Contacts of the helix formed by residues 82 - 102 (chain C) in PDB entry 5T5W
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 LEU 82 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ALA* 3.5 40.8 - - + +
27C LEU* 3.8 24.7 - - + +
30C SER* 3.6 32.5 - - - +
75C THR* 4.3 12.3 - - + +
79C ASP* 3.1 32.6 + - + +
81C ALA* 1.3 76.6 - - - +
83C GLY* 1.3 59.3 + - - +
84C ASP 3.2 1.4 + - - -
85C VAL* 3.5 5.9 + - + +
86C LEU* 3.4 25.4 + - + +
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Residues in contact with GLY 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ALA* 4.0 25.5 - - - +
79C ASP 2.9 13.7 + - - -
80C PRO 3.0 7.7 + - - -
82C LEU* 1.3 75.4 - - - +
84C ASP* 1.3 63.2 + - - +
85C VAL 3.2 1.1 - - - -
86C LEU* 3.8 4.7 - - - -
87C ASP* 3.3 23.9 + - - +
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Residues in contact with ASP 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN* 5.0 9.7 + - - +
80C PRO 3.2 8.4 + - - +
81C ALA* 3.5 14.8 - - - +
82C LEU 3.2 1.0 - - - -
83C GLY* 1.3 78.6 - - - +
85C VAL* 1.3 69.2 + - + +
87C ASP* 4.2 8.4 + - - +
88C GLN 5.4 0.2 + - - -
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Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ALA 4.5 2.0 - - - +
22C ARG* 3.5 28.0 - - + +
23C ALA* 3.5 34.1 - - + +
26C ALA* 4.4 11.9 - - + -
81C ALA 5.5 2.2 - - - +
82C LEU* 3.5 8.5 + - + +
83C GLY 3.2 0.2 - - - -
84C ASP* 1.3 87.7 - - + +
86C LEU* 1.3 57.6 + - + +
87C ASP 3.2 5.5 + - - -
88C GLN* 4.0 2.3 + - - +
89C PRO* 3.1 21.3 - - - +
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Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ALA* 3.6 25.6 - - + -
26C ALA* 6.2 0.2 - - + -
27C LEU* 3.7 40.4 - - + -
72C LEU* 4.3 20.0 - - + +
75C THR* 4.2 16.6 - - + -
76C ALA* 4.3 15.5 - - + +
82C LEU* 3.4 24.5 + - + +
83C GLY* 3.7 5.8 + - - -
84C ASP 3.6 0.2 - - - -
85C VAL* 1.3 76.4 - - + +
87C ASP* 1.3 62.6 + - - +
88C GLN 3.5 0.4 - - - -
89C PRO* 3.4 7.2 - - + +
90C LEU* 2.9 35.9 + - + +
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Residues in contact with ASP 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 5.2 1.6 + - - -
58A SER* 3.0 26.8 + - - -
59A TYR* 2.8 37.5 + - - +
60A ARG* 2.9 21.6 + - + +
63A GLN* 5.2 3.3 - - - +
76C ALA* 6.2 1.1 - - - -
83C GLY 3.3 18.0 + - - +
84C ASP* 4.3 8.1 - - - +
85C VAL 3.2 2.2 - - - -
86C LEU* 1.3 78.2 - - - +
88C GLN* 1.3 68.3 + - - +
90C LEU* 3.3 1.3 + - - -
91C HIS* 3.2 18.5 + - - +
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Residues in contact with GLN 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER 4.3 11.5 + - - +
80A SER* 3.6 32.3 - - - +
15C ARG* 5.1 3.4 + - - +
16C GLU* 3.0 28.4 + - - +
19C ALA* 3.9 15.9 - - + +
22C ARG* 5.3 2.8 + - - -
85C VAL 4.0 1.9 + - - +
87C ASP* 1.3 80.9 + - - +
89C PRO* 1.3 72.0 - - + +
91C HIS* 3.3 8.3 + - + +
92C THR* 3.1 21.1 + - - -
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Residues in contact with PRO 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLU* 5.1 0.9 - - - +
19C ALA* 3.7 26.5 - - + +
20C PHE* 3.4 33.2 - - + -
23C ALA* 4.0 13.7 - - + -
72C LEU* 6.0 2.0 - - + -
85C VAL 3.1 22.2 - - - +
86C LEU* 3.4 9.2 - - + +
88C GLN* 1.3 94.3 - - + +
90C LEU* 1.3 60.8 + - + +
92C THR* 3.1 3.4 + - - -
93C LEU* 2.9 35.1 + - + +
145C LEU* 6.2 0.2 - - + -
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 3.5 38.3 - - + -
69C LEU* 3.5 30.3 - - + +
72C LEU* 3.7 32.8 - - + +
73C ASP* 3.6 26.2 - - + +
76C ALA* 5.2 3.8 - - + -
86C LEU* 2.9 42.0 + - + +
87C ASP* 3.6 2.0 - - - +
89C PRO* 1.3 76.2 - - + +
91C HIS* 1.3 63.2 + - - +
93C LEU* 3.4 2.4 + - + -
94C HIS* 2.9 25.6 + - - +
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Residues in contact with HIS 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU 5.7 2.8 + - - -
58A SER 6.0 1.2 - - - -
59A TYR* 3.7 25.6 + - + +
80A SER* 3.5 24.9 - - - -
82A TYR 2.7 26.0 + - - -
83A GLY* 4.5 2.0 - - - -
84A ASP 3.4 29.2 - - - -
85A HIS* 3.5 16.1 - + - -
87C ASP* 3.2 11.4 + - - +
88C GLN* 3.6 9.4 - - + +
90C LEU* 1.3 78.8 - - - +
92C THR* 1.3 65.1 + - - +
94C HIS* 3.5 4.7 + - - +
95C HIS* 3.1 20.6 + - + +
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Residues in contact with THR 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A SER* 3.3 8.7 + - - -
82A TYR* 4.3 17.7 - - + -
12C LEU* 6.0 1.8 - - + -
16C GLU* 3.0 41.8 + - + +
20C PHE* 4.0 13.9 - - + -
88C GLN 3.1 9.7 + - - -
89C PRO 3.1 7.8 + - - -
91C HIS* 1.3 76.6 - - - +
93C LEU* 1.3 67.6 + - - +
95C HIS* 2.9 6.3 + - - +
96C ILE* 2.9 40.3 + - + +
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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
----------------------------------------------------------
20C PHE* 3.8 26.0 - - + -
65C LEU* 3.7 27.3 - - + +
68C THR* 4.1 25.8 - - + -
69C LEU* 3.7 21.8 - - + +
72C LEU* 4.4 14.6 - - + -
89C PRO* 2.9 24.9 + - + +
90C LEU* 5.2 1.6 - - + -
92C THR* 1.3 71.8 - - - +
94C HIS* 1.3 63.8 + - - +
96C ILE* 3.4 8.0 + - + +
97C LEU* 2.9 24.8 + - - +
145C LEU* 4.4 6.5 - - + -
148C LEU* 4.9 1.6 - - + -
149C LEU* 3.9 20.4 - - + -
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Residues in contact with HIS 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 4.4 18.5 + + + -
69C LEU* 3.7 27.1 - - + +
90C LEU 2.9 17.0 + - - +
91C HIS* 3.6 6.1 - - - +
93C LEU* 1.3 78.7 - - - +
95C HIS* 1.3 61.0 + - + +
97C LEU* 3.2 5.1 + - + +
98C SER* 2.9 32.3 + - - -
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Residues in contact with HIS 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 3.8 17.1 - + + +
83A GLY* 3.6 41.1 + - - +
84A ASP* 5.6 2.7 - - - -
108A VAL* 6.0 4.0 - - + +
8C GLN* 4.7 4.9 - - - -
9C PHE* 3.9 16.7 - + - -
91C HIS* 3.1 14.6 + - + +
92C THR* 2.9 11.1 + - - +
94C HIS* 1.3 80.5 - - + +
96C ILE* 1.3 67.0 + - - +
98C SER* 3.1 11.0 + - - -
99C GLN* 2.9 53.4 + - + +
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Residues in contact with ILE 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 6.0 0.4 - - + -
6C ILE* 5.5 0.2 - - - +
9C PHE* 4.0 28.7 - - + -
12C LEU* 4.8 11.4 - - + -
65C LEU* 3.7 17.5 - - + -
92C THR* 2.9 37.0 + - + +
93C LEU* 3.8 8.5 - - + +
95C HIS* 1.3 76.1 - - - +
97C LEU* 1.3 53.2 + - - +
99C GLN* 3.0 3.6 + - - +
100C LEU* 2.7 37.1 + - + +
148C LEU* 6.1 0.9 - - + -
149C LEU* 4.4 14.8 - - + -
153C LEU* 3.8 43.1 - - + -
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Residues in contact with LEU 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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62C GLU* 3.7 34.3 - - + +
65C LEU* 3.6 18.0 - - + +
66C ALA* 3.9 17.3 - - - +
69C LEU* 3.8 24.5 - - + -
93C LEU 2.9 18.0 + - - +
94C HIS* 3.5 6.5 - - - +
96C ILE* 1.3 75.2 - - - +
98C SER* 1.3 63.3 + - - +
100C LEU* 3.2 2.6 + - + -
101C ARG* 3.0 68.2 + - - +
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Residues in contact with SER 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C HIS* 2.9 22.3 + - - -
95C HIS* 3.1 16.6 + - - -
97C LEU* 1.3 79.7 - - - +
99C GLN* 1.3 62.5 + - - +
101C ARG* 3.4 14.4 + - - +
102C ALA* 3.5 10.7 + - - +
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Residues in contact with GLN 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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4C CYS* 5.3 0.3 - - - -
5C HIS* 4.0 41.6 + - - +
6C ILE* 3.7 14.8 - - + +
8C GLN* 4.5 8.3 - - - +
9C PHE* 3.8 19.7 - - + -
95C HIS* 2.9 46.0 + - + +
96C ILE 3.6 6.3 - - - +
98C SER* 1.3 76.9 - - - +
100C LEU* 1.3 61.9 + - - +
102C ALA* 3.3 22.7 + - - +
103C CYS* 3.9 4.2 - - - -
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 3.9 29.1 - - + +
58C PRO* 4.3 13.5 - - + +
61C LEU* 3.7 24.0 - - + +
62C GLU* 3.6 35.4 - - + +
65C LEU* 4.3 13.9 - - + -
96C ILE* 2.7 20.7 + - + +
97C LEU* 3.6 7.4 - - + +
98C SER 3.2 0.2 - - - -
99C GLN* 1.3 70.7 - - - +
101C ARG* 1.3 62.2 + - + +
102C ALA 3.0 6.1 + - - -
103C CYS* 3.1 13.4 + - + +
104C ILE* 3.5 15.7 - - - +
153C LEU* 5.0 6.3 - - + -
156C VAL* 4.1 15.0 - - + -
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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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62C GLU* 3.6 31.1 + - + -
66C ALA* 4.2 7.7 - - - +
97C LEU* 3.0 50.8 + - - +
98C SER* 3.4 8.7 + - - +
100C LEU* 1.3 75.2 - - - +
102C ALA* 1.3 59.4 + - - +
103C CYS 3.3 1.0 + - - -
104C ILE* 3.6 24.4 + - + +
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C CYS* 3.6 24.0 + - - +
98C SER 3.5 8.9 + - - +
99C GLN* 3.3 18.5 + - - +
100C LEU 3.0 1.4 - - - -
101C ARG* 1.3 77.5 - - - +
103C CYS* 1.3 59.8 + - - +
104C ILE 3.4 2.7 + - - +
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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