Contacts of the helix formed by residues 90 - 100 (chain C) in PDB entry 3QSV
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 PHE 90 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79C ASP 3.9 17.3 - - - -
80C GLY* 3.7 13.9 - - - -
81C ARG* 3.9 22.9 - - + -
89C GLY* 1.3 77.7 - - - -
91C PRO* 1.3 59.9 - - + +
92C HIS* 3.5 15.3 - + + -
93C VAL* 3.0 16.1 + - + +
94C ILE* 2.7 36.6 + - - +
97C ARG* 5.9 0.4 - - - +
106C LYS* 5.3 21.8 - - + -
119C PHE* 3.5 33.9 - + - -
1003G A 5.6 5.4 - - - -
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Residues in contact with PRO 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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74C ILE* 4.4 14.4 - - + -
76C ARG* 6.5 0.9 - - + -
80C GLY 3.0 25.8 - - - +
81C ARG 4.8 0.4 - - - +
82C LEU* 4.2 19.7 - - + -
89C GLY 4.0 3.3 - - - +
90C PHE* 1.3 89.7 - - + +
92C HIS* 1.3 70.9 + - - +
94C ILE* 3.0 13.4 + - + +
95C TYR* 3.1 24.5 + - + -
119C PHE* 4.7 2.9 - - + -
126C VAL* 4.7 14.1 - - + -
128C VAL* 4.1 17.0 - - + -
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Residues in contact with HIS 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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90C PHE* 3.7 24.2 - + + -
91C PRO* 1.3 80.7 - - - +
93C VAL* 1.3 71.1 + - + +
95C TYR* 3.5 1.6 + - - +
96C ALA* 3.0 25.4 + - - +
106C LYS 5.4 2.0 + - - -
109C LEU* 3.5 31.1 + - + +
119C PHE* 3.4 49.8 - + + -
126C VAL* 5.2 1.3 - - + +
127C CYS 4.1 4.0 - - - +
128C VAL* 4.3 16.3 - - - +
130C PRO* 5.5 0.7 - - - +
133C TYR* 3.8 41.7 - + + +
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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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90C PHE* 3.0 17.1 + - + +
92C HIS* 1.3 100.4 - - + +
94C ILE* 1.3 69.0 + - - +
96C ALA* 2.8 7.6 + - - +
97C ARG* 2.7 51.9 + - - +
104C LEU* 3.8 19.3 - - + -
106C LYS* 4.3 30.1 - - + +
109C LEU* 4.2 8.3 - - + -
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Residues in contact with ILE 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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31C GLU* 5.9 1.7 - - - +
35C PHE* 4.4 32.3 - - + -
39C ALA* 4.5 14.1 - - + -
82C LEU* 4.8 9.6 - - + +
84C VAL* 4.8 6.7 - - + -
87C ARG* 5.4 5.6 - - + +
88C LYS 5.1 1.8 - - - +
89C GLY* 3.9 22.4 - - - +
90C PHE 2.7 30.3 + - - +
91C PRO* 3.4 7.9 - - + +
93C VAL* 1.3 75.9 - - - +
95C TYR* 1.3 71.7 + - + +
97C ARG* 3.5 24.7 + - - +
98C LEU* 3.2 24.6 + - + +
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Residues in contact with TYR 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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39C ALA* 2.7 43.8 + - + -
40C ILE* 4.5 2.7 - - - -
42C SER* 4.0 4.3 + - - -
43C LEU* 3.4 33.3 + - + +
46C LYS* 5.0 1.0 + - - -
74C ILE* 5.3 3.9 - - + +
82C LEU* 4.0 28.8 - - + +
91C PRO* 3.1 25.9 + - + +
92C HIS 4.3 1.3 - - - +
93C VAL 3.1 0.8 - - - -
94C ILE* 1.3 79.7 - - + +
96C ALA* 1.3 64.5 + - - +
98C LEU* 3.4 14.7 + - + -
99C TRP* 3.2 49.3 + + + +
128C VAL* 3.3 37.7 - - + +
130C PRO* 4.1 2.8 - - + +
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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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92C HIS 3.0 19.4 + - - +
93C VAL* 2.8 4.2 + - - +
95C TYR* 1.3 73.1 - - - +
97C ARG* 1.3 57.6 + - - +
98C LEU 3.0 4.7 - - - -
100C ARG* 2.9 29.9 + - - +
101C TRP* 3.1 21.2 + - + -
104C LEU* 3.9 16.6 - - + -
109C LEU* 4.5 7.6 - - + -
130C PRO* 4.1 21.3 - - + +
133C TYR* 5.9 1.6 - - + -
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Residues in contact with ARG 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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28C GLN* 5.0 0.2 - - - +
30C GLY* 4.2 5.3 - - - -
31C GLU* 3.5 30.8 + - + +
87C ARG* 5.6 2.4 - - - +
89C GLY* 5.8 1.8 - - - -
90C PHE 5.9 0.6 - - - +
93C VAL* 2.7 41.0 + - - +
94C ILE* 3.7 24.1 - - - +
96C ALA* 1.3 73.3 - - - +
98C LEU* 1.3 59.8 + - - +
99C TRP 3.7 0.2 + - - -
100C ARG 4.5 0.2 + - - -
101C TRP 3.0 24.8 + - - +
102C PRO* 3.4 35.0 - - + +
103C ASP* 5.0 0.8 - - - +
104C LEU* 2.7 37.3 + - + +
105C HIS* 4.8 2.2 - - - +
106C LYS* 5.5 7.3 - - - +
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Residues in contact with LEU 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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27C ARG* 3.2 22.7 - - + +
28C GLN 3.0 23.3 + - - -
30C GLY 5.2 1.5 + - - +
31C GLU* 4.4 26.2 - - + +
35C PHE* 5.2 2.7 - - + -
36C ALA* 3.9 32.3 - - + +
39C ALA* 4.4 12.3 - - + -
40C ILE* 3.9 30.7 - - + -
94C ILE* 3.2 16.5 + - + +
95C TYR* 3.6 17.7 - - + +
96C ALA 3.0 0.4 - - - -
97C ARG* 1.3 80.6 - - - +
99C TRP* 1.3 64.4 + - + +
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Residues in contact with TRP 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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23C LEU* 2.9 41.1 + - + -
26C HIS 3.3 28.0 - - - +
27C ARG* 3.6 3.9 - - - +
28C GLN* 3.4 23.4 + - - +
40C ILE* 3.5 36.8 - - + +
43C LEU* 4.4 14.4 - - + -
57C LEU* 4.6 5.4 - - + -
61C ILE* 3.6 46.1 - - + +
64C ASN* 4.9 4.2 - - - +
95C TYR* 3.2 51.3 + + + +
96C ALA 3.3 1.8 + - - -
98C LEU* 1.3 88.7 + - + +
100C ARG* 1.3 68.9 + - + +
128C VAL* 5.7 0.2 - - + -
130C PRO* 4.1 5.6 - - + -
131C TYR* 4.8 5.4 + - - +
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Residues in contact with ARG 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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28C GLN* 4.0 6.9 - - - +
96C ALA 2.9 8.1 + - - +
97C ARG 4.5 0.2 - - - -
98C LEU 3.8 0.6 - - - -
99C TRP* 1.3 90.9 - - + +
101C TRP* 1.3 113.2 + - + +
102C PRO* 3.5 10.6 - - - +
130C PRO* 3.2 35.9 + - + -
131C TYR* 3.2 50.2 - - + +
133C TYR 3.3 14.3 + - - -
134C GLU* 5.5 4.0 - - - +
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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