Contacts of the helix formed by residues 543 - 552 (chain A) in PDB entry 4Y5U
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 543 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476A PHE* 3.5 16.3 - - - -
479A GLN* 4.7 5.4 + - - -
542A ILE* 1.3 77.1 - - - +
544A LYS* 1.3 65.9 + - - +
545A GLN* 3.2 26.7 + - - +
546A TYR* 3.4 20.6 + - - +
547A VAL* 3.2 23.4 + - - +
562A ARG* 3.8 5.2 - - - +
565A ASP* 4.1 6.5 - - - -
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Residues in contact with LYS 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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543A SER* 1.3 75.7 - - - +
545A GLN* 1.3 74.9 + - + +
547A VAL* 3.5 12.0 + - - +
548A THR* 3.4 19.1 - - - +
562A ARG* 3.4 30.3 - - - +
565A ASP* 4.4 0.4 + - - +
588A ASN* 3.8 24.0 + - - +
639B ARG* 3.8 17.0 + - - +
640B GLY* 3.7 19.6 + - - -
641B PTR 3.2 50.7 + - - +
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Residues in contact with GLN 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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485A ASN* 5.0 7.8 - - - +
543A SER* 3.2 21.8 + - - +
544A LYS* 1.3 90.5 - - + +
546A TYR* 1.3 60.1 + - - +
547A VAL 3.1 1.6 - - - -
548A THR* 2.5 27.4 + - - -
549A SER* 3.2 5.4 + - - -
565A ASP* 5.3 3.0 + - - -
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Residues in contact with TYR 546 (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 LEU* 6.2 0.2 - - + -
476A PHE* 3.8 23.1 - + + -
487A LEU* 4.4 29.6 - - + -
542A ILE* 3.3 30.3 - - + -
543A SER* 3.4 20.9 + - - +
545A GLN* 1.3 78.4 - - - +
547A VAL* 1.3 60.3 + - - +
548A THR 3.3 0.2 - - - -
549A SER* 3.3 24.9 + - - -
550A LEU* 3.4 26.8 + - + +
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Residues in contact with VAL 547 (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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542A ILE* 3.8 21.5 - - + -
543A SER 3.2 18.3 + - - +
544A LYS* 3.6 9.6 - - - +
545A GLN 3.1 0.8 - - - -
546A TYR* 1.3 76.9 - - - +
548A THR* 1.3 65.2 + - + +
550A LEU* 3.4 4.8 + - - +
551A LEU* 3.2 33.5 + - + +
560A LEU* 3.7 27.1 - - + -
562A ARG* 4.0 6.3 - - - -
574A ALA* 3.6 27.1 - - + -
586A ILE* 4.6 5.4 - - + -
588A ASN* 4.4 7.4 - - - +
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Residues in contact with THR 548 (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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544A LYS 3.4 15.9 - - - +
545A GLN* 2.5 23.8 + - - -
547A VAL* 1.3 76.0 - - + +
549A SER* 1.3 60.2 + - - +
552A LEU* 3.1 40.4 + - - +
586A ILE* 4.3 26.4 - - + +
588A ASN* 5.8 2.5 - - - +
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Residues in contact with SER 549 (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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545A GLN 3.2 17.7 + - - -
546A TYR* 3.3 19.4 + - - -
548A THR* 1.3 76.7 + - - +
550A LEU* 1.3 64.9 + - - +
552A LEU* 4.0 5.8 + - - +
553A ASN* 4.3 12.5 + - - +
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Residues in contact with LEU 550 (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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539A ILE* 4.6 5.4 - - + -
542A ILE* 4.0 24.9 - - + -
546A TYR* 3.4 27.6 + - + +
547A VAL* 3.4 6.5 + - - +
549A SER* 1.3 80.5 - - - +
551A LEU* 1.3 63.6 + - + +
553A ASN* 3.3 19.8 - - - +
554A GLU* 3.5 13.5 - - - +
560A LEU* 4.3 17.9 - - + -
616A TYR* 3.3 38.2 - - + +
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Residues in contact with LEU 551 (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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547A VAL* 3.2 17.7 + - + +
550A LEU* 1.3 82.0 - - + +
552A LEU* 1.3 58.1 + - - +
553A ASN 3.3 1.1 - - - -
554A GLU* 2.9 28.2 + - + +
558A THR* 4.1 14.8 - - + +
559A PHE* 4.6 1.6 - - - -
560A LEU* 3.6 33.4 - - + -
574A ALA* 3.9 6.5 - - + +
575A HIS* 3.8 31.6 - - - +
576A VAL* 3.5 15.7 - - + +
586A ILE* 3.3 20.4 - - + -
616A TYR* 4.2 21.8 - - + -
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Residues in contact with LEU 552 (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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548A THR* 3.1 25.5 + - - +
549A SER* 4.0 3.8 + - - +
550A LEU 3.5 1.0 - - - -
551A LEU* 1.3 76.6 - - - +
553A ASN* 1.3 57.8 + - - +
576A VAL* 4.7 0.9 - - + -
578A ARG* 3.1 22.0 + - - -
584A PRO* 3.7 39.0 - - + +
586A ILE* 3.4 31.2 - - + +
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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