Contacts of the helix formed by residues 89 - 100 (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 ILE 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B PHE* 3.8 14.3 - - + -
8B LEU* 3.8 24.9 - - + -
11B THR* 3.7 32.3 - - + -
12B LEU* 3.9 17.7 - - + -
15B LEU* 4.2 2.0 - - + -
40B THR* 3.6 31.4 - - + -
56B ILE* 4.4 16.4 - - + -
86B GLN 4.3 2.7 - - - +
87B ASP 3.6 0.6 + - - +
88B ASN* 1.3 75.5 + - - +
90B ALA* 1.3 57.2 + - - +
91B ASP 3.4 1.3 - - - -
92B ALA* 3.2 14.9 + - + +
93B VAL* 3.0 33.8 + - + +
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Residues in contact with ALA 90 (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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15B LEU* 4.1 25.8 - - + +
88B ASN* 2.9 22.6 + - - +
89B ILE* 1.3 70.2 - - - +
91B ASP* 1.3 67.8 + - - +
93B VAL* 3.3 4.2 + - - +
94B ALA* 3.0 22.5 + - - +
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Residues in contact with ASP 91 (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* 3.8 26.0 - - + +
83B ALA* 4.3 8.4 - - + +
86B GLN* 3.0 31.2 + - - +
88B ASN* 4.6 2.0 + - - +
89B ILE 3.4 0.4 - - - -
90B ALA* 1.3 80.1 - - - +
92B ALA* 1.3 57.5 - - - +
94B ALA* 3.2 7.5 + - - +
95B CYS* 2.9 29.3 + - - +
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Residues in contact with ALA 92 (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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55B GLY* 6.4 0.2 - - - -
56B ILE* 4.7 8.1 - - + +
57B PHE* 4.6 13.2 - - + +
59B ILE* 3.7 5.8 - - + +
83B ALA 5.1 1.9 + - - +
84B LEU* 3.6 35.3 - - + +
88B ASN 5.3 0.4 + - - -
89B ILE* 3.2 20.5 + - + +
91B ASP* 1.3 78.0 - - - +
93B VAL* 1.3 52.7 + - - +
95B CYS* 3.2 2.3 + - - +
96B ALA* 2.7 36.4 + - - +
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Residues in contact with VAL 93 (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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12B LEU* 3.9 26.9 - - + -
15B LEU* 3.9 26.9 - - + -
17B MET* 3.6 30.5 - - + -
57B PHE* 4.1 9.9 - - + -
89B ILE* 3.0 22.8 + - + +
90B ALA 3.7 6.5 - - - +
92B ALA* 1.3 71.5 - - - +
94B ALA* 1.3 62.9 + - - +
96B ALA* 3.2 7.5 + - - +
97B LYS* 2.8 41.7 + - - +
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Residues in contact with ALA 94 (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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90B ALA 3.0 13.7 + - - +
91B ASP* 3.6 9.9 - - - +
93B VAL* 1.3 77.6 - - - +
95B CYS* 1.3 63.0 + - - +
97B LYS* 3.3 16.6 - - + +
98B ARG* 3.2 20.7 + - - +
101B ARG* 5.2 0.7 + - - -
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Residues in contact with CYS 95 (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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59B ILE* 3.9 28.0 - - - -
63B TYR* 4.3 1.8 - - - -
77B CYS* 2.0 51.6 - - + -
79B LEU* 4.2 4.0 - - + -
84B LEU* 4.2 17.9 - - + -
91B ASP 2.9 16.9 + - - +
92B ALA 3.6 4.5 - - - +
94B ALA* 1.3 78.1 - - - +
96B ALA* 1.3 60.9 + - - +
98B ARG* 3.1 14.9 + - - +
99B VAL* 3.1 13.4 + - - +
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Residues in contact with ALA 96 (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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17B MET* 5.0 2.2 - - - -
28B TRP* 4.3 17.0 - - + -
57B PHE* 3.7 28.7 - - + -
59B ILE* 3.8 10.7 - - + +
92B ALA 2.7 21.1 + - - +
93B VAL* 3.5 5.6 - - - +
95B CYS* 1.3 72.4 - - - +
97B LYS* 1.3 63.3 + - - +
99B VAL* 3.4 6.2 + - - +
100B VAL* 3.2 28.9 + - - +
109B TRP* 4.6 3.3 - - + -
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Residues in contact with LYS 97 (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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15B LEU 2.8 29.5 + - - -
16B GLY* 4.0 7.9 + - - -
17B MET* 3.3 31.2 - - + -
20B TYR* 3.4 41.5 - - + +
93B VAL* 2.8 19.5 + - - +
94B ALA* 3.3 17.6 - - - +
96B ALA* 1.3 78.2 - - - +
98B ARG* 1.3 59.5 + - - +
100B VAL* 3.2 20.4 - - - +
101B ARG* 3.3 21.6 + - - +
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Residues in contact with ARG 98 (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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63B TYR* 5.0 0.2 - - - -
75B ASN* 3.1 62.8 + - - +
76B ALA 3.2 20.3 + - - -
77B CYS* 3.6 15.8 - - - +
78B HIS* 3.3 34.6 + - - +
94B ALA 3.2 9.9 + - - +
95B CYS* 3.1 11.1 + - - +
97B LYS* 1.3 76.7 - - - +
99B VAL* 1.3 60.1 + - - +
100B VAL 3.1 1.6 - - - -
101B ARG* 2.8 53.1 + - - +
102B ASP* 3.4 8.0 + - - +
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Residues in contact with VAL 99 (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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59B ILE* 4.3 20.0 - - + -
63B TYR* 3.6 52.2 + - + +
95B CYS* 3.1 14.9 + - - +
96B ALA 3.7 6.1 - - - +
98B ARG* 1.3 75.1 - - - +
100B VAL* 1.3 58.3 + - - +
102B ASP* 3.2 24.7 + - - +
105B GLY 4.5 4.0 + - - +
108B ALA* 4.6 13.6 - - + +
109B TRP* 3.6 30.5 - - + -
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Residues in contact with VAL 100 (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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20B TYR* 3.7 25.4 - - + -
21B ARG* 3.5 17.7 + - + +
23B ILE* 4.2 19.2 - - + +
28B TRP* 3.4 29.6 - - + -
96B ALA 3.2 10.2 + - - +
97B LYS 3.2 18.6 - - - +
98B ARG 3.1 1.0 - - - -
99B VAL* 1.3 74.6 - - - +
101B ARG* 1.3 61.7 - - - +
102B ASP 3.2 7.1 - - - +
105B GLY* 3.5 22.0 - - - -
106B ILE* 4.2 1.1 - - - +
109B TRP* 3.7 22.4 - - + -
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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