Contacts of the helix formed by residues 543 - 555 (chain B) in PDB entry 5YPO
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 543 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541B GLY 3.5 0.4 + - - -
542B PRO* 1.3 78.1 + - + +
544B LYS* 1.3 64.8 + - - +
545B ASP* 3.2 3.4 - - - +
546B ARG* 3.1 11.2 + - - +
547B ALA* 3.0 19.8 + - - +
650B ILE* 3.7 10.4 - - - +
661B ILE* 3.7 42.2 - - + +
662B ASN* 4.3 18.2 - - + +
664B ARG* 5.7 2.2 - - - +
697B PHE* 3.3 25.6 - - + -
700B ILE* 4.6 2.4 - - - +
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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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539B ILE* 3.5 49.5 + - + +
540B LEU* 4.0 10.8 - - - +
541B GLY 3.1 20.4 - - - +
542B PRO 3.2 3.4 + - - -
543B THR* 1.3 77.3 - - - +
545B ASP* 1.3 88.1 + - - +
547B ALA* 3.3 2.8 + - - +
548B ASN* 2.8 37.8 + - - +
629B ASP* 2.8 35.8 + - - +
630B VAL 4.9 4.9 + - - -
650B ILE* 4.1 3.6 - - + -
7C GLN* 5.8 4.2 - - - +
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Residues in contact with ASP 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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543B THR 3.1 1.2 + - - -
544B LYS* 1.3 107.9 + - - +
546B ARG* 1.3 65.1 + - - +
548B ASN* 3.3 10.8 + - - +
549B ASP* 3.0 32.7 + - - +
629B ASP* 4.0 11.6 - - - +
-2C ARG* 4.4 20.2 + - - -
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Residues in contact with ARG 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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543B THR* 3.1 13.7 + - - +
545B ASP* 1.3 78.8 - - - +
547B ALA* 1.3 61.2 + - - +
549B ASP* 3.4 8.0 + - + +
550B ASP* 3.0 38.5 + - - +
661B ILE 4.5 1.6 + - - -
664B ARG* 3.3 33.7 - - - +
697B PHE* 3.4 54.5 - - + +
698B GLU* 4.2 14.5 + - - -
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Residues in contact with ALA 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B ILE* 4.3 17.0 - - + -
543B THR 3.0 12.5 + - - +
544B LYS* 3.6 11.2 - - - +
546B ARG* 1.3 76.4 - - - +
548B ASN* 1.3 62.2 + - - +
550B ASP* 3.4 1.4 + - - +
551B LEU* 3.1 31.0 + - - +
650B ILE* 4.7 6.1 - - + -
697B PHE* 3.7 20.0 - - + -
700B ILE* 5.9 0.2 - - + -
701B TYR* 3.9 12.1 - - + -
704B VAL* 5.0 7.0 - - + -
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Residues in contact with ASN 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B ILE* 5.4 0.2 - - - +
539B ILE* 3.3 31.5 + - - +
544B LYS* 2.8 27.7 + - - +
545B ASP* 3.3 19.9 + - - +
547B ALA* 1.3 74.1 - - - +
549B ASP* 1.3 68.7 + - - +
550B ASP 3.2 0.2 + - - -
551B LEU* 3.3 5.8 + - - +
552B LEU* 3.2 29.3 + - + +
627B ILE* 3.4 28.0 - - + +
628B LEU 4.0 16.2 + - - +
629B ASP* 4.6 9.5 - - - +
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Residues in contact with ASP 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 ASP* 3.0 25.3 + - - +
546B ARG* 3.8 6.9 - - - +
548B ASN* 1.3 78.0 - - - +
550B ASP* 1.3 62.1 + - - +
552B LEU* 3.4 11.6 + - - +
553B SER* 3.0 31.5 + - - -
-3C ALA* 4.8 17.6 + - - +
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Residues in contact with ASP 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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546B ARG* 3.0 27.1 + - - +
547B ALA 3.8 0.2 - - - +
548B ASN 3.1 0.2 - - - -
549B ASP* 1.3 79.6 - - - +
551B LEU* 1.3 66.1 + - - +
553B SER* 3.2 7.9 + - - -
554B GLU* 2.9 30.7 + - + +
697B PHE* 3.4 27.5 - - - -
701B TYR* 3.3 29.7 - - + +
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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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539B ILE* 3.8 25.6 - - + -
547B ALA 3.1 21.5 + - - +
548B ASN 3.3 3.8 + - - +
550B ASP* 1.3 76.3 - - - +
552B LEU* 1.3 62.9 + - - +
555B PHE* 3.0 24.6 + - + -
559B PHE* 3.6 41.5 - - + -
627B ILE* 3.8 17.0 - - + -
701B TYR* 3.7 11.2 - - + +
704B VAL* 4.2 5.6 - - + -
705B LYS* 3.7 31.9 - - + -
708B ILE* 3.9 17.7 - - + -
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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 ASN* 3.2 17.5 + - + +
549B ASP* 3.8 13.7 - - - +
551B LEU* 1.3 79.6 - - - +
553B SER* 1.3 61.2 + - - +
554B GLU 3.6 0.2 + - - -
556B PRO* 3.6 23.6 - - - +
559B PHE* 3.6 35.2 - - + +
560B GLY* 3.8 19.1 - - - +
561B SER* 3.5 18.4 - - - +
627B ILE* 4.0 16.2 - - + -
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Residues in contact with SER 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B ASP 3.0 17.8 + - - -
550B ASP* 3.2 13.3 + - - -
552B LEU* 1.3 78.6 - - - +
554B GLU* 1.3 61.6 + - - +
556B PRO* 4.0 6.2 - - - +
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Residues in contact with GLU 554 (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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550B ASP* 2.9 16.1 + - + +
553B SER* 1.3 81.1 + - - +
555B PHE* 1.3 81.6 + - + +
556B PRO* 3.2 9.8 - - - +
701B TYR* 2.6 29.5 + - + -
705B LYS* 2.9 24.9 + - - -
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Residues in contact with PHE 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B LEU* 3.0 18.0 + - + -
554B GLU* 1.3 115.3 - - + +
556B PRO* 1.3 66.0 - - - +
557B ASP* 3.0 14.6 - - - +
558B LYS* 3.0 15.7 + - + -
559B PHE* 3.0 39.2 + + + +
701B TYR* 4.3 0.2 - - - -
705B LYS* 3.6 26.7 - - + -
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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