Contacts of the helix formed by residues 550 - 567 (chain B) in PDB entry 6O81
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 ILE 550 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549B ASP* 1.3 78.6 - - + +
551B LYS* 1.3 59.1 + - - +
553B PHE* 3.5 7.3 + - - +
554B GLN* 2.9 30.1 + - - +
595B VAL* 5.7 2.8 - - + +
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Residues in contact with LYS 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B ASP 3.3 5.0 - - - +
550B ILE* 1.3 76.2 - - - +
552B VAL* 1.3 59.9 + - - +
554B GLN* 3.4 6.5 + - - +
555B ASN* 2.9 29.7 + - - +
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Residues in contact with VAL 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B ASP* 3.7 13.8 + - - +
550B ILE 3.4 0.4 - - - -
551B LYS* 1.3 78.4 - - - +
553B PHE* 1.3 57.0 + - - +
555B ASN* 3.4 6.6 + - - +
556B GLU* 2.9 29.6 + - - +
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Residues in contact with PHE 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B ASP 3.5 10.8 + - - +
550B ILE* 3.5 10.5 + - - +
551B LYS 3.3 0.4 - - - -
552B VAL* 1.3 76.5 - - - +
554B GLN* 1.3 59.3 + - - +
556B GLU* 3.4 6.6 + - - +
557B VAL* 2.9 29.9 + - - +
581B LEU* 5.6 3.4 - - + +
585B TYR* 3.8 28.7 - - + -
595B VAL* 5.7 3.8 - - + -
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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
----------------------------------------------------------
550B ILE 2.9 17.6 + - - +
551B LYS* 3.7 7.4 - - - +
553B PHE* 1.3 77.5 - - - +
555B ASN* 1.3 57.3 + - - +
557B VAL* 3.4 6.4 + - - +
558B LEU* 2.9 29.3 + - - +
595B VAL* 4.8 21.7 - - + +
598B HIS* 6.4 2.0 - - + -
599B VAL* 4.9 3.4 - - + +
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Residues in contact with ASN 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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551B LYS 2.9 18.2 + - - +
552B VAL* 3.8 7.0 - - - +
554B GLN* 1.3 76.2 - - - +
556B GLU* 1.3 57.9 + - - +
558B LEU* 3.4 6.3 + - - +
559B GLY* 2.9 25.3 + - - -
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Residues in contact with GLU 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B VAL 2.9 18.0 + - - +
553B PHE* 3.7 7.2 - - - +
554B GLN 3.3 0.2 - - - -
555B ASN* 1.3 74.6 - - - +
557B VAL* 1.3 59.3 + - - +
559B GLY* 3.4 1.6 + - - +
560B THR* 2.9 29.5 + - - -
581B LEU* 5.4 11.0 - - + -
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Residues in contact with VAL 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B PHE 2.9 17.6 + - - +
554B GLN* 3.8 7.2 - - - +
556B GLU* 1.3 76.1 - - - +
558B LEU* 1.3 57.7 + - - +
560B THR* 3.4 6.4 + - - -
561B LEU* 2.9 29.6 + - - +
581B LEU* 5.7 7.8 - - + +
595B VAL* 5.3 9.0 - - + +
596B LEU* 5.6 4.0 - - + +
599B VAL* 4.8 10.7 - - + +
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Residues in contact with LEU 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 18.3 + - - +
555B ASN* 3.7 7.2 - - - +
557B VAL* 1.3 77.3 - - - +
559B GLY* 1.3 56.5 + - - +
561B LEU* 3.4 6.3 + - - +
562B GLN* 2.9 29.5 + - - +
599B VAL* 4.5 15.6 - - + +
602B GLU* 6.5 0.4 - - + -
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Residues in contact with GLY 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B ASN 2.9 17.1 + - - -
556B GLU* 3.8 1.6 - - - -
558B LEU* 1.3 77.1 - - - +
560B THR* 1.3 55.6 + - - +
562B GLN* 3.4 7.2 + - - +
563B LYS* 2.9 29.3 + - - +
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Residues in contact with THR 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 GLU 2.9 18.2 + - - -
557B VAL* 3.8 7.6 - - - -
559B GLY* 1.3 76.5 - - - +
561B LEU* 1.3 57.4 + - - +
563B LYS* 3.4 5.8 + - - +
564B GLY* 2.9 25.5 + - - -
577B GLU* 5.1 16.6 - - - -
578B ILE* 6.5 0.2 - - - -
628B TRP* 4.3 2.6 - - - -
379S ARG* 5.4 11.9 - - - -
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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 VAL 2.9 18.3 + - - +
558B LEU* 3.8 7.0 - - - +
560B THR* 1.3 73.0 - - - +
562B GLN* 1.3 60.3 + - - +
565B LYS* 2.9 27.9 + - - +
599B VAL* 5.6 7.2 - - + +
603B PHE* 6.1 4.7 - - + -
628B TRP* 3.3 28.5 - - + -
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Residues in contact with GLN 562 (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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558B LEU 2.9 17.8 + - - +
559B GLY* 3.7 7.4 - - - +
561B LEU* 1.3 76.7 - - - +
563B LYS* 1.3 56.8 + - - +
565B LYS* 3.4 6.3 + - - +
566B GLU* 2.9 31.4 + - - +
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Residues in contact with LYS 563 (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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559B GLY 2.9 17.2 + - - +
560B THR* 3.8 7.2 - - - +
562B GLN* 1.3 76.3 - - - +
564B GLY* 1.3 58.0 + - - +
566B GLU* 4.5 4.5 - - - +
567B GLU* 2.9 36.9 + - + +
569B ILE* 5.4 0.2 - - - -
379S ARG* 5.6 9.2 - - + -
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Residues in contact with GLY 564 (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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560B THR 2.9 16.2 + - - -
562B GLN 3.3 0.2 - - - -
563B LYS* 1.3 77.4 - - - +
565B LYS* 1.3 57.9 + - - +
568B ASN* 3.2 7.3 + - - -
569B ILE* 3.0 42.2 + - - +
574B LEU* 6.1 0.2 - - - -
628B TRP* 3.6 20.1 - - - -
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Residues in contact with LYS 565 (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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561B LEU 2.9 17.2 + - - +
562B GLN* 3.8 6.5 - - - +
564B GLY* 1.3 76.8 - - - +
566B GLU* 1.3 61.9 + - - +
568B ASN* 4.0 5.2 + - - +
628B TRP* 3.6 15.0 - - + +
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Residues in contact with GLU 566 (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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562B GLN 2.9 18.4 + - - +
563B LYS* 4.1 4.0 - - - +
565B LYS* 1.3 79.0 - - - +
567B GLU* 1.3 61.0 + - - +
568B ASN* 3.3 2.8 + - - +
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Residues in contact with GLU 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B LYS* 2.9 17.7 + - + +
566B GLU* 1.3 75.8 - - + +
568B ASN* 1.3 69.5 + - - +
569B ILE* 3.6 5.0 + - + +
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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