Contacts of the strand formed by residues 504 - 510 (chain A) in PDB entry 1DY7
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 504 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A THR* 2.7 50.5 + - + +
460A LEU* 3.4 21.0 + - - +
461A ASN 3.0 25.2 + - - -
462A PRO* 4.9 7.9 + - - +
467A SER* 3.8 10.3 - - - +
502A GLN 4.0 8.9 + - - +
503A PRO* 1.3 77.7 - - - +
505A VAL* 1.3 63.7 + - - +
506A VAL* 3.7 0.5 + - - +
520A SER 3.5 0.5 - - - +
522A TRP* 2.9 54.2 + - + +
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Residues in contact with VAL 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A ASP* 4.1 4.5 - - + +
458A ALA 4.8 0.2 + - - -
459A THR* 2.7 31.9 + - - -
467A SER 2.8 15.0 + - - +
468A GLY* 3.5 31.6 - - - +
469A SER 4.5 2.2 - - - +
470A VAL* 3.8 27.6 - - + -
492A ILE* 3.8 27.8 - - + -
493A ALA* 3.9 10.5 - - + +
504A ARG* 1.3 73.5 - - - +
506A VAL* 1.3 56.3 + - - +
519A PHE* 3.9 11.0 - - + -
520A SER 3.2 10.1 - - - +
521A VAL* 4.4 5.4 - - + -
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Residues in contact with VAL 506 (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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443A LEU* 4.2 4.9 - - + -
444A PHE* 3.7 25.1 - - + -
457A ASP* 3.7 1.6 - - - -
459A THR* 3.5 26.9 - - + +
504A ARG 4.4 1.8 - - - +
505A VAL* 1.3 80.2 - - - +
507A GLN* 1.3 72.2 + - + +
519A PHE* 4.6 3.4 - - - -
520A SER* 2.9 45.1 + - - +
522A TRP* 4.2 20.4 - - + -
554A THR* 4.5 14.1 - - - +
556A LYS* 3.1 5.7 + - - -
602A DHE 4.4 9.0 - - + -
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Residues in contact with GLN 507 (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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444A PHE* 3.5 35.7 - - + -
457A ASP* 2.9 19.6 + - - +
506A VAL* 1.3 74.8 - - + +
508A GLY* 1.3 72.0 + - - +
509A GLU* 4.6 4.2 + - - -
518A TRP 3.3 0.9 - - - +
519A PHE* 4.0 2.9 - - - -
554A THR 5.1 0.9 - - - +
555A GLY* 3.4 6.6 - - - -
556A LYS* 2.7 88.6 + - - +
557A PHE* 3.5 13.1 - - - -
602A DHE 3.2 26.4 + - + +
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Residues in contact with GLY 508 (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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444A PHE* 4.7 6.6 + - - +
446A LYS* 3.3 34.9 + - - +
457A ASP* 4.7 0.6 + - - -
507A GLN* 1.3 83.0 + - - +
509A GLU* 1.3 60.1 - - - +
517A VAL* 4.0 7.2 - - - -
518A TRP 3.2 9.0 - - - -
519A PHE* 3.5 24.4 - - - -
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Residues in contact with GLU 509 (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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169A PHE* 3.7 12.8 - - + -
391A ARG* 3.9 9.2 + - - -
446A LYS* 3.4 25.9 + - - +
507A GLN* 4.6 1.8 + - - +
508A GLY* 1.3 74.1 - - - +
510A PHE* 1.3 69.8 + - - +
517A VAL* 3.5 4.7 - - - +
518A TRP* 2.8 36.4 + - - +
556A LYS* 3.5 36.6 - - + +
557A PHE* 3.5 3.2 - - - +
558A ASN* 2.7 35.9 + - - +
561A ASN* 4.2 9.5 - - - +
562A THR* 3.8 7.8 + - - -
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Residues in contact with PHE 510 (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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169A PHE* 3.6 3.9 - - - -
446A LYS* 3.9 20.5 - - + +
447A THR* 3.5 36.6 - - - -
448A HIS* 3.7 26.7 - - + -
451A SER* 4.0 3.6 - - - -
455A TYR* 3.8 23.3 - + - -
509A GLU* 1.3 79.6 + - - +
511A ASN* 1.3 66.4 + - - +
514A GLY* 3.8 14.8 - - - -
516A GLU 3.3 16.2 - - - -
517A VAL* 4.0 14.8 - - + -
536A ASP* 3.7 25.1 - - + -
558A ASN* 3.2 17.3 - - - +
561A ASN* 3.0 21.8 + - - +
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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