Contacts of the helix formed by residues 529 - 534 (chain A) in PDB entry 4YOZ
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 GLN 529 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496A ILE* 5.5 1.0 - - - +
527A ASN 3.8 3.6 + - - +
528A LEU* 1.3 69.6 - - - +
530A PRO* 1.3 72.1 - - - +
531A PHE 4.3 2.1 + - - +
532A TYR* 3.1 34.0 + - + +
533A PHE* 2.9 28.3 + - - +
571A ASP* 3.7 19.4 + - - -
572A SER* 3.5 8.8 + - - -
573A ALA* 2.9 35.3 + - + -
576A GLU* 5.5 2.2 + - - -
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Residues in contact with PRO 530 (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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523A ILE* 4.1 17.5 - - + -
528A LEU 3.3 7.2 - - - +
529A GLN* 1.3 92.5 - - + +
531A PHE* 1.3 62.7 + - - +
533A PHE* 4.3 6.7 - - + -
534A TYR* 3.3 20.6 + - - -
562A ILE* 3.4 32.7 - - + +
566A LEU* 4.0 35.0 - - + +
567A ALA* 4.1 1.6 - - - +
569A SER* 5.9 0.2 - - - +
572A SER* 5.5 2.9 - - - +
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Residues in contact with PHE 531 (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* 3.2 1.0 - - + +
530A PRO* 1.3 81.0 - - - +
532A TYR* 1.3 82.5 + + - +
534A TYR* 3.1 26.1 - + - -
535A LYS* 4.5 2.9 - - - +
567A ALA* 4.4 7.5 - - + +
572A SER* 3.9 9.2 + - - +
573A ALA* 4.0 9.2 - - + +
574A LEU* 3.7 45.5 - - + +
577A ALA* 4.0 28.5 - - + -
784A ARG* 5.0 0.7 - - - -
787A SER* 4.0 31.4 - - - -
788A LEU* 4.4 2.7 - - + -
791A PHE* 3.5 41.1 - + + -
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Residues in contact with TYR 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A ILE* 3.8 35.9 - - + +
500A SER* 4.5 3.7 + - - -
529A GLN* 3.1 28.0 + - + +
531A PHE* 1.3 103.7 - + - +
533A PHE* 1.3 65.4 + - - +
534A TYR 3.4 0.5 + - - -
535A LYS* 3.4 29.5 + - - +
536A VAL 4.7 0.2 + - - -
573A ALA* 3.5 27.2 + - + +
576A GLU* 5.2 6.8 + - - +
577A ALA* 6.1 0.3 - - - +
784A ARG* 3.3 42.9 + - - +
787A SER* 5.4 1.8 - - - -
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Residues in contact with PHE 533 (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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496A ILE* 5.5 0.2 - - - +
500A SER* 3.3 46.4 - - - +
503A ALA* 3.9 10.1 - - + -
504A CYS* 3.8 28.0 - - + -
507A GLU* 5.5 2.5 - - + -
519A PHE* 3.8 22.7 - + - -
522A ILE* 5.6 0.2 - - + -
523A ILE* 3.9 24.5 - - + -
528A LEU* 4.5 7.0 - - + -
529A GLN 2.9 19.2 + - - +
530A PRO* 3.3 4.0 + - + +
532A TYR* 1.3 78.3 - - - +
534A TYR* 1.3 65.1 + - - +
535A LYS 2.9 2.1 + - - -
536A VAL* 3.0 27.7 + - + +
537A ILE* 4.2 17.7 - - + -
558A ILE* 4.6 4.9 - - + -
562A ILE* 3.7 14.1 - - + -
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Residues in contact with TYR 534 (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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530A PRO 3.3 8.2 + - - +
531A PHE* 3.1 30.1 - + - -
533A PHE* 1.3 79.1 - - - +
535A LYS* 1.3 84.5 + - + +
536A VAL 3.2 0.9 + - - -
537A ILE* 3.2 33.9 + - + +
538A GLU* 4.3 0.7 + - - +
559A GLU* 4.1 18.2 - - + +
562A ILE* 3.7 30.7 - - + -
563A LEU* 4.3 7.4 - - + -
787A SER 4.4 1.3 + - - -
790A LEU* 3.4 14.3 - - + +
791A PHE* 3.1 50.4 + + + +
794A LYS* 3.7 34.9 + - + -
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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