Contacts of the helix formed by residues 535 - 545 (chain A) in PDB entry 4FYT
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 THR 535 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522A GLN* 3.4 20.4 - - + +
534A THR* 1.3 89.1 + - - +
536A VAL* 1.3 65.3 + - - +
537A ARG* 3.8 9.3 + - - +
538A ASP* 3.1 27.3 + - - +
539A ILE* 3.0 23.0 + - - +
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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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487A LEU* 4.5 5.6 - - + -
490A PHE* 5.7 1.8 - - + -
491A LEU* 4.9 4.3 - - + -
518A TRP* 4.2 20.9 - - + +
521A LEU* 4.1 23.8 - - + -
522A GLN* 2.7 29.9 + - - +
525A VAL* 3.9 27.8 - - + -
532A LEU* 4.1 11.6 - - + +
534A THR 3.9 0.2 + - - -
535A THR* 1.3 70.1 - - - +
537A ARG* 1.3 58.0 + - - +
539A ILE* 3.3 7.6 + - - +
540A MET* 2.8 47.8 + - + +
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Residues in contact with ARG 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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515A LEU* 3.6 38.8 + - + +
518A TRP* 3.7 28.3 - - + +
519A ASP* 3.3 31.5 + - - -
522A GLN* 4.4 1.4 + - - +
535A THR* 3.8 9.3 + - - +
536A VAL* 1.3 79.1 - - - +
538A ASP* 1.3 67.4 + - - +
541A ASN* 2.7 53.7 + - - +
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Residues in contact with ASP 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 THR* 3.7 25.3 + - + +
535A THR* 3.1 17.2 + - - +
537A ARG* 1.3 89.5 - - - +
539A ILE* 1.3 66.8 + - - +
541A ASN* 4.3 7.8 + - - +
542A ARG* 3.4 24.8 + - - +
580A PHE* 5.7 3.6 - - - -
585A ILE* 3.9 6.6 - - + +
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Residues in contact with ILE 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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490A PHE* 4.1 11.0 - - + -
532A LEU* 4.1 23.6 - - + -
533A PRO* 4.4 4.3 - - + -
534A THR* 3.8 24.0 - - + +
535A THR 3.0 19.8 + - - +
536A VAL* 3.8 5.8 - - - +
538A ASP* 1.3 81.1 - - - +
540A MET* 1.3 79.1 + - + +
542A ARG* 3.2 12.8 + - - +
543A TRP* 3.3 17.8 + - - +
585A ILE* 4.0 27.3 - - + +
587A PRO* 5.8 0.4 - - + -
601A TRP* 4.1 35.0 - - + -
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Residues in contact with MET 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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483A VAL* 3.0 42.2 - - + +
486A MET* 4.7 2.9 - - + -
487A LEU* 3.8 39.0 - - + -
490A PHE* 4.1 8.5 - - + -
518A TRP* 3.4 32.1 - - + -
536A VAL* 2.8 27.3 + - + +
539A ILE* 1.3 86.7 - - + +
541A ASN* 1.3 65.7 + - - +
542A ARG 3.1 1.8 - - - -
543A TRP* 3.0 22.4 + - + +
544A THR* 2.8 21.7 + - - -
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Residues in contact with ASN 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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514A TYR* 3.5 13.3 - - - -
515A LEU* 4.4 5.5 - - - +
518A TRP* 2.9 22.6 + - - -
537A ARG* 2.7 46.4 + - - +
538A ASP* 4.3 9.3 + - - +
539A ILE 3.4 0.2 - - - -
540A MET* 1.3 73.4 - - - +
542A ARG* 1.3 57.1 + - - +
544A THR* 4.3 3.6 - - - -
545A LEU* 3.0 46.3 + - + +
580A PHE* 3.6 24.8 - - + -
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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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538A ASP* 3.4 19.5 + - - +
539A ILE 3.4 8.7 - - - +
540A MET 3.1 0.8 - - - -
541A ASN* 1.3 77.9 - - - +
543A TRP* 1.3 59.1 + - + +
546A GLN* 3.0 32.1 + - - +
580A PHE* 3.5 40.3 + - - -
583A VAL* 3.0 40.8 + - - +
584A TRP* 3.0 26.7 + - + -
585A ILE* 3.8 36.2 - - + +
603A ILE 5.0 2.8 + - - -
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Residues in contact with TRP 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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455A LEU* 4.0 6.8 - - - +
479A LYS* 3.4 27.2 + - - +
483A VAL* 4.0 20.2 - - + -
486A MET* 3.5 32.8 - - + +
539A ILE* 3.3 26.2 + - + +
540A MET* 3.0 18.4 + - + +
542A ARG* 1.3 77.6 - - - +
544A THR* 1.3 59.2 + - - +
545A LEU 3.9 0.2 - - - -
546A GLN 4.3 3.8 - - - +
548A GLY 4.9 2.2 - - - -
549A PHE* 4.4 0.7 - - + -
550A PRO* 3.6 29.2 - - + -
584A TRP* 3.5 27.7 - + + +
585A ILE 3.1 28.7 + - - +
586A VAL* 4.1 13.2 - - + -
587A PRO* 4.9 0.8 - - - +
629A TYR* 3.1 50.5 - + + -
630A TYR* 4.8 0.2 - - + -
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Residues in contact with THR 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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408A TRP* 3.9 24.3 - - + +
454A PRO* 3.6 0.7 - - - +
455A LEU* 3.3 21.6 + - + +
456A SER* 2.9 50.0 + - - +
483A VAL* 4.9 2.3 - - - +
514A TYR* 4.3 6.1 - - + -
518A TRP* 3.3 22.6 - - + -
540A MET* 2.8 20.8 + - - +
541A ASN* 4.1 4.3 - - - -
543A TRP* 1.3 81.8 - - - +
545A LEU* 1.3 67.7 + - + +
546A GLN 3.6 1.3 - - - -
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Residues in contact with LEU 545 (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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454A PRO* 3.6 17.6 - - - +
456A SER* 4.1 18.1 - - - +
514A TYR* 3.6 40.8 - - + +
541A ASN* 3.0 46.8 + - + +
544A THR* 1.3 81.0 - - + +
546A GLN* 1.3 59.8 + - - +
576A ARG* 5.6 0.5 - - - -
578A SER* 5.4 1.2 + - - -
579A GLU* 4.2 10.3 - - - +
580A PHE* 3.9 15.5 - - + -
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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