Contacts of the helix formed by residues 855 - 862 (chain B) in PDB entry 6WCZ
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 HIS 855 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A ASP* 4.6 1.6 - - - -
171A ASP* 2.5 32.5 + - - -
172A VAL* 3.5 35.5 - - + +
175A PHE* 4.7 24.6 - + + +
332B PRO* 5.6 1.2 - - - +
852B LEU* 3.3 34.1 + - + +
853B ILE 3.1 6.0 + - - +
854B GLY* 1.3 76.7 + - - +
856B ARG* 1.3 72.7 + - + +
857B PRO* 3.4 25.0 - - + +
858B ARG* 4.4 2.6 - - + +
859B THR* 2.7 29.5 + - - -
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Residues in contact with ARG 856 (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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171A ASP* 5.6 1.8 - - - +
854B GLY 4.1 15.8 + - - -
855B HIS* 1.3 80.9 + - + +
857B PRO* 1.4 72.2 - - + +
859B THR* 3.4 10.6 + - - +
860B THR* 2.9 35.3 + - + +
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Residues in contact with PRO 857 (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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168A ASP* 4.3 19.7 - - - +
171A ASP* 5.0 0.7 - - - +
172A VAL* 5.8 0.7 - - + -
331B LYS* 5.6 2.0 - - + -
332B PRO* 3.8 22.4 - - + -
855B HIS* 3.4 33.7 - - + +
856B ARG* 1.4 88.2 - - + +
858B ARG* 1.3 57.5 + - - +
860B THR* 2.4 33.4 + - - +
861B TRP* 2.9 17.6 - - + +
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Residues in contact with ARG 858 (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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332B PRO* 4.1 1.2 - - + +
333B TRP* 5.0 2.3 - - + -
772B ARG* 3.7 26.7 + - - +
773B ASP* 2.8 31.7 + - - +
776B LEU* 5.0 8.3 - - - +
852B LEU* 3.3 53.1 - - + +
853B ILE* 3.4 20.1 - - - +
854B GLY 4.8 2.4 - - - +
855B HIS* 4.0 2.6 + - + +
856B ARG 3.5 0.4 - - - -
857B PRO* 1.3 78.9 - - - +
859B THR* 1.3 53.8 + - - +
861B TRP* 3.5 25.0 - - + +
862B ALA* 2.6 51.3 + - + +
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Residues in contact with THR 859 (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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854B GLY* 4.0 15.9 + - - -
855B HIS 2.7 23.5 + - - -
856B ARG* 3.7 13.3 + - - +
857B PRO 3.2 0.6 - - - -
858B ARG* 1.3 80.4 + - - +
860B THR* 1.3 60.4 + - + +
862B ALA* 3.3 5.7 + - - +
863B GLU* 3.0 51.9 + - + +
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Residues in contact with THR 860 (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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331B LYS* 6.0 0.3 - - - +
856B ARG* 2.9 26.4 + - + +
857B PRO* 2.4 30.7 + - - +
859B THR* 1.3 77.4 - - + +
861B TRP* 1.3 59.2 + - - -
863B GLU* 2.8 26.8 + - - +
864B ASN* 2.9 11.4 - - - +
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Residues in contact with TRP 861 (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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329B LEU 4.1 18.6 - - - -
330B SER* 4.9 0.2 - - - -
331B LYS* 3.6 50.7 - - + +
332B PRO* 3.2 25.7 - - + +
333B TRP* 3.6 32.3 - + - -
776B LEU* 6.0 7.0 - - + -
777B MET* 4.8 15.0 - - + -
857B PRO* 2.9 35.4 + - + -
858B ARG* 3.5 18.0 - - + +
860B THR* 1.3 77.6 + - - +
862B ALA* 1.3 62.7 + - + +
863B GLU 3.1 1.1 - - - -
864B ASN* 2.9 32.4 - - - +
865B ILE* 3.3 17.2 - - + +
868B THR* 5.2 8.5 - - + +
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Residues in contact with ALA 862 (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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776B LEU* 6.4 2.0 - - + -
858B ARG* 2.6 40.0 + - + +
859B THR* 3.4 7.6 - - - +
860B THR 3.1 0.2 - - - -
861B TRP* 1.3 84.9 - - + +
863B GLU* 1.3 58.6 + - - +
864B ASN 3.5 0.4 - - - -
865B ILE* 3.3 20.6 - - + +
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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