - - - +
705A SER* 6.3 0.4 - - - -
602D SER 3.0 12.2 + - - +
603D ALA 3.5 7.6 - - - +
605D VAL* 1.3 78.1 - - - +
607D ALA* 1.3 62.1 + - - +
609D LEU* 3.3 12.1 + - - +
610D GLU* 2.7 50.5 + - - +
636D THR* 2.6 46.3 + - - +
637D SER* 5.5 0.2 - - - +
638D ILE* 3.7 25.4 - - + +
643D LEU* 4.3 9.6 - - + +
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Residues in contact with ALA 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603D ALA 2.9 15.9 + - - +
604D GLU* 3.7 7.0 - - + +
605D VAL 3.3 0.2 - - - -
606D LYS* 1.3 76.1 - - - +
608D TRP* 1.3 64.6 + - - +
610D GLU* 3.1 22.9 + - - +
611D THR* 3.4 16.3 + - - +
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Residues in contact with TRP 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604D GLU* 3.0 13.9 + - + +
605D VAL 3.4 8.5 - - - +
607D ALA* 1.3 76.9 - - - +
609D LEU* 1.3 68.2 + - + +
611D THR* 2.7 34.1 + - + -
613D GLU* 6.2 0.8 - - - +
614D GLY* 3.4 23.7 - - - +
617D VAL* 3.5 30.7 - - + -
618D ILE* 3.6 17.7 - - + -
671D LEU* 3.5 31.2 - - + -
674D TYR* 3.7 44.1 - + - -
675D PHE* 4.2 20.0 - + + -
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Residues in contact with LEU 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605D VAL* 2.9 36.4 + - + +
606D LYS* 3.3 5.6 + - - +
608D TRP* 1.3 99.3 - - + +
610D GLU* 1.3 61.0 + - + +
611D THR 3.3 6.7 + - - +
614D GLY 4.8 2.2 - - - +
615D PHE* 4.0 15.4 + - - +
618D ILE* 3.9 17.0 - - + -
634D LEU* 4.0 25.2 - - + +
636D THR* 4.0 23.3 - - + -
643D LEU* 4.3 2.9 - - + -
645D ILE* 4.0 26.9 - - + -
647D PHE* 6.2 1.3 - - + -
671D LEU* 4.1 10.1 - - + -
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Residues in contact with GLU 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584A LEU 4.5 9.6 - - - +
606D LYS* 2.7 51.5 + - + +
607D ALA* 3.1 15.9 + - - +
608D TRP 3.0 1.4 - - - -
609D LEU* 1.3 79.8 - - + +
611D THR* 1.3 60.0 + - - +
612D SER 4.0 0.7 + - - -
615D PHE* 5.7 0.2 - - - -
636D THR* 3.5 6.8 + - + +
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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