Contacts of the strand formed by residues 580 - 590 (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 SER 580 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599B ALA* 6.0 0.2 - - - +
600B CYS* 3.6 26.4 - - - -
547C ASP* 3.3 10.2 + - - -
578C GLY 5.4 0.2 + - - -
579C ALA* 1.3 76.9 + - - +
581C SER* 1.3 59.1 + - - +
582C ARG* 4.7 1.8 - - - -
708C CYS* 3.0 3.4 - - - -
709C GLU* 2.8 42.9 + - - +
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Residues in contact with SER 581 (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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600B CYS* 5.3 0.2 - - - -
546C LEU* 3.6 8.2 - - - +
547C ASP* 2.6 29.2 + - - -
580C SER* 1.3 73.7 - - - +
582C ARG* 1.3 76.0 + - - +
706C VAL* 4.5 3.6 - - - -
707C VAL* 3.1 14.1 - - - -
708C CYS* 3.7 12.6 - - - -
840C ARG* 2.8 49.4 + - - +
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Residues in contact with ARG 582 (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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600B CYS* 3.5 44.7 + - - +
603B ALA* 4.0 27.4 - - + -
547C ASP* 4.0 10.3 + - - -
580C SER* 4.7 1.4 - - - -
581C SER* 1.3 91.4 + - - +
583C VAL* 1.3 66.6 + - - +
584C LEU* 3.7 2.8 + - + -
706C VAL* 3.4 4.9 - - - +
707C VAL* 3.0 38.4 + - + +
840C ARG* 4.1 13.9 - - - +
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Residues in contact with VAL 583 (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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582C ARG* 1.3 75.3 - - - +
584C LEU* 1.3 62.9 + - - +
585C ALA* 3.5 25.4 - - - +
586C ASP* 4.7 2.2 - - + -
704C LYS* 4.5 5.4 - - + -
705C SER 3.5 6.1 - - - +
706C VAL* 4.3 9.4 - - + -
836C ARG* 4.0 42.8 - - + +
840C ARG* 3.9 30.5 - - + +
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Residues in contact with LEU 584 (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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603B ALA* 3.7 36.6 - - + +
606B LYS* 3.8 27.0 - - + +
610B GLU* 4.4 8.3 - - - +
638B ILE* 3.7 35.7 - - + +
582C ARG* 4.1 6.3 - - + +
583C VAL* 1.3 76.4 - - - +
585C ALA* 1.3 60.5 + - - +
705C SER* 2.7 27.4 + - - +
706C VAL 4.4 7.4 - - - -
707C VAL* 4.0 20.4 - - + -
796C THR* 4.5 6.7 - - + -
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Residues in contact with ALA 585 (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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606B LYS* 5.4 5.2 - - - +
583C VAL* 3.5 11.8 - - - +
584C LEU* 1.3 79.9 - - + +
586C ASP* 1.3 65.2 + - - +
648C GLN* 5.9 4.9 - - - +
650C ARG* 5.8 2.0 - - - +
700C GLU 5.9 2.9 - - - +
701C GLY* 6.3 0.2 - - - -
703C GLY 4.1 1.3 - - - +
704C LYS* 3.5 1.4 - - - -
705C SER* 3.0 39.0 + - - +
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Residues in contact with ASP 586 (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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583C VAL* 4.7 6.7 - - + -
585C ALA* 1.3 79.0 - - - +
587C GLY* 1.3 56.3 + - - +
588C MET 4.9 0.9 + - - -
632C GLN* 2.6 32.2 + - - +
648C GLN* 4.9 1.6 - - - -
650C ARG* 3.2 40.4 + - - +
651C SER* 5.4 2.8 + - - -
652C GLY 5.0 5.9 - - - +
703C GLY* 3.3 5.0 - - - +
704C LYS* 2.9 43.0 + - + +
832C GLY* 5.1 1.4 - - - +
836C ARG* 3.9 18.7 + - - +
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Residues in contact with GLY 587 (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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586C ASP* 1.3 80.6 + - - +
588C MET* 1.3 65.8 + - - -
589C THR* 3.8 2.4 + - - +
632C GLN* 3.7 6.3 - - - -
648C GLN* 3.0 27.5 + - - +
649C SER 3.4 12.3 - - - -
650C ARG* 4.4 0.7 - - - -
703C GLY* 2.9 28.8 + - - -
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Residues in contact with MET 588 (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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586C ASP* 4.9 1.0 + - - -
587C GLY* 1.3 74.3 - - - +
589C THR* 1.3 61.5 + - - +
647C PHE 3.8 0.2 - - - +
648C GLN* 3.3 2.6 - - - -
649C SER 2.9 31.9 + - - +
650C ARG* 5.1 0.2 - - - +
651C SER* 4.6 5.3 + - - +
655C MET* 3.1 56.3 - - + +
656C GLY 3.9 3.8 - - - +
657C MET* 4.1 3.1 - - - +
660C ILE* 3.8 27.4 - - + +
702C ARG* 3.3 32.8 - - - +
703C GLY* 4.0 14.9 - - - +
801C GLU* 3.8 29.4 - - + -
802C ILE 5.3 0.2 - - - +
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Residues in contact with THR 589 (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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587C GLY 3.8 5.4 + - - +
588C MET* 1.3 84.9 - - - +
590C ARG* 1.3 60.6 + - - +
646C ARG* 3.7 34.1 - - + +
647C PHE 3.0 8.1 - - - +
648C GLN* 3.7 24.5 - - + +
657C MET* 3.3 9.7 - - - +
660C ILE* 4.1 3.8 - - - -
688C CYS* 2.6 26.5 + - - -
701C GLY 4.8 0.2 - - - +
702C ARG* 3.0 39.7 + - + +
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Residues in contact with ARG 590 (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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589C THR* 1.3 75.9 - - - +
591C GLY* 1.3 58.2 + - - +
592C PRO* 3.4 6.8 - - + +
646C ARG* 3.6 0.8 - - - -
647C PHE* 2.9 29.9 + - - +
657C MET* 3.3 29.1 - - + +
660C ILE* 3.9 11.0 - - + +
661C SER* 3.1 29.0 + - - +
664C THR* 3.5 26.9 - - + +
683C VAL* 3.4 27.3 + - + +
684C SER* 3.6 16.4 + - - -
688C CYS* 3.5 28.8 - - - -
690C ASP* 4.1 1.2 - - - +
203D MAH 3.0 32.1 + - - +
862D LEU* 3.9 17.9 - - - +
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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