Contacts of the helix formed by residues 85 - 96 (chain Z) in PDB entry 6QXT
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 85 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209Y PHE 5.1 6.6 - - - +
211Y GLN* 5.8 7.3 - - - +
84Z ARG* 1.3 73.9 - - - +
86Z ASP* 1.3 60.0 + - - +
87Z SER 3.1 2.0 + - - -
88Z SER* 3.7 13.6 + - - -
89Z LEU* 4.2 5.9 + - - +
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Residues in contact with ASP 86 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84Z ARG* 3.1 9.2 - - + +
85Z HIS* 1.3 76.1 - - - +
87Z SER* 1.3 57.8 + - - +
88Z SER 3.4 0.2 - - - -
89Z LEU* 3.5 10.9 + - + +
90Z GLN* 2.9 29.6 + - + +
195Z CYS 5.1 5.8 - - - +
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Residues in contact with SER 87 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200Y GLN* 5.4 1.6 - - - -
81Z TYR 5.7 2.2 - - - -
82Z TYR* 5.7 3.6 - - - -
83Z ALA 5.5 4.0 - - - -
84Z ARG* 3.2 18.3 + - - +
85Z HIS 3.1 1.2 - - - -
86Z ASP* 1.3 75.1 - - - +
88Z SER* 1.3 61.2 + - - +
90Z GLN* 2.9 5.3 + - - +
91Z ILE* 2.9 29.3 + - - +
195Z CYS 5.0 0.4 + - - -
196Z GLY* 3.6 38.6 - - - +
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Residues in contact with SER 88 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200Y GLN* 3.8 33.7 - - - +
208Y GLN* 4.1 26.8 - - - +
209Y PHE 4.8 3.1 - - - -
210Y ASN 4.4 1.3 - - - -
211Y GLN* 4.2 21.5 - - - -
85Z HIS 3.7 9.6 + - - -
86Z ASP 3.4 0.2 - - - -
87Z SER* 1.3 78.9 - - - +
89Z LEU* 1.3 59.4 + - - +
91Z ILE* 3.7 12.2 + - - +
92Z ALA* 4.2 4.2 + - - +
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Residues in contact with LEU 89 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208Y GLN* 5.0 7.8 + - + +
85Z HIS 4.2 2.5 + - - +
86Z ASP* 3.5 14.8 + - + +
87Z SER 3.2 0.6 - - - -
88Z SER* 1.3 77.9 - - - +
90Z GLN* 1.3 61.7 + - - +
91Z ILE 3.3 0.4 + - - -
92Z ALA* 3.7 12.9 + - - +
93Z ARG* 3.9 8.5 + - - +
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Residues in contact with GLN 90 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86Z ASP* 2.9 18.8 + - + +
87Z SER* 2.9 8.5 + - - +
89Z LEU* 1.3 74.9 - - - +
91Z ILE* 1.3 60.8 + - - +
93Z ARG* 3.2 9.8 + - + +
94Z GLN* 2.9 28.6 + - - +
195Z CYS 4.5 11.9 - - - +
197Z CYS* 4.8 14.6 - - + +
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Residues in contact with ILE 91 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200Y GLN* 5.3 9.4 - - + -
201Y ILE* 6.2 1.3 - - + +
87Z SER 2.9 13.6 + - - +
88Z SER* 3.9 10.5 - - - +
89Z LEU 3.3 0.4 - - - -
90Z GLN* 1.3 76.7 - - - +
92Z ALA* 1.3 57.6 + - - +
94Z GLN* 3.2 8.4 + - - +
95Z ILE* 2.9 29.3 + - - +
196Z GLY 5.4 3.1 + - - +
197Z CYS* 5.8 2.0 - - - +
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Residues in contact with ALA 92 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208Y GLN* 5.8 7.9 - - + -
88Z SER 4.2 4.5 + - - +
89Z LEU* 3.7 10.6 + - - +
90Z GLN 3.3 0.4 - - - -
91Z ILE* 1.3 78.2 - - - +
93Z ARG* 1.3 57.8 + - - +
95Z ILE* 3.4 7.1 + - - +
96Z ALA* 3.0 28.2 + - - +
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Residues in contact with ARG 93 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89Z LEU 3.9 4.1 + - - +
90Z GLN* 3.2 16.8 + - + +
92Z ALA* 1.3 77.8 - - - +
94Z GLN* 1.3 59.9 + - - +
96Z ALA* 3.0 9.2 + - - +
97Z TRP* 3.0 26.7 + - - +
278Z ASN* 5.2 15.3 - - + -
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Residues in contact with GLN 94 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90Z GLN 2.9 13.8 + - - +
91Z ILE* 3.2 11.0 + - - +
93Z ARG* 1.3 75.5 - - - +
95Z ILE* 1.3 62.0 + - - +
97Z TRP* 3.4 20.6 + - - +
197Z CYS* 4.8 16.4 - - + -
198Z MET* 5.0 9.6 - - + +
201Z ILE* 6.3 3.1 - - + -
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Residues in contact with ILE 95 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91Z ILE 2.9 16.5 + - - +
92Z ALA* 3.8 7.0 - - - +
94Z GLN* 1.3 77.0 - - - +
96Z ALA* 1.3 57.5 + - - +
97Z TRP 3.3 4.9 + - - +
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Residues in contact with ALA 96 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92Z ALA 3.0 17.3 + - - +
93Z ARG* 3.0 10.7 + - - +
95Z ILE* 1.3 75.2 - - - +
97Z TRP* 1.3 64.8 + - - +
98Z LYS* 3.8 1.7 + - - +
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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