Contacts of the helix formed by residues 543 - 552 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476B PHE* 3.7 20.2 - - - -
479B GLN* 4.6 6.0 + - - -
487B LEU* 5.8 0.5 - - - +
542B ILE* 1.3 76.7 - - - +
544B LYS* 1.3 64.8 + - - +
545B GLN* 3.3 20.5 + - - +
546B TYR* 3.3 23.2 + - - +
547B VAL* 3.0 26.5 + - - +
562B ARG* 3.9 1.1 - - - -
565B ASP* 4.1 10.5 - - - -
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Residues in contact with LYS 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639A ARG* 4.1 7.1 - - - +
640A GLY* 3.9 28.3 + - - +
641A PTR 3.4 38.5 + - - +
543B SER* 1.3 73.4 - - - +
545B GLN* 1.3 77.6 + - - +
547B VAL* 3.4 14.2 + - - +
548B THR* 3.2 17.3 + - - -
562B ARG* 3.4 31.2 - - - +
565B ASP* 4.4 1.6 + - - +
588B ASN* 3.4 30.3 + - - +
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Residues in contact with GLN 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485B ASN* 5.1 6.4 - - - +
543B SER* 3.3 22.0 + - - +
544B LYS* 1.3 95.1 - - - +
546B TYR* 1.3 58.6 + - - +
547B VAL 3.5 0.2 + - - -
548B THR* 3.5 13.6 + - - -
549B SER* 3.4 13.7 + - - -
565B ASP* 5.7 0.2 - - - +
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Residues in contact with TYR 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476B PHE* 3.8 19.3 - + + -
487B LEU* 3.9 35.0 - - + -
542B ILE* 3.4 26.5 - - + -
543B SER* 3.3 19.0 + - - +
545B GLN* 1.3 75.9 - - - +
547B VAL* 1.3 62.9 + - - +
548B THR 3.2 0.7 - - - -
549B SER* 3.5 13.8 + - - -
550B LEU* 3.2 45.0 + - + +
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Residues in contact with VAL 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542B ILE* 3.8 16.4 - - + -
543B SER 3.0 19.2 + - - +
544B LYS* 3.5 11.2 - - - +
545B GLN 3.2 0.6 - - - -
546B TYR* 1.3 75.3 - - - +
548B THR* 1.3 61.6 + - - +
549B SER 3.2 0.2 - - - -
550B LEU* 3.7 6.9 - - - +
551B LEU* 3.0 40.5 + - + +
560B LEU* 3.8 26.5 - - + -
562B ARG* 4.0 8.3 - - - -
574B ALA* 3.5 28.5 - - + -
586B ILE* 4.9 5.4 - - + -
588B ASN* 4.9 4.0 - - - +
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Residues in contact with THR 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544B LYS 3.2 12.8 + - - -
545B GLN* 3.7 10.3 - - - -
546B TYR 3.2 0.2 - - - -
547B VAL* 1.3 79.7 - - - +
549B SER* 1.3 61.5 + - - +
552B LEU* 3.2 39.4 + - + +
586B ILE* 4.0 31.0 - - + +
588B ASN* 5.6 1.0 + - - -
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Residues in contact with SER 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545B GLN 3.4 12.5 + - - -
546B TYR* 3.6 20.6 + - - -
547B VAL 3.2 0.2 - - - -
548B THR* 1.3 78.1 - - - +
550B LEU* 1.3 65.5 + - - +
551B LEU 3.5 0.3 + - - -
552B LEU* 4.0 7.5 + - - +
553B ASN* 4.4 9.7 + - - +
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Residues in contact with LEU 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539B ILE* 4.9 3.6 - - + -
542B ILE* 4.1 21.3 - - + -
546B TYR* 3.2 38.2 + - + +
547B VAL* 3.7 7.4 - - - +
549B SER* 1.3 80.2 - - - +
551B LEU* 1.3 65.7 + - + +
553B ASN* 3.4 8.7 - - - +
554B GLU* 3.4 20.1 - - - +
560B LEU* 4.2 15.0 - - + -
616B TYR* 4.1 38.1 - - + +
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Residues in contact with LEU 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547B VAL* 3.0 35.6 + - + +
550B LEU* 1.3 82.4 - - + +
552B LEU* 1.3 63.6 + - - +
553B ASN 3.3 2.7 - - - -
554B GLU* 3.2 12.9 + - + -
558B THR* 4.3 24.0 - - + +
560B LEU* 3.8 22.4 - - + -
574B ALA 4.0 4.9 - - - +
575B HIS* 3.8 31.4 - - - +
576B VAL* 3.3 25.7 - - + +
586B ILE* 3.4 16.4 - - + -
616B TYR* 4.4 12.1 - - + -
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Residues in contact with LEU 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B THR* 3.2 29.3 + - + +
549B SER* 4.6 4.9 - - - +
550B LEU 3.5 1.2 - - - -
551B LEU* 1.3 77.9 - - - +
553B ASN* 1.3 52.8 + - + +
576B VAL* 4.6 0.4 - - - -
578B ARG* 2.6 28.2 + - - -
584B PRO* 3.7 42.8 - - + +
586B ILE* 3.8 27.1 - - + +
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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