Contacts of the strand formed by residues 565 - 571 (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 VAL 565 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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524A TRP* 4.3 7.2 - - + -
531A PRO* 4.2 11.2 - - + -
533A ILE* 4.4 9.9 - - + -
546A GLN* 4.3 8.1 - - - +
563A TRP* 3.6 28.7 - - + +
564A HIS* 1.3 74.3 - - - +
566A PRO* 1.3 64.5 - - + +
567A LEU* 3.1 23.7 + - + -
581A LEU* 3.5 2.8 - - - +
582A LEU* 2.8 42.7 + - + +
608A TYR* 3.5 36.8 - - + -
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Residues in contact with PRO 566 (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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447A MET* 4.0 40.4 - - + +
448A LEU* 6.0 0.2 - - - -
451A TYR* 4.1 30.1 - - + -
520A MET* 4.6 7.4 - - - -
524A TRP* 4.7 0.7 - - - +
564A HIS 3.6 8.3 - - - +
565A VAL* 1.3 81.4 - - + +
567A LEU* 1.3 62.6 + - - +
568A THR* 3.8 4.7 + - - +
580A PHE 3.9 2.9 - - - +
581A LEU* 3.6 12.5 - - + -
606A GLY* 5.7 0.5 - - - -
608A TYR* 3.8 10.9 + - - -
1949A EDO 3.8 20.1 + - - +
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Residues in contact with LEU 567 (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* 3.7 33.7 - - + -
544A MET* 3.6 34.1 - - + -
565A VAL* 3.1 19.6 + - + +
566A PRO* 1.3 74.2 - - - +
568A THR* 1.3 61.2 + - - +
569A PHE* 5.4 0.7 - - - -
579A ARG* 3.4 5.2 - - - +
580A PHE* 2.8 43.7 + - + +
582A LEU* 3.8 25.8 - - + -
600A PHE* 4.2 16.4 - - + -
608A TYR* 3.6 21.5 - - + +
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Residues in contact with THR 568 (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* 6.1 3.4 - - + -
566A PRO 3.8 3.4 + - - +
567A LEU* 1.3 78.8 - - - +
569A PHE* 1.3 67.5 + - - +
577A VAL* 4.1 17.7 - - + -
578A HIS 3.1 11.9 - - - +
579A ARG* 4.5 10.3 - - + +
600A PHE* 3.3 5.5 - - - -
601A ASN* 2.9 27.7 + - - -
602A VAL* 3.1 27.9 + - + +
605A ASN* 5.9 2.5 - - + +
608A TYR* 3.6 5.0 + - - -
1949A EDO 3.9 17.7 - - - +
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Residues in contact with PHE 569 (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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567A LEU 5.3 2.0 - - - -
568A THR* 1.3 78.8 - - - +
570A ILE* 1.3 69.6 + - - +
571A THR* 4.1 7.0 - - + -
577A VAL* 3.8 0.3 - - - -
578A HIS* 3.0 73.3 + + + +
579A ARG 4.8 1.3 - - - -
580A PHE* 5.1 4.9 - - + -
589A LEU* 3.7 41.3 - - + -
591A LEU* 4.0 18.8 - - + -
598A ILE* 3.8 18.8 - - + -
599A LYS 3.2 14.1 - - - +
600A PHE* 3.5 33.4 - + + -
602A VAL* 3.6 4.9 - - - +
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Residues in contact with ILE 570 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569A PHE* 1.3 79.8 - - - +
571A THR* 1.3 70.1 + - - +
574A SER 4.5 4.9 - - - +
575A ASP* 4.1 11.7 - - - +
576A MET 3.9 17.0 - - - +
577A VAL* 4.1 14.6 - - + -
578A HIS* 5.0 0.9 - - - -
597A TRP* 4.1 21.5 - - + -
598A ILE* 3.5 2.1 - - - +
599A LYS* 3.0 39.0 + - + +
602A VAL* 3.9 20.6 - - + -
630A ALA 4.9 5.4 - - - +
631A VAL* 4.3 16.6 - - + -
635A ASP* 4.4 14.1 - - - +
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Residues in contact with THR 571 (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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569A PHE* 4.1 16.2 - - + -
570A ILE* 1.3 82.2 - - - +
572A SER* 1.3 62.0 - - - +
573A LYS* 3.2 16.8 + - - +
574A SER* 3.0 29.7 + - - +
576A MET 5.2 0.2 + - - -
578A HIS* 5.1 7.6 + - + -
591A LEU* 4.6 7.2 - - + -
595A VAL* 3.8 20.4 - - + +
597A TRP* 3.4 23.9 - - - +
598A ILE* 4.0 20.0 - - + -
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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