Contacts of the strand formed by residues 580 - 590 (chain D) 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 SER 580 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600A CYS* 3.6 25.5 - - - -
547D ASP* 3.3 10.0 - - - -
578D GLY 5.1 0.9 + - - -
579D ALA* 1.3 76.8 + - - +
581D SER* 1.3 60.7 + - - +
582D ARG* 4.7 2.0 - - - -
708D CYS* 3.3 3.6 - - - -
709D GLU* 2.9 39.9 + - - +
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Residues in contact with SER 581 (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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600A CYS* 5.1 0.7 - - - -
546D LEU* 3.9 10.4 - - - +
547D ASP* 2.7 33.4 + - - +
580D SER* 1.3 75.6 - - - +
582D ARG* 1.3 83.6 + - - +
706D VAL* 4.5 4.0 - - - -
707D VAL* 3.1 15.0 - - - -
708D CYS* 4.2 7.9 - - - -
840D ARG* 3.2 34.0 + - - +
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Residues in contact with ARG 582 (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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600A CYS* 3.5 45.6 + - - +
603A ALA* 4.0 24.9 - - + -
547D ASP* 4.0 10.9 + - - -
580D SER* 4.7 1.8 - - - -
581D SER* 1.3 92.3 + - - +
583D VAL* 1.3 65.4 + - - +
584D LEU* 3.6 3.6 + - + -
706D VAL* 3.4 6.4 - - - +
707D VAL* 3.0 43.6 + - + +
840D ARG* 5.0 1.8 - - - +
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Residues in contact with VAL 583 (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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582D ARG* 1.3 74.6 - - - +
584D LEU* 1.3 64.6 + - - +
585D ALA 3.5 22.4 - - - +
586D ASP* 4.9 2.9 - - + -
704D LYS* 4.7 8.7 - - + -
705D SER 3.5 6.7 - - - +
706D VAL* 4.5 7.0 - - + +
836D ARG* 4.1 35.9 - - + +
839D ALA* 5.4 0.4 - - + -
840D ARG* 3.7 35.6 - - + +
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Residues in contact with LEU 584 (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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603A ALA* 3.7 33.0 - - + +
606A LYS* 4.4 25.8 + - + +
610A GLU* 4.7 10.4 - - - +
638A ILE* 4.1 28.0 - - + +
582D ARG* 4.0 6.3 - - + +
583D VAL* 1.3 78.2 - - - +
585D ALA* 1.3 59.7 + - + +
705D SER* 2.7 26.6 + - - +
706D VAL 4.2 9.6 - - - +
707D VAL* 4.2 26.2 - - + -
796D THR* 4.8 6.1 - - + -
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Residues in contact with ALA 585 (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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606A LYS* 5.6 4.5 - - - +
583D VAL* 3.5 9.4 - - - +
584D LEU* 1.3 81.4 - - + +
586D ASP* 1.3 64.6 + - - +
587D GLY 5.5 0.2 - - - +
648D GLN* 5.6 6.1 - - - +
700D GLU 5.9 2.7 - - - +
703D GLY 4.1 1.3 - - - +
704D LYS* 3.4 3.1 - - - -
705D SER* 3.0 40.1 + - - +
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Residues in contact with ASP 586 (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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583D VAL* 4.9 4.3 - - + -
585D ALA* 1.3 80.5 - - - +
587D GLY* 1.3 63.7 + - - +
588D MET 5.0 0.7 + - - -
632D GLN* 5.0 3.6 - - - +
648D GLN* 4.8 1.6 - - - -
650D ARG* 3.2 46.2 + - - +
651D SER* 5.2 5.0 + - - -
652D GLY 4.9 5.2 - - - +
703D GLY* 3.2 5.4 - - - +
704D LYS* 2.8 38.9 + - + +
836D ARG* 3.3 31.4 + - - +
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Residues in contact with GLY 587 (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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586D ASP* 1.3 79.6 + - - +
588D MET* 1.3 66.8 + - - -
589D THR* 3.8 2.6 - - - +
632D GLN* 5.9 0.2 - - - -
648D GLN* 3.1 32.2 + - - +
649D SER 3.3 12.6 - - - -
650D ARG 4.6 0.2 - - - -
703D GLY* 2.8 29.3 + - - -
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Residues in contact with MET 588 (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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586D ASP* 5.0 1.2 + - - -
587D GLY* 1.3 74.5 - - - +
589D THR* 1.3 69.9 + - - +
647D PHE 3.7 0.2 - - - +
648D GLN* 3.4 2.1 - - - -
649D SER 2.9 31.2 + - - +
651D SER* 4.6 5.5 + - - +
655D MET* 3.3 42.0 - - + +
656D GLY 3.9 15.7 - - - -
657D MET* 4.0 9.2 - - + +
660D ILE* 4.0 22.6 - - + +
702D ARG* 3.4 29.8 - - - +
703D GLY* 4.0 13.5 - - - +
801D GLU* 3.9 29.2 - - + -
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Residues in contact with THR 589 (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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587D GLY 3.8 10.1 - - - +
588D MET* 1.3 86.7 - - - +
590D ARG* 1.3 61.4 + - - +
646D ARG* 3.7 33.4 - - + +
647D PHE 3.0 12.8 - - - +
648D GLN* 3.9 12.8 - - + +
657D MET* 3.2 9.9 - - - +
660D ILE* 3.9 4.5 - - - -
688D CYS* 2.6 26.8 + - - +
701D GLY 4.8 0.2 - - - +
702D ARG* 2.8 41.6 + - + +
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Residues in contact with ARG 590 (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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862C LEU* 3.9 11.3 - - - +
4D NAP 2.5 32.3 + - - -
203D MAH 3.3 32.5 + - - +
589D THR* 1.3 75.7 - - - +
591D GLY* 1.3 66.5 + - - +
592D PRO* 3.4 3.5 - - - +
645D ILE 3.3 2.8 - - - +
646D ARG* 3.5 1.3 - - - -
647D PHE* 2.9 30.9 + - + +
657D MET* 3.5 18.2 - - - +
660D ILE* 3.4 13.4 - - + +
661D SER* 3.1 18.3 + - - +
664D THR* 3.4 30.7 - - + +
683D VAL* 3.5 25.2 + - + +
684D SER* 3.6 8.9 + - - -
688D CYS* 3.3 23.6 - - - -
690D ASP* 4.0 2.0 - - - +
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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