Contacts of the helix formed by residues 572 - 581 (chain A) in PDB entry 4YOS
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 SER 572 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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529A GLN* 3.4 9.2 + - - -
530A PRO* 6.0 0.9 - - - -
531A PHE* 3.9 9.4 + - - +
566A LEU 4.6 0.4 - - - -
567A ALA* 2.5 36.5 + - - -
569A SER* 3.0 22.3 + - - -
570A HIS 3.3 1.1 - - - +
571A ASP* 1.3 82.5 + - - +
573A ALA* 1.3 61.6 + - - +
574A LEU* 3.0 15.2 + - - +
575A TRP* 3.3 21.3 + - - +
576A GLU* 4.2 4.4 + - - +
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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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529A GLN* 3.1 21.1 + - + +
531A PHE* 4.0 9.0 - - + +
532A TYR* 3.5 42.0 + - + +
571A ASP 3.7 0.2 + - - -
572A SER* 1.3 70.9 + - - +
574A LEU* 1.3 63.8 + - - +
575A TRP 3.2 0.4 - - - -
576A GLU* 3.1 24.9 + - - +
577A ALA* 3.0 21.7 + - - +
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Residues in contact with LEU 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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531A PHE* 3.5 36.6 - - + -
567A ALA 3.6 12.3 - - - +
568A TRP* 3.5 38.8 - - + -
572A SER* 3.0 16.3 + - - +
573A ALA* 1.3 78.3 - - - +
575A TRP* 1.3 71.3 + - + +
577A ALA* 3.1 2.1 + - - +
578A LEU* 2.8 28.0 + - + +
788A LEU* 3.7 19.7 - - + -
791A PHE* 3.9 19.3 - - + -
792A TYR* 4.2 7.0 - - + +
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Residues in contact with TRP 575 (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 ALA 4.8 0.2 + - - -
568A TRP* 3.6 42.9 + + - -
569A SER 2.8 30.1 + - - -
570A HIS 3.7 13.2 - - - +
572A SER* 3.3 20.7 + - - +
573A ALA 3.2 1.0 - - - -
574A LEU* 1.3 84.1 - - + +
576A GLU* 1.3 58.9 + - + +
578A LEU* 3.5 28.7 + - + +
579A GLN* 2.9 29.5 + - - +
583A ASN* 5.1 0.5 - - - +
832A PRO* 3.4 33.4 - - + -
833A ASP* 4.9 1.1 - - - -
836A LYS* 3.5 42.8 - - + +
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Residues in contact with GLU 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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529A GLN* 5.5 2.1 + - - -
532A TYR* 5.0 5.2 + - - +
571A ASP 5.1 3.1 - - - +
572A SER 4.4 4.2 - - - +
573A ALA* 3.3 29.2 + - + +
575A TRP* 1.3 79.6 - - + +
577A ALA* 1.3 61.4 + - - +
579A GLN* 3.2 12.7 + - - +
580A VAL* 3.1 29.2 + - + +
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Residues in contact with ALA 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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531A PHE* 3.9 22.4 - - + -
532A TYR* 6.1 0.4 - - - +
573A ALA 3.0 12.7 + - - +
574A LEU 3.1 7.8 + - - +
576A GLU* 1.3 73.6 - - - +
578A LEU* 1.3 64.8 + - - +
580A VAL* 3.2 23.1 - - + +
581A SER* 3.3 13.2 + - - -
787A SER* 5.4 3.4 - - - -
788A LEU* 3.5 18.9 - - + +
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Residues in contact with LEU 578 (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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574A LEU* 2.8 15.9 + - + +
575A TRP* 3.7 33.4 - - + +
577A ALA* 1.3 76.4 - - - +
579A GLN* 1.3 58.0 + - - +
581A SER* 3.1 8.5 + - - -
582A ALA 3.4 0.2 + - - -
583A ASN* 2.7 43.6 + - + +
584A LYS 3.7 21.3 - - - +
585A VAL* 3.7 35.0 - - + -
788A LEU* 3.9 21.2 - - + +
792A TYR* 3.9 13.0 - - + +
832A PRO* 4.4 7.2 - - + -
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Residues in contact with GLN 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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575A TRP 2.9 19.1 + - - +
576A GLU* 3.4 11.9 + - - +
577A ALA 3.2 0.2 - - - -
578A LEU* 1.3 77.3 - - - +
580A VAL* 1.3 62.0 + - + +
582A ALA* 3.0 19.6 + - - -
583A ASN* 3.5 15.5 + - - +
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Residues in contact with VAL 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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576A GLU* 3.1 14.8 + - + +
577A ALA* 3.2 22.4 - - - +
579A GLN* 1.3 80.1 - - + +
581A SER* 1.3 60.5 + - - +
582A ALA* 3.1 4.0 + - - +
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Residues in contact with SER 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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577A ALA 3.3 3.9 + - - -
578A LEU* 3.1 8.7 + - - -
579A GLN 3.0 1.2 - - - -
580A VAL* 1.3 81.7 - - - +
582A ALA* 1.3 69.6 + - - +
583A ASN 3.2 0.4 - - - -
584A LYS* 3.3 23.2 + - - +
784A ARG* 4.6 8.7 + - - -
788A LEU* 3.2 30.4 - - - +
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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