Contacts of the helix formed by residues 80 - 86 (chain B) in PDB entry 1QSW
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 SER 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B CYS* 3.9 4.7 - - - -
79B LEU* 1.3 90.0 - - - +
81B CYS* 1.3 62.7 + - - +
82B SER* 3.7 8.4 + - - -
83B ALA* 3.1 26.7 + - - +
84B LEU 4.0 0.2 + - - -
50C ARG 5.5 0.7 + - - -
66C ASN 4.7 14.8 - - - -
67C ASP* 4.8 13.0 - - - -
68C GLY* 5.1 6.5 - - - -
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Residues in contact with CYS 81 (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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54B TYR* 3.5 42.1 - - + +
61B SER* 4.5 0.2 - - - -
64B CYS* 2.0 61.6 + - - -
65B ALA* 3.4 16.4 - - - -
80B SER* 1.3 70.2 - - - +
82B SER* 1.3 60.1 - - - +
84B LEU* 3.0 28.0 + - - +
85B LEU* 4.2 0.3 - - - +
54C TYR* 4.9 2.2 - - - +
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Residues in contact with SER 82 (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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54B TYR* 5.4 0.2 - - - -
80B SER* 3.2 9.5 - - - -
81B CYS* 1.3 78.1 - - - +
83B ALA* 1.3 62.3 + - - +
84B LEU 3.0 0.4 - - - -
85B LEU* 3.1 14.0 + - - +
86B GLN 3.9 1.0 + - - -
45C TYR* 3.4 19.7 + - - -
50C ARG* 3.7 21.5 - - - -
51C SER* 3.3 5.4 - - - -
52C THR* 2.7 40.6 + - - -
54C TYR* 5.4 1.1 + - - -
61C SER* 4.0 7.1 + - - -
67C ASP* 5.0 3.8 + - - -
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Residues in contact with ALA 83 (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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79B LEU* 4.1 22.7 - - + -
80B SER* 3.1 23.9 + - - +
82B SER* 1.3 78.8 - - - +
84B LEU* 1.3 59.4 + - - +
85B LEU 3.2 0.2 - - - -
86B GLN* 2.7 44.5 + - - +
88B ASN 5.0 1.9 - - - +
91B ASP* 4.3 10.5 - - + +
92B ALA* 5.1 2.1 + - - +
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Residues in contact with LEU 84 (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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40B THR* 3.7 1.7 - - - +
54B TYR* 4.0 17.5 - - + +
55B GLY* 3.4 21.5 - - - -
56B ILE 4.7 0.5 + - - -
59B ILE* 3.9 35.9 - - + +
64B CYS* 4.0 26.0 - - + -
79B LEU* 3.9 26.9 - - + -
81B CYS 3.0 11.1 + - - +
82B SER 3.0 1.4 - - - -
83B ALA* 1.3 76.3 - - - +
85B LEU* 1.3 59.0 + - - +
86B GLN 3.6 1.2 - - - +
92B ALA* 3.6 40.0 - - + +
95B CYS* 4.2 8.5 - - + -
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Residues in contact with LEU 85 (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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40B THR* 3.3 23.2 + - - +
41B ARG* 3.5 30.9 + - - +
42B ALA 3.7 19.3 - - - +
43B THR* 3.8 15.5 - - + -
54B TYR* 4.0 19.5 - - + -
55B GLY 3.8 9.2 - - - +
81B CYS 4.2 0.7 - - - +
82B SER* 3.1 7.2 + - - +
84B LEU* 1.3 77.6 - - - +
86B GLN* 1.3 64.5 + - - +
43C THR* 6.0 0.2 - - - -
45C TYR* 3.6 29.7 - - + -
52C THR* 3.5 37.2 - - + +
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Residues in contact with GLN 86 (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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40B THR* 3.5 15.5 - - - +
82B SER 3.9 0.6 + - - -
83B ALA* 2.7 34.6 + - - +
84B LEU 3.6 1.4 - - - +
85B LEU* 1.3 82.1 - - - +
87B ASP* 1.3 64.2 + - - +
88B ASN* 3.3 27.3 + - - +
89B ILE* 4.3 2.3 - - - +
91B ASP* 3.0 29.2 + - - +
45C TYR* 3.7 26.2 - - + +
50C ARG* 3.4 36.9 - - + +
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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