Contacts of the helix formed by residues 885 - 889 (chain A) in PDB entry 5WRZ
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 PRO 885 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710A TYR* 4.0 18.6 - - + +
713A LEU* 4.3 10.3 - - + -
714A SER* 3.5 20.4 - - - +
717A GLN* 3.0 25.8 - - + +
758A VAL* 3.9 25.4 - - + -
762A ALA* 4.1 16.2 - - + -
884A ALA* 1.3 85.3 - - + +
886A VAL* 1.3 59.3 + - - +
887A THR 3.1 0.4 - - - -
888A GLY 2.8 20.3 + - - -
889A TYR* 3.4 11.1 - - - -
981B ASP* 6.1 0.2 - - - +
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Residues in contact with VAL 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A GLN* 3.6 1.6 + - - +
884A ALA 3.2 6.1 + - - -
885A PRO* 1.3 70.8 - - - +
887A THR* 1.3 59.3 + - - +
888A GLY 3.2 1.4 + - - -
889A TYR* 3.3 22.2 + - - +
892A GLY* 3.6 14.4 - - - -
893A LYS* 4.1 25.4 - - + +
937A HIS* 3.7 12.6 + - - +
938A ILE 3.5 26.9 - - - +
939A SER* 4.6 6.7 - - - +
934B HIS* 3.1 47.8 - - + +
981B ASP* 6.2 0.9 - - + -
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Residues in contact with THR 887 (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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717A GLN* 2.9 27.5 + - + +
721A SER* 5.9 1.8 - - - +
755A ALA* 5.1 15.3 - - + -
758A VAL* 5.0 9.0 - - + -
759A GLN* 3.9 11.5 - - + +
885A PRO* 3.0 0.6 + - - -
886A VAL* 1.3 73.3 - - - +
888A GLY* 1.3 59.0 + - - +
889A TYR 3.2 6.4 + - - -
937A HIS* 3.6 37.7 - - - +
934B HIS* 3.8 18.0 + - - +
935B ALA* 5.4 0.3 + - - +
983B SER* 4.7 1.7 + - - -
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Residues in contact with GLY 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A GLN* 4.4 0.4 + - - -
758A VAL* 4.4 10.3 - - - +
759A GLN* 3.5 41.8 + - - +
762A ALA* 4.7 3.5 - - - +
885A PRO* 2.8 15.5 + - - +
887A THR* 1.3 76.7 - - - +
889A TYR* 1.3 72.4 + - - +
1101A 7U3 5.5 2.3 + - - -
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Residues in contact with TYR 889 (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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710A TYR* 3.8 12.8 - - - -
759A GLN* 5.4 0.9 - - - +
762A ALA* 3.9 15.3 - - + +
763A GLU* 5.3 2.0 - - + -
766A ASP* 2.9 40.8 + - - -
880A ALA* 3.5 15.6 - - + +
884A ALA* 3.8 2.9 - - + +
885A PRO 3.4 23.8 - - - -
886A VAL 3.3 3.6 - - - +
887A THR 3.2 1.0 - - - -
888A GLY* 1.3 85.5 - - - +
890A MET* 1.3 59.7 + - - +
891A PHE 3.2 0.4 - - - -
892A GLY 2.9 34.7 + - - +
893A LYS* 3.7 28.7 - - + -
896A TYR* 3.5 7.4 - + + +
937A HIS* 2.9 21.9 + - - -
1101A 7U3 3.8 27.6 - - + -
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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