Contacts of the helix formed by residues 85 - 96 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209O PHE 5.1 6.3 - - - +
211O GLN* 5.9 7.1 - - + +
84P ARG* 1.3 74.7 - - - +
86P ASP* 1.3 59.9 + - - +
87P SER 3.1 2.2 + - - -
88P SER* 3.7 13.8 + - - -
89P LEU* 4.2 5.7 + - - +
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Residues in contact with ASP 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84P ARG* 3.1 8.7 - - + +
85P HIS* 1.3 76.0 - - - +
87P SER* 1.3 58.5 + - - +
88P SER 3.4 0.4 - - - -
89P LEU* 3.5 10.3 + - + +
90P GLN* 2.9 29.7 + - + +
195P CYS 5.1 5.8 - - - +
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Residues in contact with SER 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200O GLN* 5.4 0.9 - - - -
82P TYR* 5.7 3.6 - - - -
83P ALA* 5.5 4.0 - - - -
84P ARG* 3.2 19.4 + - - +
85P HIS 3.1 1.2 - - - -
86P ASP* 1.3 75.0 - - - +
88P SER* 1.3 60.9 + - - +
90P GLN* 2.9 4.1 + - - +
91P ILE* 2.9 29.5 + - - +
195P CYS 5.0 0.4 + - - -
196P GLY* 3.6 38.9 - - - +
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Residues in contact with SER 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200O GLN* 3.9 33.7 - - - +
208O GLN* 4.1 27.5 - - - +
209O PHE 4.8 2.9 - - - -
210O ASN 4.5 0.4 - - - -
211O GLN* 4.3 21.5 - - - -
85P HIS 3.7 8.9 + - - -
86P ASP 3.4 0.2 - - - -
87P SER* 1.3 79.4 - - - +
89P LEU* 1.3 60.4 + - - +
91P ILE* 3.7 12.1 + - - +
92P ALA* 4.2 4.9 + - - +
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Residues in contact with LEU 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208O GLN* 5.0 8.0 + - + +
85P HIS 4.2 2.8 + - - +
86P ASP* 3.5 15.7 + - + +
87P SER 3.2 0.6 - - - -
88P SER* 1.3 78.6 - - - +
90P GLN* 1.3 61.0 + - - +
91P ILE 3.6 0.2 + - - -
92P ALA* 3.7 12.9 + - - +
93P ARG* 3.9 8.1 + - - +
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Residues in contact with GLN 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86P ASP* 2.9 18.6 + - + +
87P SER* 2.9 8.9 + - - +
89P LEU* 1.3 75.7 - - - +
91P ILE* 1.3 60.4 + - - +
92P ALA 3.3 0.2 - - - -
93P ARG* 3.2 10.4 + - + +
94P GLN* 2.9 28.1 + - - +
195P CYS 4.5 11.9 - - - +
197P CYS* 4.8 14.6 - - + +
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Residues in contact with ILE 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200O GLN* 5.3 9.0 - - + -
201O ILE* 6.5 0.7 - - + -
87P SER 2.9 14.3 + - - +
88P SER* 3.9 10.8 - - - +
89P LEU 3.3 0.6 - - - -
90P GLN* 1.3 77.1 - - - +
92P ALA* 1.3 57.1 + - - +
94P GLN* 3.2 8.2 + - - +
95P ILE* 2.9 28.8 + - - +
196P GLY 5.4 2.9 + - - +
197P CYS* 5.8 2.0 - - - +
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Residues in contact with ALA 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208O GLN* 5.8 7.6 - - + -
88P SER 4.2 5.1 + - - +
89P LEU* 3.7 10.5 + - - +
90P GLN 3.3 0.8 - - - -
91P ILE* 1.3 78.3 - - - +
93P ARG* 1.3 56.6 + - - +
95P ILE* 3.4 7.8 + - - +
96P ALA* 3.0 28.2 + - - +
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Residues in contact with ARG 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89P LEU 3.9 4.3 + - - +
90P GLN* 3.2 16.8 + - + +
92P ALA* 1.3 77.5 - - - +
94P GLN* 1.3 59.0 + - - +
96P ALA* 3.0 8.0 + - - +
97P TRP* 3.0 26.5 + - - +
278P ASN* 5.2 15.9 - - + -
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Residues in contact with GLN 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90P GLN 2.9 13.3 + - - +
91P ILE* 3.6 11.2 - - - +
93P ARG* 1.3 76.7 - - - +
95P ILE* 1.3 61.2 + - - +
97P TRP* 3.4 19.8 + - - +
197P CYS* 4.8 17.5 - - + -
198P MET* 5.0 9.9 - - + +
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Residues in contact with ILE 95 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91P ILE 2.9 16.7 + - - +
92P ALA* 3.8 7.4 - - - +
94P GLN* 1.3 76.3 - - - +
96P ALA* 1.3 58.7 + - - +
97P TRP 3.3 4.7 + - - +
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Residues in contact with ALA 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92P ALA 3.0 17.9 + - - +
93P ARG* 3.0 10.0 + - - +
95P ILE* 1.3 75.9 - - - +
97P TRP* 1.3 64.8 + - - +
98P 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