Contacts of the helix formed by residues 548 - 561 (chain B) in PDB entry 6RKU
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 ASP 548 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531B GLN* 5.4 3.3 - - - +
534B LEU* 4.5 6.3 - - - -
535B TYR* 4.6 0.2 - - - -
546B ILE* 3.7 3.1 - - - +
547B LYS* 1.3 117.0 - - - +
549B ASP* 1.3 61.0 + - - +
550B GLU* 4.3 3.4 - - + +
551B ALA* 3.4 18.1 + - + +
552B MET* 2.9 29.3 + - - +
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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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534B LEU* 4.7 6.2 - - + +
535B TYR* 5.1 10.2 + - + -
548B ASP* 1.3 73.9 - - - +
550B GLU* 1.3 58.6 + - - +
552B MET* 3.2 8.2 + - - +
553B ASP* 2.9 43.6 + - - +
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Residues in contact with GLU 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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548B ASP* 3.4 3.9 - - + +
549B ASP* 1.3 79.1 - - - +
551B ALA* 1.3 57.0 - - - +
553B ASP* 3.3 11.0 + - + +
554B GLN* 2.9 53.3 + - + +
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Residues in contact with ALA 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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546B ILE* 4.1 13.0 - - + -
547B LYS* 5.0 5.2 - - + +
548B ASP* 3.4 25.0 + - + +
549B ASP 3.2 0.4 - - - -
550B GLU* 1.3 78.8 - - - +
552B MET* 1.3 57.4 + - - +
554B GLN* 3.3 10.4 + - - +
555B TYR* 2.9 30.1 + - - +
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Residues in contact with MET 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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535B TYR* 4.2 29.8 - - + -
537B VAL* 3.9 13.0 - - + -
546B ILE* 3.5 31.7 - - + +
548B ASP 2.9 14.0 + - - +
549B ASP* 3.2 11.6 + - - +
551B ALA* 1.3 76.1 - - - +
553B ASP* 1.3 59.2 + - - +
555B TYR* 3.3 9.7 + - + +
556B GLN* 2.9 72.9 + - + +
734B LEU* 6.5 0.4 - - + -
736B ILE* 3.7 27.1 - - + -
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Residues in contact with ASP 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B ASP* 2.9 38.6 + - - +
550B GLU* 3.5 13.4 - - + +
551B ALA 3.2 0.2 - - - -
552B MET* 1.3 79.2 - - - +
554B GLN* 1.3 58.1 + - + +
556B GLN* 3.3 14.4 + - - +
557B ILE* 2.9 40.1 + - + +
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Residues in contact with GLN 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 GLU* 2.9 47.8 + - + +
551B ALA* 3.8 7.5 - - - +
553B ASP* 1.3 77.7 - - + +
555B TYR* 1.3 57.1 + - - +
557B ILE* 3.3 12.7 + - + +
558B SER* 2.9 30.0 + - - -
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Residues in contact with TYR 555 (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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537B VAL* 3.6 21.2 + - + +
539B LYS* 3.2 32.6 + - - +
542B GLN* 3.6 27.4 + - - +
544B GLN* 3.9 32.7 - - + +
546B ILE* 3.7 20.4 - - + -
551B ALA 2.9 17.5 + - - +
552B MET* 3.6 13.7 - - + +
553B ASP 3.2 0.2 - - - -
554B GLN* 1.3 77.2 - - - +
556B GLN* 1.3 59.5 + - + +
558B SER* 3.3 7.4 + - - -
559B ILE* 2.9 50.1 + - + +
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Residues in contact with GLN 556 (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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552B MET* 2.9 55.4 + - + +
553B ASP* 3.7 12.7 + - - +
555B TYR* 1.3 76.6 - - + +
557B ILE* 1.3 59.8 + - + +
559B ILE* 3.3 6.3 + - - +
560B ALA* 2.9 30.5 + - - +
730B SER* 5.1 1.2 + - - -
731B ARG* 2.4 48.1 + - + +
734B LEU* 6.2 3.1 - - + -
736B ILE* 4.9 6.1 - - - +
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Residues in contact with ILE 557 (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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553B ASP* 2.9 29.9 + - + +
554B GLN* 3.6 12.3 - - + +
555B TYR 3.3 0.2 - - - -
556B GLN* 1.3 77.7 - - + +
558B SER* 1.3 58.4 + - - +
560B ALA* 3.2 5.5 + - - +
561B LEU* 2.9 51.3 + - + +
581B GLU 5.8 1.8 - - - +
584B VAL* 5.2 7.0 - - + -
585B SER* 5.7 9.0 - - - +
588B ASN* 4.2 22.9 - - + +
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Residues in contact with SER 558 (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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554B GLN 2.9 17.4 + - - -
555B TYR* 3.3 9.1 + - - -
557B ILE* 1.3 78.4 - - - +
559B ILE* 1.3 64.0 + - - +
561B LEU* 3.3 17.0 + - - +
562B ASP* 2.8 18.2 + - - +
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Residues in contact with ILE 559 (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 LYS* 3.7 27.4 - - + +
542B GLN* 4.4 13.0 - - - +
555B TYR* 2.9 57.6 + - + +
556B GLN* 3.8 5.8 - - - +
557B ILE 3.3 0.2 - - - -
558B SER* 1.3 80.2 - - - +
560B ALA* 1.3 57.2 + - - +
562B ASP* 2.8 17.9 - - - +
709B ARG* 2.5 40.7 + - - +
730B SER* 4.2 15.7 - - - +
734B LEU* 5.2 2.5 - - + -
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Residues in contact with ALA 560 (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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556B GLN 2.9 16.5 + - - +
557B ILE* 3.7 6.3 - - - +
559B ILE* 1.3 78.1 - - - +
561B LEU* 1.3 65.3 + - + +
562B ASP 3.4 2.7 + - - -
564B ALA* 5.3 1.4 - - - +
709B ARG* 4.0 15.2 + - - +
726B LEU* 4.6 16.0 - - + +
727B VAL* 4.5 21.8 - - + +
730B SER* 3.7 25.3 - - - +
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Residues in contact with LEU 561 (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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557B ILE* 2.9 36.5 + - + +
558B SER* 3.4 9.6 - - - +
559B ILE 3.2 0.4 - - - -
560B ALA* 1.3 82.8 - - + +
562B ASP* 1.3 52.1 + - - +
563B GLY* 2.6 17.2 + - - -
564B ALA* 4.4 9.8 + - + +
580B LEU* 4.7 17.3 - - + -
581B GLU* 3.9 48.5 - - + +
584B VAL* 4.5 25.8 - - + -
726B LEU* 5.4 10.5 - - + -
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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