Contacts of the helix formed by residues 89 - 102 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C PHE* 3.9 14.3 - - + -
8C LEU* 3.7 30.7 - - + -
11C THR* 3.8 26.9 - - + -
12C LEU* 4.3 13.0 - - + -
15C LEU* 4.1 5.6 - - + -
40C THR* 3.7 31.9 - - + -
56C ILE* 4.2 17.3 - - + -
86C GLN 4.4 2.9 - - - +
87C ASP 3.6 0.6 + - - +
88C ASN* 1.3 72.8 + - - +
90C ALA* 1.3 53.9 + - - +
91C ASP 3.3 2.9 - - - -
92C ALA* 3.0 15.6 + - + +
93C VAL* 2.7 38.2 + - + +
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Residues in contact with ALA 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 4.3 28.5 - - + +
88C ASN* 3.1 21.7 + - - +
89C ILE* 1.3 75.0 - - - +
91C ASP* 1.3 67.8 + - - +
93C VAL* 3.2 5.7 + - - +
94C ALA* 3.1 21.3 + - - +
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Residues in contact with ASP 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ARG* 5.2 1.7 + - - -
79C LEU* 3.6 23.1 - - + +
83C ALA* 4.3 7.0 - - + +
86C GLN* 3.0 31.1 + - - +
88C ASN 4.7 1.7 + - - +
89C ILE 3.3 0.2 - - - -
90C ALA* 1.3 76.5 - - - +
92C ALA* 1.3 61.7 + - - +
94C ALA* 3.5 8.7 + - - +
95C CYS* 3.0 28.2 + - - +
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ILE* 4.8 14.1 - - + +
57C PHE* 4.4 5.2 - - + -
59C ILE* 3.8 5.8 - - + +
83C ALA 4.9 1.7 + - - +
84C LEU* 3.7 33.6 - - + +
88C ASN 5.3 0.4 + - - -
89C ILE* 3.0 23.1 + - + +
91C ASP* 1.3 78.6 - - - +
93C VAL* 1.3 60.6 + - - +
95C CYS* 3.3 2.8 + - - +
96C ALA* 2.9 29.0 + - - +
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 4.1 15.3 - - + -
15C LEU* 3.8 31.6 - - + +
17C MET* 3.7 28.0 - - + +
57C PHE* 4.1 19.3 - - + -
89C ILE* 2.7 24.3 + - + +
90C ALA 3.5 8.3 - - - +
92C ALA* 1.3 74.0 - - - +
94C ALA* 1.3 60.6 + - - +
96C ALA* 3.3 6.6 + - - +
97C LYS* 3.0 35.5 + - + +
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Residues in contact with ALA 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ALA 3.1 11.9 + - - +
91C ASP* 3.5 12.6 - - - +
93C VAL* 1.3 74.4 - - - +
95C CYS* 1.3 63.3 + - - +
97C LYS* 3.3 14.8 + - - +
98C ARG* 3.1 24.5 + - - +
101C ARG* 5.0 0.5 + - - -
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Residues in contact with CYS 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ILE* 3.7 31.2 - - + -
63C TYR* 4.4 1.6 - - - -
77C CYS* 2.0 52.7 - - + -
79C LEU* 4.1 13.9 - - + -
84C LEU* 4.3 4.5 - - + -
91C ASP 3.0 17.4 + - - +
92C ALA 3.8 3.8 - - - +
93C VAL 3.2 0.2 - - - -
94C ALA* 1.3 76.9 - - - +
96C ALA* 1.3 53.2 + - - +
98C ARG* 2.8 31.3 + - - +
99C VAL* 3.0 6.0 + - - +
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Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C MET* 4.4 2.5 - - + -
28C TRP* 4.2 19.1 - - + -
57C PHE* 3.9 26.2 - - + -
59C ILE* 3.6 12.7 - - + +
92C ALA 2.9 19.1 + - - +
93C VAL 3.3 4.7 + - - +
95C CYS* 1.3 70.7 - - - +
97C LYS* 1.3 62.5 + - - +
99C VAL* 3.3 7.2 + - - +
100C VAL* 3.0 30.7 + - - +
109C TRP* 4.9 2.5 - - + -
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Residues in contact with LYS 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU 2.8 26.2 + - - -
16C GLY* 3.7 14.5 + - - -
17C MET* 3.3 28.7 - - - -
20C TYR* 3.6 43.4 - - + +
28C TRP* 5.2 0.4 - - - -
93C VAL* 3.0 23.2 + - + +
94C ALA* 3.3 13.9 - - - +
96C ALA* 1.3 78.5 - - - +
98C ARG* 1.3 62.8 - - - +
100C VAL* 3.6 12.4 + - - +
101C ARG* 3.1 23.4 + - - +
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Residues in contact with ARG 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ASN* 3.6 46.4 - - - +
76C ALA 3.4 14.4 + - - +
77C CYS* 3.9 13.6 - - - +
78C HIS* 3.2 38.3 + - - +
94C ALA 3.1 14.4 + - - +
95C CYS* 2.8 15.7 + - - +
97C LYS* 1.3 74.6 - - - +
99C VAL* 1.3 63.7 + - - +
101C ARG* 3.1 41.5 + - - +
102C ASP 3.9 2.1 + - - -
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Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ILE* 4.1 18.4 - - + -
63C TYR* 3.8 52.0 - - + +
95C CYS* 3.0 17.4 + - - +
96C ALA* 3.3 10.1 + - - +
98C ARG* 1.3 76.0 - - - +
100C VAL* 1.3 59.7 + - - +
101C ARG 3.0 5.7 + - - -
102C ASP* 3.0 23.9 + - - +
105C GLY 5.1 0.7 + - - +
108C ALA* 4.9 12.6 - - + -
109C TRP* 3.7 27.1 - - + -
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Residues in contact with VAL 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C TYR* 4.0 19.5 - - + -
21C ARG* 4.5 16.7 + - + +
23C ILE* 3.8 26.5 - - + -
28C TRP* 3.3 29.8 - - + -
96C ALA 3.0 11.4 + - - +
97C LYS 3.6 13.7 - - - +
99C VAL* 1.3 74.3 - - - +
101C ARG* 1.3 60.1 - - - +
102C ASP 3.3 1.6 - - - +
105C GLY* 3.4 25.2 - - - -
106C ILE 4.4 4.3 - - - +
109C TRP* 3.6 24.2 - - + -
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Residues in contact with ARG 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C TYR* 2.7 32.1 + - + -
21C ARG* 4.7 20.6 - - + +
75C ASN* 4.3 17.6 + - - +
94C ALA 5.0 0.4 + - - -
97C LYS* 3.1 25.4 + - - +
98C ARG* 3.1 46.9 + - - +
99C VAL 3.0 1.2 + - - -
100C VAL* 1.3 78.1 - - - +
102C ASP* 1.3 63.5 + - - +
103C PRO* 3.5 7.1 - - - +
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Residues in contact with ASP 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C TYR* 2.8 31.7 + - - +
74C VAL* 4.5 5.4 - - + -
75C ASN* 3.0 46.9 + - - +
98C ARG 4.0 0.2 - - - +
99C VAL 3.0 12.3 + - - +
100C VAL 3.7 1.4 - - - +
101C ARG* 1.3 77.4 - - - +
103C PRO* 1.3 60.8 - - + +
104C GLN* 2.5 23.3 + - + +
105C GLY 2.9 14.4 + - - -
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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