Contacts of the strand formed by residues 578 - 583 (chain C) in PDB entry 5YDI
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 VAL 578 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478C ILE* 3.4 26.7 - - + -
480C THR* 4.8 2.2 - - + -
568C ALA* 3.6 32.1 - - + +
571C TYR* 3.8 4.3 - - + -
572C ALA* 3.5 24.5 - - - +
576C ASN 3.3 17.6 + - - +
577C ASN* 1.3 74.7 - - - +
579C TYR* 1.3 73.6 + - - +
656C LYS* 3.6 4.2 - - - +
657C HIS* 2.7 50.8 + - + +
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Residues in contact with TYR 579 (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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478C ILE 2.9 11.7 + - - +
479C LEU* 3.5 11.7 - - + -
480C THR 3.0 27.7 + - - +
577C ASN* 4.3 17.7 + - + +
578C VAL* 1.3 82.2 - - - +
580C MET* 1.3 61.9 + - - +
636C PHE* 3.8 17.0 - + - -
640C GLY 3.5 21.5 + - - -
641C ASN* 2.7 30.0 + - - +
642C PRO* 3.6 27.8 - - + -
654C TRP* 3.7 28.3 - + + +
655C PRO 3.9 13.9 - - - -
656C LYS* 3.6 39.7 - - + +
657C HIS* 4.3 1.1 - - - +
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Residues in contact with MET 580 (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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480C THR* 3.1 22.9 - - + +
481C GLY* 4.0 13.2 - - - -
482C SER* 5.1 0.9 - - - -
564C VAL* 4.1 3.8 - - - +
565C ASN* 3.4 36.6 - - - +
568C ALA* 3.5 26.7 - - + -
579C TYR* 1.3 72.9 - - - +
581C TYR* 1.3 63.2 + - - +
654C TRP* 2.9 19.8 + - - +
657C HIS* 3.3 43.3 - - + +
663C HIS 4.1 0.6 + - - +
664C TYR* 3.3 18.5 - - + -
665C LEU 3.0 14.7 + - - -
677C GLY 4.0 1.8 - - - +
678C PRO* 4.0 10.5 - - + -
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Residues in contact with TYR 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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384C LEU 4.5 2.0 - - - -
385C GLN* 3.3 34.8 - - + +
479C LEU* 4.3 3.8 - - + -
480C THR* 3.0 27.0 + - - -
481C GLY* 3.2 48.2 + - - -
482C SER 3.3 7.2 + - - -
483C ASN* 4.3 3.4 - - - -
580C MET* 1.3 81.4 - - - +
582C LEU* 1.3 63.5 + - - +
583C TYR* 3.7 26.7 - + + -
603C GLU* 3.7 11.1 + - + +
633C TRP* 3.6 31.1 - + - -
654C TRP* 3.5 21.8 - + + -
664C TYR* 4.6 1.6 - - - -
665C LEU 3.3 10.8 - - - +
667C LEU* 3.7 20.0 - - + -
678C PRO* 4.8 2.4 - - - +
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Residues in contact with LEU 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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482C SER* 3.4 17.3 - - - +
483C ASN 4.2 16.2 - - - +
484C THR* 4.1 11.0 - - + -
561C THR* 5.3 2.2 - - + -
581C TYR* 1.3 74.4 - - - +
583C TYR* 1.3 60.7 + - - +
584C THR* 3.4 25.1 + - + +
664C TYR* 3.6 38.5 - - + +
665C LEU 3.0 8.9 + - - -
666C GLU* 3.6 3.3 - - + +
667C LEU 3.0 23.1 + - - -
678C PRO* 3.7 28.0 - - + -
679C ARG* 6.2 2.5 - - + -
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Residues in contact with TYR 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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482C SER 3.1 7.7 + - - -
483C ASN* 3.4 21.4 - - - +
484C THR* 3.2 26.0 + - - +
581C TYR* 3.7 14.5 - + + -
582C LEU* 1.3 69.1 - - - +
584C THR* 1.3 59.0 + - - +
585C HIS* 3.3 31.2 + - + -
598C VAL* 3.5 25.4 - - + +
602C ASP 3.6 4.5 + - - -
603C GLU* 3.8 38.4 - - + -
606C TYR* 3.1 34.7 - - - -
625C PHE* 3.6 21.5 - + - -
629C ILE* 4.8 10.5 - - + -
667C LEU* 3.7 23.6 - - + -
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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