Contacts of the helix formed by residues 716 - 720 (chain B) in PDB entry 6CNC
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 ASN 716 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B HIS* 4.1 18.8 + - + -
119B ARG* 4.1 11.1 - - - +
175B ASN 4.7 2.9 - - - +
176B GLU* 4.2 10.8 - - - +
177B CYS* 4.0 24.9 - - - +
714B ALA* 3.4 16.3 - - - +
715B TYR* 1.3 76.8 - - - +
717B GLN* 1.3 67.8 + - - +
718B PHE 3.2 2.2 - - - -
719B LYS* 2.8 22.9 + - + -
720B ARG* 3.3 31.6 + - + +
63J TYR* 3.5 21.2 - - + -
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Residues in contact with GLN 717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B GLY 4.2 0.8 + - - -
712B ALA* 2.8 30.5 + - - +
713B ILE* 4.4 9.4 - - + -
714B ALA 2.9 14.0 + - - +
715B TYR 3.0 3.0 + - - -
716B ASN* 1.3 79.3 + - - +
718B PHE* 1.3 70.5 + - + +
720B ARG* 3.2 24.9 - - - +
725B LEU* 4.5 8.1 - - + +
727B LEU* 3.0 55.0 - - + +
728B MET 4.9 2.4 + - - +
788B ARG* 5.3 2.9 + - - -
60J PHE* 3.0 32.5 - - + -
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Residues in contact with PHE 718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B TYR 5.0 0.2 + - - -
716B ASN 3.2 0.8 - - - -
717B GLN* 1.3 99.7 - - + +
719B LYS* 1.3 69.1 + - + +
720B ARG 3.1 9.6 + - - +
727B LEU* 4.3 9.2 - - + -
786B GLU* 4.7 1.6 - - - -
788B ARG* 3.6 31.4 + - - +
883B GLN* 3.4 17.6 - - - +
899B LEU* 5.4 1.9 - - - +
91C VAL* 3.6 45.1 - - + -
93C GLN* 3.8 20.6 - - + +
1J MET* 4.6 13.9 - - + -
60J PHE* 4.1 25.5 - + + -
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Residues in contact with LYS 719 (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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116B HIS* 3.4 13.3 + - - +
120B LEU* 4.6 9.4 - - - +
175B ASN* 3.5 39.4 + - - +
716B ASN* 2.8 16.7 + - + +
718B PHE* 1.3 76.9 - - + +
720B ARG* 1.3 57.0 + - - +
721B ILE* 4.2 2.1 + - - +
883B GLN* 4.5 25.1 + - - +
63J TYR* 3.6 30.5 - - + +
64J ASN 5.0 1.8 - - - -
65J PRO* 3.2 42.5 - - + +
32L ALA* 5.6 8.2 + - - +
57L LEU* 5.1 6.3 - - - +
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Residues in contact with ARG 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B HIS* 3.5 24.0 - - + -
119B ARG* 3.5 34.7 - - - +
120B LEU* 5.0 0.2 - - - -
191B GLU* 4.6 6.3 + - - -
460B ARG* 3.0 50.0 - - - +
713B ILE* 4.6 10.4 - - - +
714B ALA* 5.3 1.8 - - - +
716B ASN* 3.3 27.2 + - - +
717B GLN* 3.2 26.0 - - - +
718B PHE 3.1 5.7 - - - +
719B LYS* 1.3 78.4 - - - +
721B ILE* 1.3 63.5 + - - +
722B ASP* 3.5 29.8 + - - +
725B LEU* 4.7 13.2 - - + +
788B ARG* 5.4 4.7 - - - -
899B LEU* 4.8 3.3 - - - +
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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