Contacts of the strand formed by residues 478 - 483 (chain A) in PDB entry 5YDJ
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 ILE 478 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A LEU* 3.6 32.3 - - + -
382A ALA* 3.6 13.9 - - + -
384A LEU* 3.9 17.0 - - + -
477A GLU* 1.3 82.6 - - - +
479A LEU* 1.3 68.5 + - - +
480A THR* 4.1 15.9 - - + -
567A PHE* 4.4 9.0 - - + -
568A ALA* 5.5 0.9 - - - -
571A TYR* 3.3 39.7 - - + -
577A ASN 3.2 5.4 + - - +
578A VAL* 3.4 18.5 - - + -
579A TYR* 3.0 27.4 + - - -
636A PHE* 3.4 5.4 - - - -
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Residues in contact with LEU 479 (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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382A ALA 3.3 5.9 + - - -
383A ILE* 3.2 25.0 - - + +
384A LEU* 2.9 23.9 + - - +
478A ILE* 1.3 73.6 - - - +
480A THR* 1.3 61.7 + - - +
579A TYR* 3.5 13.5 - - + +
581A TYR* 4.3 4.7 - - + -
632A TYR 4.2 4.3 - - - +
633A TRP* 3.8 23.8 - - + -
636A PHE* 3.4 33.6 - - + -
642A PRO* 3.8 28.3 - - + -
654A TRP* 3.7 30.5 - - + -
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Residues in contact with THR 480 (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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384A LEU* 2.6 36.1 + - - +
387A GLY 4.4 0.9 + - - -
478A ILE* 4.1 14.6 - - + -
479A LEU* 1.3 75.2 - - - +
481A GLY* 1.3 62.6 + - - +
564A VAL* 3.3 20.9 - - + +
567A PHE* 5.6 4.1 - - + -
568A ALA* 3.8 29.6 - - + +
578A VAL* 4.6 4.9 - - + -
579A TYR 3.1 9.4 + - - +
580A MET* 3.2 7.4 - - - -
581A TYR* 2.9 32.1 + - - -
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Residues in contact with GLY 481 (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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384A LEU 3.4 1.5 + - - +
386A SER* 2.7 34.5 + - - -
480A THR* 1.3 82.1 + - - +
482A SER* 1.3 60.4 + - - -
564A VAL* 4.1 4.7 - - - +
580A MET* 3.9 9.0 - - - -
581A TYR* 3.2 30.9 + - - -
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Residues in contact with SER 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A SER* 3.6 1.8 - - - -
481A GLY* 1.3 75.9 + - - -
483A ASN* 1.3 70.3 + - - +
486A GLU* 3.6 13.0 - - - -
561A THR* 3.4 46.7 + - - +
564A VAL* 3.9 9.6 - - - +
565A ASN* 4.8 1.4 + - - -
580A MET* 5.1 0.9 - - - -
581A TYR* 3.3 8.5 + - - -
582A LEU* 3.5 10.3 - - - -
583A TYR 2.9 23.0 + - - -
678A PRO* 5.1 3.6 - - - +
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Residues in contact with ASN 483 (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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386A SER* 3.6 10.3 + - - -
482A SER* 1.3 85.8 - - - +
484A THR* 1.3 64.5 + - - +
485A GLU 3.5 1.1 - - - +
486A GLU* 3.0 27.8 + - - +
561A THR* 4.2 4.3 + - - -
581A TYR* 4.1 2.3 - - - -
582A LEU* 4.1 6.6 - - - +
583A TYR* 3.5 32.3 - - - +
598A VAL* 3.7 13.9 - - + +
599A MET 2.9 23.1 + - - +
600A HIS* 4.2 0.2 - - - +
601A GLY 3.7 3.2 - - - +
602A ASP 3.8 2.2 - - - +
603A GLU* 2.9 30.0 + - - +
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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