Contacts of the strand formed by residues 861 - 864 (chain A) 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 TRP 861 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820A ASP* 4.9 3.4 - - - -
824A ARG* 3.6 72.9 - - + +
825A ILE* 3.3 24.0 - - - -
826A ARG* 3.6 42.0 - - + -
829A ASP* 5.8 0.4 - - - -
852A PHE* 3.8 6.1 - - - -
853A LYS* 3.4 32.3 + - + +
855A THR* 4.6 13.4 - - + +
859A SER* 4.6 8.2 + - - -
860A ASN* 1.3 81.9 - - - +
862A TRP* 1.3 62.3 + - - +
863A VAL* 3.9 7.3 + - + -
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Residues in contact with TRP 862 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815A PHE* 3.8 5.4 - - - -
824A ARG* 3.3 3.6 - - - -
825A ILE* 2.7 46.0 + - + -
827A MET* 3.4 53.9 - - + +
843A ARG* 4.5 21.8 - - + -
846A LEU* 3.5 51.3 - - + +
847A LYS* 4.5 4.0 - - + -
850A ALA* 3.7 27.1 - - + -
851A ASP 3.9 2.9 - - - -
852A PHE* 4.4 33.3 - + + -
860A ASN 5.1 1.1 - - - -
861A TRP* 1.3 73.4 - - - +
863A VAL* 1.3 63.4 + - - +
864A LEU 3.7 0.9 + - - -
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Residues in contact with VAL 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822A PRO* 3.8 28.5 - - + +
823A ARG 3.6 6.1 - - - +
824A ARG* 4.0 18.2 - - + +
850A ALA* 3.3 1.3 - - - -
851A ASP* 2.6 46.4 + - + +
853A LYS* 3.7 28.7 - - + -
861A TRP* 4.5 7.6 - - + -
862A TRP* 1.3 73.2 - - - +
864A LEU* 1.3 72.1 + - - +
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Residues in contact with LEU 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815A PHE* 3.6 30.5 - - + -
822A PRO* 4.6 7.0 - - + +
823A ARG* 2.8 48.2 + - + +
849A CYS* 3.3 21.1 - - + +
850A ALA* 4.3 0.2 - - - +
851A ASP* 5.8 0.2 - - - -
862A TRP 3.7 2.0 + - - -
863A VAL* 1.3 83.0 - - - +
865A LYS* 1.3 73.8 + - - +
866A SER* 3.5 2.4 + - - -
868A PHE* 3.7 27.1 - - + +
870A LEU* 4.4 20.2 - - + -
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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