Contacts of the helix formed by residues 719 - 726 (chain B) in PDB entry 6MZL
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 MET 719 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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699B CYS* 4.1 16.4 - - + -
702B LEU* 3.8 30.5 - - + -
716B PRO* 5.4 0.2 - - - +
717B PRO 3.9 0.4 + - - -
718B ALA* 1.3 75.8 - - + +
720B LYS* 1.3 62.4 + - - +
721B SER* 3.2 8.5 + - - -
722B LEU* 3.1 39.1 + - + +
723B PHE* 3.2 9.7 + - - +
753B MET* 3.7 30.0 - - + +
756B ALA* 4.0 14.8 - - + -
757B MET* 3.6 42.7 - - + +
760B LEU* 3.9 15.5 - - - -
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Residues in contact with LYS 720 (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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717B PRO* 4.1 21.6 - - + +
718B ALA 2.9 11.4 + - - +
719B MET* 1.3 76.0 - - - +
721B SER* 1.3 59.2 + - - +
723B PHE* 3.1 8.7 + - - +
724B THR* 2.9 29.8 + - - +
757B MET* 3.6 17.7 - - + +
770B GLU* 2.6 56.2 + - - +
771B VAL* 4.7 9.0 - - + +
774B PHE* 5.2 17.3 - - + -
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Residues in contact with SER 721 (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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683B ASP* 5.7 0.3 + - - -
716B PRO* 5.0 12.7 - - - +
717B PRO 5.0 1.2 + - - -
718B ALA 5.0 0.2 - - - -
719B MET 4.2 10.3 + - - +
720B LYS* 1.3 78.7 - - - +
722B LEU* 1.3 65.9 + - - +
724B THR* 3.3 11.6 - - - -
725B ARG* 2.8 53.3 + - - +
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Residues in contact with LEU 722 (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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683B ASP* 3.8 29.4 - - + +
686B GLU* 3.3 24.2 - - + +
687B GLN* 3.3 25.8 - - + +
702B LEU* 4.2 1.3 - - + -
719B MET* 3.1 40.9 + - + +
721B SER* 1.3 83.7 - - - +
723B PHE* 1.3 65.4 + - - +
725B ARG* 6.1 1.3 - - - -
726B MET* 3.2 38.2 + - - +
727B PHE* 3.6 0.7 - - - -
753B MET* 3.7 20.2 - - + -
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Residues in contact with PHE 723 (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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719B MET 3.2 4.0 + - - +
720B LYS 3.1 8.9 + - - +
722B LEU* 1.3 75.8 - - - +
724B THR* 1.3 66.8 + - - +
727B PHE* 3.3 44.3 - + + +
736B VAL* 3.4 17.3 - - + +
750B GLN* 4.8 14.6 - - + -
753B MET* 3.5 42.2 - - + -
754B PRO* 3.9 13.2 - - + -
757B MET* 4.0 12.1 - - + -
774B PHE* 3.4 40.8 - + + -
778B LEU* 4.4 15.9 - - + -
794B TYR* 5.4 4.7 - - - -
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Residues in contact with THR 724 (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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720B LYS* 2.9 15.9 + - - +
721B SER* 3.3 14.7 - - - -
722B LEU 3.2 0.2 - - - -
723B PHE* 1.3 79.7 - - - +
725B ARG* 1.3 68.6 + - + +
726B MET 3.2 5.4 + - - -
727B PHE 3.5 13.5 + - - +
728B CYS* 4.9 5.5 - - - -
732B CYS* 5.9 0.2 - - - +
736B VAL* 5.3 1.6 - - - -
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Residues in contact with ARG 725 (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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687B GLN* 4.5 19.3 - - - +
721B SER* 2.8 36.3 + - - +
722B LEU* 6.1 1.1 - - - -
724B THR* 1.3 82.4 - - + +
726B MET* 1.3 60.2 + - - +
727B PHE 3.6 0.2 - - - -
728B CYS* 6.1 1.8 - - - -
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Residues in contact with MET 726 (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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686B GLU* 3.6 25.4 - - - +
687B GLN* 3.4 41.5 - - + +
695B ARG* 5.0 2.0 - - - +
722B LEU* 3.2 29.9 + - - +
724B THR 3.2 0.8 - - - -
725B ARG* 1.3 78.7 - - - +
727B PHE* 1.3 80.2 + - + +
728B CYS* 4.2 1.2 + - - -
749B LEU* 3.7 24.5 - - + -
753B MET* 5.1 2.9 - - - +
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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