Contacts of the helix formed by residues 534 - 544 (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 TYR 534 (chain A).
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Specific contacts
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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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Residues in contact with LYS 535 (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* 5.9 5.1 - - - +
531A PHE 5.1 3.4 - - - -
532A TYR* 3.6 21.0 + - - +
533A PHE 2.9 1.2 + - - -
534A TYR* 1.3 112.3 - - + +
536A VAL* 1.3 60.2 + - - +
537A ILE 3.6 0.3 + - - -
538A GLU* 4.0 9.4 + - - +
539A VAL* 3.7 15.6 + - - +
784A ARG* 5.7 1.8 - - - +
787A SER* 3.9 25.1 - - - +
790A LEU* 3.5 27.6 - - + -
794A LYS* 5.8 1.3 - - - +
1004A SO4 5.3 3.0 + - - -
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Residues in contact with VAL 536 (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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497A PHE* 4.3 20.6 - - + +
500A SER* 3.6 29.6 - - - +
501A LEU* 3.8 39.0 - - + +
504A CYS* 4.0 14.4 - - + -
532A TYR 4.7 0.2 + - - -
533A PHE* 3.0 23.4 + - + +
535A LYS* 1.3 76.6 - - - +
537A ILE* 1.3 62.5 + - + +
539A VAL* 2.9 10.8 + - + +
540A VAL* 2.8 28.1 + - + +
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Residues in contact with ILE 537 (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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504A CYS* 4.4 12.1 - - - -
533A PHE* 4.2 18.6 - - + -
534A TYR* 3.2 24.6 + - + +
536A VAL* 1.3 78.3 - - + +
538A GLU* 1.3 58.6 + - - +
540A VAL* 3.2 8.0 + - - +
541A ILE* 2.9 41.4 + - + +
555A LEU* 3.5 40.2 - - + +
556A ASN* 4.9 0.4 - - - +
558A ILE* 3.9 12.8 - - + -
559A GLU* 3.6 40.4 - - + +
562A ILE* 4.5 0.7 - - + -
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Residues in contact with GLU 538 (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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534A TYR 4.3 1.0 + - - -
535A LYS* 4.0 8.2 + - - +
536A VAL 3.3 0.4 - - - -
537A ILE* 1.3 80.5 - - - +
539A VAL* 1.3 62.1 + - + +
541A ILE* 4.0 9.0 - - + +
542A ARG* 3.1 43.9 + - + +
559A GLU* 4.6 10.9 + - - +
790A LEU* 5.2 4.9 - - - +
793A ARG* 4.6 12.5 + - - -
794A LYS* 3.9 23.9 + - - +
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Residues in contact with VAL 539 (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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471A ILE* 5.6 1.1 - - + -
475A VAL* 3.8 31.0 - - + -
497A PHE* 4.4 18.8 - - + -
501A LEU* 6.1 0.9 - - + -
535A LYS 3.7 16.6 - - - +
536A VAL* 2.9 14.8 + - + +
538A GLU* 1.3 76.3 - - + +
540A VAL* 1.3 59.7 + - + +
542A ARG* 3.3 25.0 + - - +
543A SER* 2.8 37.5 + - - +
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Residues in contact with VAL 540 (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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471A ILE* 4.3 23.6 - - + -
501A LEU* 3.7 29.8 - - + -
504A CYS* 3.8 25.1 - - + -
505A CYS* 5.8 0.7 - - - -
508A ILE* 5.1 5.6 - - + -
536A VAL* 2.8 16.3 + - + +
537A ILE 3.5 7.6 - - - +
539A VAL* 1.3 76.1 - - - +
541A ILE* 1.3 62.2 + - - +
543A SER 3.8 0.4 - - - +
544A GLU* 3.0 26.2 + - - +
547A LEU* 3.7 22.6 - - + +
555A LEU* 4.1 11.2 - - + -
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Residues in contact with ILE 541 (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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537A ILE* 2.9 33.1 + - + +
538A GLU* 4.0 8.3 - - + +
540A VAL* 1.3 76.3 - - - +
542A ARG* 1.3 64.0 + - + +
544A GLU 3.6 12.6 - - - +
545A GLU* 4.5 7.4 - - - +
547A LEU* 4.6 5.8 - - - -
552A VAL* 4.1 27.8 - - + +
555A LEU* 4.0 23.1 - - + -
556A ASN* 3.4 31.4 - - - +
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Residues in contact with ARG 542 (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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475A VAL* 6.1 2.6 - - - +
478A GLN* 5.1 13.1 + - - +
538A GLU* 3.1 31.9 + - + +
539A VAL* 3.5 33.4 - - - +
541A ILE* 1.3 81.7 - - + +
543A SER* 1.3 67.3 + - - +
544A GLU 3.6 0.3 + - - -
545A GLU* 4.6 14.0 - - - +
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Residues in contact with SER 543 (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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471A ILE* 3.9 15.9 - - - +
474A THR* 3.3 35.7 + - - +
475A VAL* 3.3 31.2 - - - +
478A GLN* 4.8 6.1 + - - +
539A VAL* 2.8 21.0 + - - +
540A VAL 3.1 0.4 + - - -
542A ARG* 1.3 84.3 + - - +
544A GLU* 1.3 62.4 + - - +
545A GLU* 4.1 1.7 + - - -
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Residues in contact with GLU 544 (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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400A ILE* 3.7 16.6 - - + +
467A LEU* 4.9 2.9 - - + -
470A LYS* 2.7 42.0 + - - +
471A ILE* 4.3 20.3 - - + +
474A THR* 5.6 0.2 + - - -
540A VAL 3.0 12.6 + - - +
541A ILE 3.6 12.4 - - - +
543A SER* 1.3 81.8 - - - +
545A GLU* 1.3 63.0 + - - +
546A GLY* 2.8 28.5 + - - +
547A LEU* 3.6 41.9 + - + +
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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