Contacts of the helix formed by residues 78 - 100 (chain C) in PDB entry 3UX9
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 ASP 78 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C MET* 5.5 2.5 + - - +
23C ARG* 3.4 20.3 + - + +
77C TRP* 1.3 73.5 - - - +
79C GLU* 1.3 68.5 + - - +
80C ASP* 3.6 11.8 + - - +
81C LEU* 3.6 43.3 + - + +
82C LEU* 3.0 26.9 + - - +
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Residues in contact with GLU 79 (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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77C TRP 3.5 3.0 + - - -
78C ASP* 1.3 77.3 + - - +
80C ASP* 1.3 66.7 + - - +
82C LEU* 3.7 3.7 - - - +
83C ASP* 3.0 23.9 + - - +
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Residues in contact with ASP 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ASP* 3.6 11.7 + - - +
79C GLU* 1.3 78.7 - - - +
81C LEU* 1.3 69.0 + - + +
83C ASP* 3.1 13.5 + - - +
84C LYS* 3.1 47.3 + - - +
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Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 4.4 12.9 - - + +
20C GLN* 3.5 45.1 - - + +
21C MET* 3.9 25.8 - - + -
78C ASP* 3.6 29.6 + - + +
79C GLU 3.4 0.2 - - - -
80C ASP* 1.3 82.3 - - + +
82C LEU* 1.3 59.5 + - - +
84C LYS* 3.2 18.7 + - + +
85C PHE* 2.9 28.8 + - - +
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Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C MET* 4.3 7.9 - - + -
68C PHE* 3.9 33.4 - - + +
73C SER* 3.8 22.2 - - - +
74C SER* 3.8 25.8 - - - -
77C TRP* 4.2 18.4 - - + +
78C ASP 3.0 18.8 + - - +
79C GLU* 3.7 3.8 - - - +
81C LEU* 1.3 80.2 - - - +
83C ASP* 1.3 57.7 + - - +
85C PHE* 3.4 8.2 + - + +
86C CYS* 2.9 38.8 + - - -
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Residues in contact with ASP 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C GLU* 3.0 13.0 + - + +
80C ASP* 3.1 11.1 + - - +
82C LEU* 1.3 74.5 - - - +
84C LYS* 1.3 63.8 + - + +
86C CYS* 3.1 4.9 + - - +
87C THR* 2.8 50.1 + - - +
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Residues in contact with LYS 84 (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 LEU* 3.9 24.9 - - + +
80C ASP* 3.4 41.9 + - - +
81C LEU* 3.5 12.9 - - + +
83C ASP* 1.3 80.9 + - - +
85C PHE* 1.3 63.6 + - - +
87C THR* 3.3 8.4 + - - -
88C GLU* 3.0 24.8 + - - +
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Residues in contact with PHE 85 (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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14C THR* 3.7 22.9 - - + -
17C LEU* 3.5 30.2 - - + +
18C LEU* 3.4 38.8 - - + -
21C MET* 4.0 19.5 - - - -
64C ILE* 4.3 9.9 - - + -
68C PHE* 3.9 31.4 - + + -
81C LEU 2.9 17.0 + - - +
82C LEU* 3.5 10.1 - - + +
83C ASP 3.2 0.2 - - - -
84C LYS* 1.3 78.9 - - - +
86C CYS* 1.3 61.7 + - - +
88C GLU* 3.4 3.3 + - - +
89C LEU* 3.1 49.7 + - + +
152C LEU* 5.3 0.7 - - + -
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Residues in contact with CYS 86 (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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65C PHE* 3.8 8.1 - - + -
68C PHE* 3.8 21.1 - - - -
69C THR* 3.7 30.5 - - + -
82C LEU* 2.9 33.9 + - - +
83C ASP* 3.7 5.4 - - - +
85C PHE* 1.3 75.8 - - - +
87C THR* 1.3 63.7 + - + +
89C LEU* 3.3 11.1 + - - +
90C TYR* 2.8 26.7 + - - +
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Residues in contact with THR 87 (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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83C ASP* 2.8 45.7 + - - +
84C LYS* 3.3 11.4 + - - -
86C CYS* 1.3 75.2 - - + +
88C GLU* 1.3 67.5 + - - +
90C TYR* 3.0 26.5 - - + +
91C GLN* 3.0 24.0 + - - +
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Residues in contact with GLU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ASP 4.8 5.1 - - - +
13C ARG* 3.6 31.9 + - + +
14C THR* 3.8 22.4 - - + -
17C LEU* 4.5 6.3 - - + -
84C LYS 3.0 14.7 + - - +
85C PHE 3.5 9.4 - - - +
86C CYS 3.2 0.2 - - - -
87C THR* 1.3 73.9 + - - +
89C LEU* 1.3 67.8 + - - +
90C TYR 3.0 0.5 + - - -
91C GLN* 3.0 24.9 + - - +
92C GLN* 2.9 32.8 + - + +
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Residues in contact with LEU 89 (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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14C THR* 4.0 11.9 - - + -
61C ILE* 3.9 17.2 - - + +
64C ILE* 4.0 22.0 - - + +
65C PHE* 3.9 32.1 - - + -
68C PHE* 5.0 0.7 - - + -
85C PHE* 3.1 43.9 + - + +
86C CYS* 3.5 14.8 - - - +
88C GLU* 1.3 78.8 - - - +
90C TYR* 1.3 57.8 + - - +
92C GLN* 3.3 24.3 + - - +
93C LEU* 2.8 34.4 + - - +
152C LEU* 5.8 2.2 - - + -
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Residues in contact with TYR 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C PHE* 4.5 22.2 - + + -
86C CYS 2.8 14.5 + - - +
87C THR* 3.0 20.4 - - + +
88C GLU 3.0 0.2 - - - -
89C LEU* 1.3 76.3 - - - +
91C GLN* 1.3 63.5 + - + +
93C LEU* 3.2 12.5 + - + +
94C ASN* 3.1 49.7 + - - -
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Residues in contact with GLN 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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87C THR* 3.0 23.8 + - - +
88C GLU* 3.7 24.7 + - - +
90C TYR* 1.3 74.0 - - + +
92C GLN* 1.3 68.8 + - - +
93C LEU 3.0 1.3 - - - -
94C ASN* 3.0 11.8 + - - +
95C ASP* 2.8 38.4 + - - +
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Residues in contact with GLN 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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9C LEU* 3.4 20.2 - - + +
10C ASP 3.6 15.9 + - - +
11C ASN* 3.0 26.9 + - - -
14C THR* 3.7 15.6 + - - +
61C ILE* 3.6 14.2 - - + +
88C GLU* 2.9 22.6 + - - +
89C LEU* 3.4 35.8 - - - +
91C GLN* 1.3 75.9 - - - +
93C LEU* 1.3 57.6 + - - +
95C ASP* 3.4 7.5 + - - +
96C LEU* 2.9 40.3 + - + +
152C LEU* 5.7 0.5 - - - +
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Residues in contact with LEU 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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58C HIS* 3.7 32.3 - - + +
61C ILE* 3.9 12.1 - - + -
62C GLN* 3.9 43.5 - - + +
65C PHE* 4.2 29.2 - - + -
89C LEU 2.8 14.5 + - - +
90C TYR* 3.2 15.5 - - + +
91C GLN 3.0 0.2 - - - -
92C GLN* 1.3 76.7 - - - +
94C ASN* 1.3 65.0 + - - +
96C LEU* 3.2 6.6 + - + +
97C GLU* 2.9 29.0 + - + +
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Residues in contact with ASN 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 TYR* 3.1 47.6 + - - +
91C GLN* 3.0 12.0 + - - +
93C LEU* 1.3 74.8 - - - +
95C ASP* 1.3 71.3 + - - +
97C GLU* 3.0 23.9 + - - +
98C ALA* 3.2 8.0 + - - +
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Residues in contact with ASP 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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91C GLN* 2.8 32.3 + - - +
92C GLN* 3.7 6.6 + - - +
94C ASN* 1.3 77.3 - - - +
96C LEU* 1.3 67.1 + - + +
97C GLU 3.0 0.9 + - - -
98C ALA* 3.4 16.9 + - - +
99C CYS* 3.8 11.6 - - - -
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Residues in contact with LEU 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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9C LEU* 4.3 26.0 - - + +
54C ILE* 3.4 23.3 - - + +
57C LEU* 4.8 1.3 - - + -
58C HIS* 3.8 32.8 - - + +
61C ILE* 3.6 32.5 - - + -
92C GLN 2.9 25.3 + - - +
93C LEU* 3.3 6.7 - - - +
95C ASP* 1.3 78.4 - - + +
97C GLU* 1.3 61.2 + - - +
99C CYS* 3.4 3.8 + - - -
100C VAL* 2.9 27.1 + - - +
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Residues in contact with GLU 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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58C HIS* 3.4 23.5 + - - +
62C GLN* 5.8 1.2 + - - -
93C LEU* 2.9 20.4 + - + +
94C ASN* 3.2 14.4 - - - +
95C ASP 3.0 0.4 - - - -
96C LEU* 1.3 75.9 - - - +
98C ALA* 1.3 70.2 + - - +
100C VAL* 3.4 20.4 + - + +
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Residues in contact with ALA 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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94C ASN 3.2 6.8 + - - +
95C ASP* 3.5 12.6 - - - +
97C GLU* 1.3 82.2 - - - +
99C CYS* 1.3 64.2 + - - +
100C VAL 3.0 4.0 + - - -
101C MET* 3.3 21.7 + - - +
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Residues in contact with CYS 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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54C ILE* 3.6 25.8 - - + +
95C ASP 3.8 14.8 - - - -
96C LEU* 3.4 2.5 + - - +
97C GLU 3.3 0.4 - - - -
98C ALA* 1.3 82.8 - - - +
100C VAL* 1.3 55.4 + - - +
101C MET* 3.0 31.7 + - + +
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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
----------------------------------------------------------
54C ILE* 4.0 21.5 - - + -
55C SER* 5.0 13.7 - - - -
58C HIS* 4.4 22.4 - - + +
96C LEU 2.9 23.6 - - - +
97C GLU* 3.8 15.5 - - + +
98C ALA 3.0 4.5 + - - -
99C CYS* 1.3 74.6 - - - +
101C MET* 1.3 56.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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