Contacts of the helix formed by residues 665 - 672 (chain B) in PDB entry 1MZC
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 665 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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620B GLN* 5.6 6.3 - - - +
623B ALA* 5.8 1.3 - - + -
627B CYS* 4.7 0.2 - - - -
663B ILE* 3.4 23.9 - - + +
664B GLY* 1.3 78.6 - - - +
666B GLU* 1.3 65.6 + - - +
667B GLU* 3.5 15.0 + - - +
668B ALA* 2.9 22.0 + - - +
669B TYR* 2.9 25.7 + - - -
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Residues in contact with GLU 666 (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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664B GLY 4.3 0.2 + - - -
665B THR* 1.3 72.4 - - - +
667B GLU* 1.3 62.6 + - - +
669B TYR* 3.9 12.9 - - + -
670B ASP* 2.9 40.5 + - - +
914B TYR* 3.6 28.0 + - + +
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Residues in contact with GLU 667 (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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620B GLN* 4.6 1.6 - - - +
623B ALA* 5.0 0.3 - - - +
624B THR* 3.2 40.7 + - - +
627B CYS* 4.1 17.4 - - + -
628B GLN* 5.8 2.6 - - - +
663B ILE* 6.1 0.2 - - - +
665B THR* 3.0 10.7 + - - +
666B GLU* 1.3 81.7 - - - +
668B ALA* 1.3 62.8 + - - +
670B ASP* 3.5 4.6 + - - +
671B ILE* 3.3 24.4 + - + +
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Residues in contact with ALA 668 (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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627B CYS* 3.6 25.8 - - - -
660B LEU* 3.4 44.5 - - + +
663B ILE* 3.9 7.9 - - + -
665B THR* 2.9 17.2 + - - +
667B GLU* 1.3 80.3 - - - +
669B TYR* 1.3 63.4 + - - +
671B ILE* 3.1 19.2 + - - +
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Residues in contact with TYR 669 (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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660B LEU* 4.6 5.8 - - + -
661B CYS* 4.3 11.7 + - - -
664B GLY* 3.4 30.0 + - - -
665B THR 2.9 19.0 + - - -
666B GLU* 3.7 11.0 - - + +
668B ALA* 1.3 73.1 - - - +
670B ASP* 1.3 63.1 + - - +
671B ILE 3.2 1.0 + - - -
672B ILE* 3.4 17.8 + - + +
907B LYS* 4.6 1.2 + - - -
910B GLN* 3.0 36.9 + - + +
911B ALA* 3.4 29.9 + - + +
914B TYR* 3.4 52.0 - + + -
915B PHE* 3.6 32.8 - + + -
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Residues in contact with ASP 670 (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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666B GLU* 2.9 32.3 + - - +
667B GLU* 4.1 4.6 - - - +
668B ALA 3.3 0.2 - - - -
669B TYR* 1.3 71.3 - - - +
671B ILE* 1.3 64.6 + - - +
672B ILE 3.2 7.4 + - - +
914B TYR* 2.7 30.5 + - - -
915B PHE* 5.8 0.2 - - - -
918B LYS* 4.2 9.9 + - - -
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Residues in contact with ILE 671 (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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627B CYS* 3.1 55.9 - - + +
630B LEU 4.7 0.7 - - - -
631B GLU* 3.9 45.3 - - + +
634B GLN* 2.8 25.6 - - - +
640B PHE* 4.6 5.2 - - + -
660B LEU* 3.9 20.0 - - + -
667B GLU* 3.3 15.2 + - + +
668B ALA 3.1 6.7 + - - +
670B ASP* 1.3 78.7 - - - +
672B ILE* 1.3 62.1 + - - +
673B ASN* 3.3 1.6 + - - +
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Residues in contact with ILE 672 (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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634B GLN* 3.6 9.0 - - - +
640B PHE* 4.3 9.2 - - + -
657B VAL* 4.4 16.6 - - + +
660B LEU* 3.6 31.4 - - + -
661B CYS* 5.5 1.8 - - - -
669B TYR* 3.7 16.7 - - + +
670B ASP* 3.2 9.0 - - - +
671B ILE* 1.3 77.0 - - - +
673B ASN* 1.3 66.2 + - - +
674B ARG* 3.1 24.2 + - + +
677B LEU* 3.9 27.8 - - + -
714B THR* 4.0 21.5 - - + -
915B PHE* 4.0 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