Contacts of the helix formed by residues 567 - 572 (chain B) in PDB entry 3MBK
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 567 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490B GLU* 3.5 12.9 + - - +
494B TRP* 3.5 34.6 - - - -
538B TYR* 2.7 23.0 + - - -
565B HIS* 4.0 1.8 - - - +
566B ALA* 1.3 78.8 - - - +
568B SER* 1.3 57.3 + - - +
569B LEU 3.3 0.6 + - - -
570B GLU* 3.6 2.0 + - - +
571B ALA* 3.0 27.4 + - - +
587B PHE* 3.6 20.7 - - - -
590B MET* 5.5 0.4 - - - -
591B VAL* 3.7 12.3 - - - +
700B SO4 4.8 0.2 + - - -
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Residues in contact with SER 568 (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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377B VAL* 3.8 8.8 - - - +
488B LEU 3.9 8.2 + - - -
538B TYR* 4.0 9.2 + - - -
564B ALA* 3.2 20.6 - - - +
565B HIS* 3.0 31.6 + - - +
567B SER* 1.3 78.6 + - - +
569B LEU* 1.3 67.8 + - - +
571B ALA* 3.8 1.3 - - - +
572B CYS* 2.9 43.1 + - - +
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Residues in contact with LEU 569 (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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377B VAL* 3.8 24.9 - - + +
378B CYS* 4.0 4.9 - - - -
379B ARG 3.9 20.4 - - - +
565B HIS 3.4 17.5 - - - +
566B ALA 3.7 10.3 - - - +
567B SER 3.3 0.8 - - - -
568B SER* 1.3 79.0 - - - +
570B GLU* 1.3 51.1 + - - +
573B THR* 2.7 35.9 + - - +
594B ILE* 4.1 26.2 - - + -
598B GLY* 3.6 23.1 - - - +
599B PHE 4.2 1.3 - - - +
600B CYS* 3.9 23.1 - - + +
613B LEU* 5.8 0.2 - - - +
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Residues in contact with GLU 570 (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* 5.9 0.9 - - + -
566B ALA 4.7 0.6 + - - -
567B SER 3.6 2.4 + - - +
569B LEU* 1.3 77.4 - - - +
571B ALA* 1.3 67.9 + - - +
572B CYS 3.2 1.8 - - - -
573B THR* 3.1 4.7 + - - +
574B CYS* 2.9 40.0 + - + +
582B GLN* 2.8 44.0 + - - +
587B PHE* 3.4 18.5 - - + -
590B MET* 3.6 28.7 - - + +
594B ILE* 5.5 0.2 - - - +
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Residues in contact with ALA 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B TYR* 3.6 21.5 - - + +
539B ILE* 3.9 28.0 - - + +
542B SER* 3.3 32.5 - - - +
543B PHE* 4.0 8.0 + - - +
567B SER 3.0 20.9 + - - +
568B SER* 4.4 1.6 - - - -
570B GLU* 1.3 77.5 - - - +
572B CYS* 1.3 62.2 + - - +
574B CYS* 4.1 4.6 + - - +
575B GLN* 5.0 1.0 + - - +
587B PHE* 4.4 0.8 - - + -
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Residues in contact with CYS 572 (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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377B VAL* 4.5 16.6 - - + -
488B LEU* 3.9 24.5 - - - -
538B TYR* 6.0 0.2 - - - -
542B SER* 4.3 13.6 - - - +
543B PHE* 5.0 3.3 - - - -
546B THR* 3.4 45.0 + - + +
562B ILE* 4.4 6.3 - - + -
568B SER* 2.9 34.6 + - - +
571B ALA* 1.3 77.7 - - - +
573B THR* 1.3 59.6 + - - +
574B CYS 3.8 0.2 - - - -
576B LEU* 4.0 9.1 + - - +
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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