Contacts of the helix formed by residues 80 - 101 (chain H) in PDB entry 5T0G
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 GLY 80 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159G TYR* 5.3 1.1 - - - -
76H TYR* 3.9 22.8 + - - -
78H GLY 3.6 2.2 + - - -
79H MET* 1.3 70.7 - - - +
81H PRO* 1.3 65.0 - - - +
83H TYR* 2.6 29.1 + - - +
84H ARG* 3.0 15.0 + - - +
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Residues in contact with PRO 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G GLN* 3.3 16.0 + - - +
157G ALA* 3.2 33.4 - - + +
158G GLY 3.3 12.9 - - - +
159G TYR* 3.7 21.9 - - + -
79H MET* 3.6 13.0 - - + -
80H GLY* 1.3 88.9 - - - +
82H ASP* 1.3 62.3 + - - +
83H TYR 3.2 0.2 + - - -
84H ARG* 3.3 16.5 + - - +
85H VAL* 3.3 16.3 + - - +
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Residues in contact with ASP 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G PHE* 4.5 2.3 - - - -
123G GLN* 2.9 29.3 + - - +
127G GLN* 4.6 3.9 + - - -
79H MET* 3.2 28.1 + - + +
80H GLY 3.2 0.6 - - - -
81H PRO* 1.3 80.2 - - - +
83H TYR* 1.3 61.1 + - - +
85H VAL* 3.7 17.1 - - - +
86H LEU* 3.7 11.6 - - - +
128H ARG* 4.4 10.4 + - - -
129H PRO 4.3 3.8 - - - +
130H PHE* 3.8 29.0 - - + -
131H GLY 3.7 11.4 + - - +
132H VAL* 3.7 19.5 - - + +
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Residues in contact with TYR 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H HIS 5.4 3.4 - - - -
64H LYS 3.6 12.9 + - - -
66H GLU* 3.3 29.2 + - + +
74H LEU* 3.6 34.4 + - + +
76H TYR* 3.5 54.7 - + + -
79H MET 4.0 7.0 - - - +
80H GLY* 2.6 23.7 + - - +
82H ASP* 1.3 70.9 - - - +
84H ARG* 1.3 73.0 + - + -
85H VAL 3.2 0.3 + - - -
86H LEU* 3.2 21.2 + - + +
87H VAL* 3.0 40.0 + - + +
132H VAL* 3.7 8.4 - - + +
134H LEU* 4.0 3.1 - - + -
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Residues in contact with ARG 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G LYS* 3.5 20.9 + - - +
119G ALA* 3.2 31.9 + - - +
120G ASP* 2.6 29.6 + - - +
123G GLN* 5.0 1.8 - - - +
158G GLY 2.5 30.3 + - - -
159G TYR* 3.7 10.9 - - - +
160G TYR* 3.6 33.2 - - + -
80H GLY 3.0 12.3 + - - +
81H PRO* 3.3 8.2 + - - +
83H TYR* 1.3 81.9 - - + +
85H VAL* 1.3 66.4 + - - +
87H VAL* 3.1 18.8 + - - +
88H HIS* 3.1 14.6 + - - +
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Residues in contact with VAL 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G ASP* 5.0 7.6 + - + +
123G GLN* 3.5 29.8 - - + -
81H PRO 3.3 18.8 - - - +
82H ASP* 3.7 12.6 - - - +
84H ARG* 1.3 80.1 - - + +
86H LEU* 1.3 64.0 + - - +
88H HIS* 3.1 4.8 + - - +
89H ARG* 3.0 29.5 + - + +
121H TYR* 5.6 2.0 - - + +
130H PHE* 4.0 24.9 - - + -
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Residues in contact with LEU 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74H LEU* 5.5 1.8 - - + -
82H ASP 3.7 11.9 - - - +
83H TYR* 3.2 28.9 - - + +
85H VAL* 1.3 76.9 - - - +
87H VAL* 1.3 68.1 + - + +
89H ARG* 3.4 13.1 - - + +
90H ALA* 2.9 24.4 + - - +
114H VAL* 5.4 9.2 - - + +
118H MET* 4.4 11.4 - - + -
130H PHE* 4.3 28.7 - - + -
132H VAL* 4.7 8.7 - - + -
134H LEU* 3.6 46.4 - - + -
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Residues in contact with VAL 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H GLU* 3.6 26.2 - - + -
68H ILE* 3.9 12.0 - - + +
74H LEU* 5.5 0.9 - - + -
83H TYR* 3.0 59.9 + - + +
84H ARG* 3.1 11.4 + - - +
86H LEU* 1.3 81.0 - - + +
88H HIS* 1.3 66.6 + - - +
90H ALA* 3.0 1.9 + - - +
91H ARG* 3.0 39.5 + - + +
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Residues in contact with HIS 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ARG* 3.9 25.9 + - - -
120G ASP* 5.7 7.6 - - - +
84H ARG 3.1 8.1 + - - +
85H VAL* 3.8 7.0 - - - +
87H VAL* 1.3 80.5 - - - +
89H ARG* 1.3 63.6 + - - +
91H ARG* 3.3 13.2 + - + +
92H LYS* 3.0 52.7 + - + +
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Residues in contact with ARG 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H VAL* 3.0 18.3 + - + +
86H LEU* 3.4 22.9 - - + +
88H HIS* 1.3 78.9 - - - +
90H ALA* 1.3 59.8 + - - +
92H LYS* 3.1 11.8 + - - +
93H LEU* 2.9 38.1 + - + +
114H VAL* 5.8 6.1 - - + -
117H VAL* 3.3 36.0 - - + +
121H TYR* 6.1 4.2 - - - -
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Residues in contact with ALA 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H ILE* 3.9 24.2 - - + +
74H LEU* 6.5 0.7 - - + -
86H LEU 2.9 19.7 + - - +
87H VAL 3.8 3.1 - - - +
89H ARG* 1.3 73.6 - - - +
91H ARG* 1.3 57.8 + - - +
93H LEU* 3.4 11.0 - - + +
94H ALA* 2.9 31.7 + - - +
110H LEU* 5.2 7.1 - - + +
114H VAL* 4.1 22.0 - - + +
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Residues in contact with ARG 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H GLU* 2.3 44.2 + - - +
67H PRO* 3.3 22.1 + - - +
68H ILE* 3.7 36.3 + - + +
87H VAL* 3.0 24.3 + - + +
88H HIS* 3.5 13.7 - - + +
90H ALA* 1.3 77.1 - - - +
92H LYS* 1.3 63.0 + - + +
93H LEU 3.2 0.5 + - - -
94H ALA* 3.7 3.2 + - - +
95H GLN* 3.1 27.1 + - - +
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Residues in contact with LYS 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H HIS* 3.0 45.0 + - + +
89H ARG* 3.7 10.5 - - - +
91H ARG* 1.3 76.9 - - - +
93H LEU* 1.3 51.5 + - - +
94H ALA 3.6 0.2 - - - -
95H GLN* 3.7 10.6 + - - +
96H GLN* 2.7 41.0 + - - +
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Residues in contact with LEU 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H ARG* 2.9 25.8 + - + +
90H ALA* 2.9 10.0 + - - +
92H LYS* 1.3 74.5 - - - +
94H ALA* 1.3 67.3 + - - +
95H GLN 3.2 1.6 - - - -
96H GLN* 2.8 19.0 + - - +
97H TYR 4.3 3.3 + - - -
105H ILE* 4.9 2.9 - - + +
110H LEU* 4.5 11.7 - - + +
113H ARG* 3.5 57.9 - - + +
114H VAL* 4.0 21.3 - - + +
117H VAL* 4.8 12.1 - - + -
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Residues in contact with ALA 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H ILE* 5.0 7.4 - - + +
69H THR* 4.8 10.5 - - + +
90H ALA 2.9 14.1 + - - +
91H ARG* 3.7 3.6 + - - +
92H LYS 3.6 0.2 - - - -
93H LEU* 1.3 76.4 - - - +
95H GLN* 1.3 66.4 + - - +
96H GLN 3.4 0.4 - - - -
97H TYR* 3.2 6.6 + - - +
98H TYR* 3.0 26.9 + - + +
105H ILE* 3.8 34.4 - - + +
110H LEU* 5.1 5.6 - - + -
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Residues in contact with GLN 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H ILE 5.7 2.4 + - - -
91H ARG* 3.1 23.2 + - - +
92H LYS* 3.9 9.9 - - - +
93H LEU 3.2 1.8 - - - -
94H ALA* 1.3 81.6 - - - +
96H GLN* 1.3 64.3 + - - +
98H TYR* 3.3 20.4 + - - +
99H LEU* 2.8 46.3 + - + +
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Residues in contact with GLN 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H LYS* 2.7 33.1 + - - +
93H LEU* 2.8 21.0 - - - +
95H GLN* 1.3 77.8 - - - +
97H TYR* 1.3 56.3 + - - +
99H LEU* 4.2 9.4 - - + -
100H VAL* 2.9 41.6 + - + +
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Residues in contact with TYR 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H LEU 4.3 3.1 + - - +
94H ALA 3.2 11.2 + - - +
96H GLN* 1.3 78.1 - - - +
98H TYR* 1.3 57.6 + - - +
100H VAL* 5.1 0.7 - - - -
101H TYR* 3.0 66.0 + + + +
103H GLU* 3.4 32.1 + - - -
105H ILE* 3.5 42.6 - - + -
106H PRO* 3.5 23.6 - - + +
109H GLN* 4.1 13.9 - - + -
113H ARG* 4.1 21.3 - - - +
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Residues in contact with TYR 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H ALA* 3.0 16.3 + - + +
95H GLN* 3.9 22.9 - - - +
97H TYR* 1.3 76.7 - - - +
99H LEU* 1.3 65.4 + - + +
102H GLN* 2.8 52.7 + - - +
103H GLU* 3.9 26.2 - - - +
104H PRO* 4.5 10.8 - - + -
105H ILE* 5.8 2.5 - - + +
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Residues in contact with LEU 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H GLN* 2.8 34.1 + - + +
96H GLN* 3.7 9.6 - - + +
98H TYR* 1.3 87.1 - - + +
100H VAL* 1.3 67.1 + - + +
102H GLN* 3.0 23.4 + - - +
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Residues in contact with VAL 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H GLN* 2.9 23.6 + - + +
97H TYR* 4.4 1.1 - - - +
99H LEU* 1.3 82.0 - - + +
101H TYR* 1.3 90.4 + - + +
102H GLN* 3.8 3.3 + - - +
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Residues in contact with TYR 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H TYR* 3.0 66.4 + + + +
100H VAL* 1.3 100.4 - - + +
102H GLN* 1.3 69.6 + - - +
103H GLU* 3.3 12.2 + - + +
113H ARG* 5.3 5.3 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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