Contacts of the strand formed by residues 570 - 577 (chain A) in PDB entry 5ON2
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 LEU 570 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568A MET* 3.7 26.0 - - + +
569A VAL* 1.3 74.1 - - - +
571A ALA* 1.3 63.6 + - - +
617A MET* 4.2 18.0 - - + +
618A SER* 3.4 4.9 - - - +
619A LYS* 3.8 19.7 - - + +
655A THR* 4.7 13.5 - - - +
656A LEU 2.8 15.6 + - - +
657A GLU* 3.9 21.7 - - + +
658A TRP* 3.0 29.3 + - - +
68B C 5.8 0.9 - - - +
69B G 3.6 43.1 - - - +
70B G 4.9 0.2 - - - -
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Residues in contact with ALA 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 VAL 4.1 0.2 + - - -
570A LEU* 1.3 76.6 - - - +
572A ASP* 1.3 64.9 + - - +
588A PRO* 5.3 2.9 - - + -
617A MET* 3.8 11.0 - - - -
618A SER* 2.8 30.5 + - - +
620A MET* 4.1 14.8 - - + -
626A ASN* 3.2 33.7 + - - +
628A ILE* 5.7 1.6 - - + -
658A TRP* 5.1 4.0 - - + -
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Residues in contact with ASP 572 (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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571A ALA* 1.3 73.1 - - - +
573A ALA* 1.3 60.0 + - - +
574A PHE* 3.9 16.5 - - + -
588A PRO* 3.3 17.3 - - + +
595A ARG* 4.0 12.0 + - - -
601A ILE* 3.5 14.6 - - - +
614A TYR* 2.7 35.9 + - + -
616A GLY 3.7 3.8 - - - -
617A MET* 3.4 25.9 - - - +
626A ASN* 3.2 22.5 - - - +
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Residues in contact with ALA 573 (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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572A ASP* 1.3 77.1 - - - +
574A PHE* 1.3 63.0 + - - +
585A TRP* 3.9 14.4 - - + -
586A VAL 5.3 0.7 - - - -
588A PRO* 5.4 0.2 - - - -
614A TYR* 3.9 2.5 - - - -
615A THR* 2.8 48.2 + - - +
616A GLY 3.4 7.3 + - - +
618A SER* 3.5 21.1 - - - +
624A LYS* 4.3 10.1 - - + +
626A ASN* 4.3 7.2 - - - +
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Residues in contact with PHE 574 (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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572A ASP* 3.9 19.7 - - + -
573A ALA* 1.3 75.2 - - - +
575A TYR* 1.3 62.8 + - - +
585A TRP* 3.3 11.6 - - - -
586A VAL* 3.0 32.3 + - + +
588A PRO* 4.0 25.6 - - + -
591A ALA* 4.0 13.5 - - + -
593A VAL* 4.0 14.6 - - + -
601A ILE* 3.9 23.6 - - + -
604A ALA* 4.0 25.6 - - + -
612A LEU* 3.9 20.9 - - + -
613A VAL 3.6 4.5 - - - -
614A TYR* 3.4 38.6 - + + -
624A LYS 4.5 0.2 - - - +
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Residues in contact with TYR 575 (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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173A ASP* 4.9 1.7 + - - -
574A PHE* 1.3 76.9 - - - +
576A TYR* 1.3 68.6 + - - +
577A VAL* 4.2 18.2 - - + +
583A ARG* 3.0 58.4 + - + -
584A ASN 3.3 16.8 - - - +
585A TRP* 3.7 27.1 - + + +
586A VAL* 4.1 2.5 - - - +
612A LEU* 3.4 5.8 - - - -
613A VAL* 2.7 71.3 + - + +
615A THR* 3.5 28.3 - - + -
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Residues in contact with TYR 576 (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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575A TYR* 1.3 80.1 - - - +
577A VAL* 1.3 75.2 - - - +
578A GLY* 3.6 1.1 + - - -
584A ASN* 3.0 71.2 + - + +
586A VAL* 3.5 27.6 - - + -
606A ASP* 5.1 0.4 - - - -
610A HIS* 4.0 42.6 - + + -
611A GLU 4.3 10.1 - - - +
612A LEU* 4.0 13.5 - - + -
613A VAL* 5.1 2.0 - - - -
93D ASN* 4.6 3.8 + - - -
94D ASN* 3.6 29.5 + - + +
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Residues in contact with VAL 577 (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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575A TYR* 4.2 18.6 - - + +
576A TYR* 1.3 84.0 - - - +
578A GLY* 1.3 75.0 + - - +
581A GLY* 3.8 21.3 - - - -
582A GLU 4.0 4.0 - - - -
583A ARG* 5.0 4.9 - - + +
613A VAL* 5.6 5.3 - - + +
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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