Contacts of the strand formed by residues 578 - 582 (chain A) in PDB entry 2YD0
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 HIS 578 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568A THR* 3.1 7.8 - - - -
569A PHE* 3.0 74.1 + + + +
570A ILE* 5.0 2.5 - - - -
571A THR* 5.1 8.5 + - + +
574A SER* 4.9 9.4 - - - -
576A MET* 3.5 48.5 + - + +
577A VAL* 1.3 72.7 - - - +
579A ARG* 1.3 63.5 + - - +
591A LEU* 5.7 3.0 - - + +
592A PRO* 6.6 0.2 - - + -
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Residues in contact with ARG 579 (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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450A GLU* 4.3 24.7 + - - +
567A LEU 3.4 4.7 - - - +
568A THR* 4.5 12.1 - - + +
569A PHE* 4.8 2.2 - - - -
576A MET* 6.2 0.6 - - + +
577A VAL* 4.4 20.7 + - - +
578A HIS* 1.3 81.5 - - - +
580A PHE* 1.3 64.4 + - - +
1949A EDO 3.2 48.3 + - - +
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Residues in contact with PHE 580 (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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544A MET* 3.9 26.5 - - + -
566A PRO* 4.7 1.1 - - - -
567A LEU* 2.8 47.2 + - + +
569A PHE* 5.1 3.1 - - + -
579A ARG* 1.3 77.8 - - - +
581A LEU* 1.3 75.9 + - - +
582A LEU* 3.4 11.1 + - + -
587A ASP* 3.3 37.0 - - + -
588A VAL 4.6 4.3 - - - -
589A LEU* 3.7 39.9 - - + -
1949A EDO 5.7 1.8 - - - -
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Residues in contact with LEU 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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451A TYR* 3.2 37.0 - - + +
514A GLY 5.2 4.5 - - - +
516A ASP 6.1 1.1 - - - +
520A MET* 3.2 31.0 - - + -
564A HIS* 4.1 2.9 - - + +
565A VAL 3.5 27.8 - - - +
566A PRO* 3.6 9.6 - - + -
580A PHE* 1.3 81.8 - - - +
582A LEU* 1.3 63.6 + - - +
583A LYS* 3.4 33.6 + - + +
587A ASP* 5.3 0.5 - - - +
1949A EDO 5.8 1.5 - - - -
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Residues in contact with LEU 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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533A ILE* 4.1 20.4 - - + -
544A MET* 4.2 13.9 - - + -
545A LYS 4.4 6.5 - - - +
546A GLN* 3.9 16.2 - - + +
563A TRP 3.5 3.6 - - - +
564A HIS* 3.5 1.3 - - - -
565A VAL* 2.8 42.2 + - + +
567A LEU* 3.8 31.2 - - + -
580A PHE* 3.4 7.2 + - + -
581A LEU* 1.3 70.8 - - - +
583A LYS* 1.3 59.8 + - - +
584A THR* 3.5 24.0 - - - +
586A THR 4.0 5.4 - - - -
587A ASP* 3.7 31.0 - - + +
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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