Contacts of the strand formed by residues 580 - 590 (chain A) 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 SER 580 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546A LEU* 4.3 0.2 - - - -
547A ASP* 3.2 12.3 + - - -
578A GLY 5.2 0.7 + - - -
579A ALA* 1.3 76.7 + - - +
581A SER* 1.3 60.8 + - - +
582A ARG* 4.9 1.3 - - - -
708A CYS* 3.4 3.7 - - - -
709A GLU* 2.9 41.3 + - - +
599D ALA* 6.0 0.2 - - - +
600D CYS* 3.8 24.9 - - - -
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Residues in contact with SER 581 (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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546A LEU* 3.7 10.9 - - - +
547A ASP* 2.6 29.4 + - - -
580A SER* 1.3 75.2 - - - +
582A ARG* 1.3 85.5 + - - +
706A VAL* 4.5 3.6 - - - -
707A VAL* 3.2 13.9 - - - -
708A CYS* 4.1 7.9 - - - -
840A ARG* 2.9 40.9 + - - +
600D CYS* 5.0 0.7 - - - -
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Residues in contact with ARG 582 (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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547A ASP* 4.1 6.7 + - - -
580A SER* 4.9 1.0 - - - -
581A SER* 1.3 98.6 + - - +
583A VAL* 1.3 65.8 + - - +
584A LEU* 3.7 2.6 + - + -
706A VAL* 3.3 6.0 - - - +
707A VAL* 3.0 39.4 + - + +
840A ARG* 4.1 13.4 - - - +
600D CYS* 3.5 45.0 + - - +
603D ALA* 3.9 29.6 - - + -
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Residues in contact with VAL 583 (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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582A ARG* 1.3 73.4 - - - +
584A LEU* 1.3 63.4 + - - +
585A ALA 3.6 23.8 - - - +
586A ASP* 4.6 3.4 - - + -
704A LYS* 4.6 7.0 - - + -
705A SER 3.4 6.3 - - - +
706A VAL* 4.2 9.6 - - + +
836A ARG* 4.0 37.7 - - + +
840A ARG* 3.6 33.7 - - + +
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Residues in contact with LEU 584 (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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582A ARG* 4.2 4.9 - - + +
583A VAL* 1.3 76.6 - - - +
585A ALA* 1.3 59.4 + - - +
705A SER* 2.7 23.7 + - - +
706A VAL 4.2 6.5 - - - +
707A VAL* 4.0 28.0 - - + +
796A THR* 4.7 5.2 - - + -
603D ALA* 3.6 36.8 - - + +
606D LYS* 3.8 27.3 - - + +
610D GLU* 4.5 8.5 - - - +
638D ILE* 3.8 33.9 - - + -
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Residues in contact with ALA 585 (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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583A VAL* 3.6 9.5 - - - +
584A LEU* 1.3 81.0 - - + +
586A ASP* 1.3 64.5 + - - +
648A GLN* 5.9 4.0 - - - +
650A ARG* 5.7 2.0 - - - +
700A GLU 5.9 3.6 - - - +
701A GLY* 6.4 0.2 - - - -
703A GLY 4.2 1.8 - - - +
704A LYS* 3.5 3.1 - - - -
705A SER* 3.0 39.1 + - - +
606D LYS* 5.4 5.2 - - - +
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Residues in contact with ASP 586 (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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583A VAL* 4.6 7.4 - - + -
585A ALA* 1.3 79.5 - - - +
587A GLY* 1.3 64.2 + - - +
588A MET 5.0 0.5 + - - -
632A GLN* 2.8 24.0 + - - +
648A GLN* 4.9 1.1 - - - -
650A ARG* 2.9 46.8 + - - +
651A SER* 5.4 2.5 + - - -
652A GLY 5.1 4.5 - - - +
703A GLY* 3.3 5.4 - - - +
704A LYS* 3.1 41.1 + - + +
832A GLY* 5.0 1.7 - - - +
836A ARG* 3.9 20.2 + - - +
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Residues in contact with GLY 587 (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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586A ASP* 1.3 80.0 + - - +
588A MET* 1.3 65.3 + - - -
589A THR* 3.9 0.2 - - - +
632A GLN* 3.6 7.9 - - - -
648A GLN* 3.1 25.9 + - - +
649A SER 3.5 11.2 - - - -
702A ARG* 3.8 1.7 - - - -
703A GLY* 2.8 31.7 + - - -
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Residues in contact with MET 588 (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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586A ASP* 5.0 0.8 + - - -
587A GLY* 1.3 75.3 - - - -
589A THR* 1.3 74.1 + - - +
648A GLN* 3.2 4.2 - - - -
649A SER 2.9 31.5 + - - +
651A SER* 4.8 4.0 + - - +
655A MET* 3.4 42.8 - - + +
656A GLY* 3.9 9.2 - - - -
657A MET* 4.1 7.9 - - - +
660A ILE* 3.8 29.6 - - + +
702A ARG* 3.3 30.7 - - - +
703A GLY* 4.1 12.2 - - - +
801A GLU* 4.1 27.6 - - + -
802A ILE 5.3 0.4 - - - +
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Residues in contact with THR 589 (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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587A GLY 3.9 4.7 - - - +
588A MET* 1.3 90.8 - - - +
590A ARG* 1.3 62.6 - - - +
646A ARG* 3.8 30.5 - - + +
647A PHE 3.1 13.9 - - - +
648A GLN* 3.7 20.6 - - + +
657A MET* 4.3 3.3 - - - +
660A ILE* 4.0 4.8 - - - +
688A CYS* 2.6 27.0 + - - -
702A ARG* 2.9 41.0 + - + +
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Residues in contact with ARG 590 (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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589A THR* 1.3 76.1 - - - +
591A GLY* 1.3 59.3 + - - +
592A PRO* 3.2 7.4 - - + +
646A ARG* 4.5 1.1 - - - -
647A PHE* 2.9 29.0 + - - -
657A MET* 3.5 24.4 + - - +
660A ILE* 3.5 20.8 - - + +
661A SER* 3.3 28.4 + - - +
664A THR* 3.6 18.8 - - - +
683A VAL* 3.5 26.4 + - + +
684A SER* 3.4 13.4 + - - -
688A CYS* 3.5 20.4 - - - -
690A ASP* 4.2 0.4 - - - +
201B MAH 3.1 53.5 + - - +
862B LEU* 4.1 11.4 - - - +
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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