Contacts of the helix formed by residues 77 - 100 (chain m) in PDB entry 5GJQ
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 77 (chain m).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437M TYR* 5.9 3.4 - - + -
438M TYR* 3.6 40.6 - - + +
15l PHE* 4.3 12.1 - - + -
21l LEU* 3.7 19.5 - - + -
121l LEU* 3.0 37.7 - - + -
159l SER 6.3 0.2 - - - -
76m GLY* 1.3 70.0 - - - -
78m THR* 1.3 66.1 + - - +
79m ALA* 3.3 4.0 + - + -
80m ASP* 3.2 27.5 - - + +
81m ALA* 3.1 19.6 + - - +
126m ARG* 3.7 2.7 - - - +
129m GLY* 2.8 17.8 + - - +
130m VAL* 3.9 2.5 - - - +
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Residues in contact with THR 78 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437M TYR 4.9 2.2 - - - +
438M TYR* 5.7 0.6 - - - +
439M ALA* 3.9 28.5 - - - +
160l GLY 5.1 0.5 - - - -
161l THR* 3.4 32.7 + - + +
60m GLN* 3.9 24.4 + - - +
74m ILE* 4.3 14.4 - - + -
76m GLY 3.2 1.3 + - - +
77m LEU* 1.3 69.1 - - - +
79m ALA* 1.3 61.2 + - - +
81m ALA* 3.2 8.9 + - - +
82m ARG* 2.9 38.6 + - - +
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Residues in contact with ALA 79 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120l ALA* 4.8 10.3 - - - +
121l LEU* 3.6 36.8 - - + -
159l SER 4.8 8.5 - - - -
160l GLY* 4.9 3.6 - - - -
161l THR* 5.3 0.6 + - - -
77m LEU* 4.0 2.7 - - + -
78m THR* 1.3 83.1 + - - +
80m ASP* 1.3 58.2 + - - +
82m ARG* 3.2 18.3 + - - +
83m LEU* 3.0 28.9 + - - +
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Residues in contact with ASP 80 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121l LEU* 3.6 5.5 - - - +
77m LEU* 3.2 22.2 + - + +
78m THR 3.4 0.4 - - - -
79m ALA* 1.3 74.5 - - - +
81m ALA* 1.3 65.7 + - - +
83m LEU* 3.3 10.1 - - - +
84m LEU* 3.0 29.3 + - - +
126m ARG* 2.6 35.2 + - - -
128m TYR* 3.4 20.1 - - + -
129m GLY* 2.7 26.0 + - - +
130m VAL* 3.8 15.7 - - + -
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Residues in contact with ALA 81 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64m LEU* 4.8 3.1 - - + +
72m ILE* 5.0 2.6 - - - +
74m ILE* 3.7 39.9 - - + -
77m LEU 3.1 14.8 + - - +
78m THR 3.3 9.2 - - - +
80m ASP* 1.3 78.6 - - - +
82m ARG* 1.3 52.0 + - - +
84m LEU* 3.5 3.6 + - - +
85m CYS* 2.8 35.4 + - - +
130m VAL* 3.8 15.9 - - + +
132m LEU* 5.3 2.2 - - - +
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Residues in contact with ARG 82 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114l GLN* 3.7 25.1 - - - -
117l SER* 3.1 39.3 + - - -
118l ASN* 1.9 40.5 + - - +
160l GLY* 4.0 12.9 - - - -
161l THR* 5.3 0.6 - - - +
162l PHE* 4.2 15.8 - - - -
64m LEU* 5.4 7.6 - - + -
78m THR* 2.9 20.9 + - - +
79m ALA* 3.7 16.9 + - - +
81m ALA* 1.3 71.5 - - - +
83m LEU* 1.3 59.6 + - - +
85m CYS* 4.0 6.7 - - - -
86m ASN* 2.9 41.6 + - - +
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Residues in contact with LEU 83 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118l ASN 6.1 0.4 - - - +
122l GLN* 4.9 15.0 - - - +
79m ALA 3.0 13.4 + - - +
80m ASP* 3.3 15.7 - - - +
82m ARG* 1.3 77.1 - - - +
84m LEU* 1.3 62.7 + - - +
86m ASN* 3.2 10.5 + - + +
87m PHE* 3.0 21.8 + - - +
115m LYS* 5.2 6.6 - - - -
128m TYR* 3.5 33.2 - - + +
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Residues in contact with LEU 84 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80m ASP 3.0 12.7 + - - +
81m ALA 3.8 3.1 - - - +
83m LEU* 1.3 80.2 - - - +
85m CYS* 1.3 57.6 + - - +
87m PHE* 3.2 8.7 + - + +
88m MET* 2.9 35.6 + - + +
112m ILE* 4.2 12.1 - - + -
115m LYS* 4.2 23.6 - - + -
116m THR* 4.0 31.2 - - + -
128m TYR* 4.2 16.8 - - + -
130m VAL* 3.9 22.9 - - + +
132m LEU* 3.9 29.2 - - + -
147m THR* 5.6 1.3 - - - +
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Residues in contact with CYS 85 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64m LEU* 3.7 36.1 - - + -
65m HIS 4.5 2.0 - - - -
66m VAL* 4.6 4.0 - - - -
72m ILE* 4.1 7.6 - - + +
81m ALA 2.8 22.8 + - - +
82m ARG* 3.6 9.4 - - - +
84m LEU* 1.3 73.6 - - - +
86m ASN* 1.3 56.5 + - - +
88m MET* 3.2 12.8 + - - +
89m ARG* 3.0 64.8 + - - +
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Residues in contact with ASN 86 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118l ASN* 4.9 15.2 + - - +
82m ARG* 2.9 28.8 + - - +
83m LEU* 3.6 11.7 + - + +
85m CYS* 1.3 75.0 - - - +
87m PHE* 1.3 59.1 + - - +
89m ARG* 3.4 27.0 + - - +
90m GLN* 2.9 29.7 + - - +
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Residues in contact with PHE 87 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83m LEU 3.0 12.9 + - - +
84m LEU* 3.4 11.7 - - + +
86m ASN* 1.3 77.0 - - - +
88m MET* 1.3 63.5 + - + +
90m GLN* 3.3 10.0 + - + +
91m GLU* 2.9 60.9 + - + +
108m LEU* 5.3 1.3 - - + -
111m LEU* 4.1 35.7 - - + -
112m ILE* 4.4 8.3 - - + -
115m LYS* 3.5 48.5 - - + -
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Residues in contact with MET 88 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66m VAL* 3.7 17.3 - - + -
70m ILE* 4.7 0.2 - - + -
72m ILE* 3.4 47.6 - - + -
84m LEU 2.9 23.2 + - - +
85m CYS* 3.2 6.7 + - - +
87m PHE* 1.3 70.2 - - + +
89m ARG* 1.3 67.5 + - - +
91m GLU* 3.3 1.9 + - - +
92m CYS* 3.0 29.1 + - - -
108m LEU* 3.6 31.9 - - + -
112m ILE* 3.4 39.3 - - + -
132m LEU* 4.2 8.3 - - - -
134m ILE* 4.2 8.7 - - + -
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Residues in contact with ARG 89 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114l GLN* 6.1 1.2 + - - -
64m LEU* 4.6 9.1 - - - +
65m HIS* 2.9 31.9 + - - +
66m VAL* 3.8 29.6 - - - +
85m CYS* 3.0 39.1 + - - +
86m ASN* 3.6 23.3 + - - +
88m MET* 1.3 77.0 - - - +
90m GLN* 1.3 61.4 - - - +
92m CYS* 3.3 4.2 + - - +
93m LEU* 2.9 31.6 + - + +
77t HIS* 3.8 49.3 + - + +
78t SER* 5.6 0.8 - - - +
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Residues in contact with GLN 90 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86m ASN 2.9 18.2 + - - +
87m PHE* 3.4 11.0 - - + +
89m ARG* 1.3 77.4 - - - +
91m GLU* 1.3 59.9 + - + +
93m LEU* 3.2 20.2 + - - +
94m ASP* 2.8 63.3 + - - +
74t MET* 4.5 13.2 - - - +
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Residues in contact with GLU 91 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87m PHE* 2.9 52.9 + - + +
88m MET 3.8 4.3 - - - +
90m GLN* 1.3 75.4 - - + +
92m CYS* 1.3 60.9 - - - +
94m ASP* 3.3 19.4 + - - +
95m SER* 3.0 27.5 + - - -
103m LEU* 4.0 10.3 - - + +
108m LEU* 4.3 4.7 - - + -
111m LEU* 3.5 29.0 - - + +
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Residues in contact with CYS 92 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66m VAL* 3.9 17.3 - - - +
67m ASP* 3.3 32.5 - - + +
69m HIS* 4.6 3.8 - - - -
70m ILE* 4.7 0.7 - - - -
88m MET 3.0 21.3 + - - +
89m ARG* 3.6 6.5 - - - +
91m GLU* 1.3 78.1 - - - +
93m LEU* 1.3 56.9 + - + +
95m SER* 3.2 5.0 + - - -
96m ARG* 2.9 32.5 + - - +
103m LEU* 4.1 25.9 + - + +
108m LEU* 4.2 10.3 - - - -
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Residues in contact with LEU 93 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67m ASP* 6.5 0.2 - - - -
89m ARG* 2.9 23.9 + - + +
90m GLN* 3.5 21.3 - - - +
92m CYS* 1.3 76.1 - - + +
94m ASP* 1.3 62.6 + - - +
96m ARG* 3.2 7.0 + - - +
97m PHE* 2.8 31.4 + - - +
70t ALA* 4.0 33.4 - - + +
73t LYS* 4.2 29.4 - - + +
74t MET* 3.3 39.9 - - + -
77t HIS* 6.3 2.0 - - + -
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Residues in contact with ASP 94 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90m GLN* 2.8 52.4 + - - +
91m GLU* 3.5 23.7 - - - +
93m LEU* 1.3 77.5 - - - +
95m SER* 1.3 56.5 + - - +
97m PHE* 3.2 7.1 + - - +
98m VAL* 2.9 36.6 + - + +
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Residues in contact with SER 95 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91m GLU 3.0 13.6 + - - -
92m CYS 3.4 8.1 - - - -
94m ASP* 1.3 77.6 - - - +
96m ARG* 1.3 58.5 + - - +
98m VAL* 5.0 0.2 - - - -
99m PHE* 3.0 37.9 + - - +
100m ASP 3.6 0.5 + - - -
101m ARG* 3.3 32.1 + - - +
103m LEU* 3.6 30.4 - - - +
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Residues in contact with ARG 96 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67m ASP* 2.9 38.0 + - - +
68m ASN* 4.3 16.6 - - - +
69m HIS* 3.8 6.3 + - - +
92m CYS 2.9 17.5 + - - +
93m LEU* 3.2 5.6 + - - +
95m SER* 1.3 76.1 - - - +
97m PHE* 1.4 60.3 + - - +
100m ASP* 2.9 33.8 + - - +
101m ARG* 4.1 12.3 - - - +
102m PRO* 3.4 42.0 - - + +
66t LYS* 5.1 4.3 - - - +
73t LYS* 3.5 29.6 - - - +
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Residues in contact with PHE 97 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93m LEU* 2.8 15.6 + - + +
94m ASP* 3.4 11.7 - - - +
96m ARG* 1.4 79.9 - - - +
98m VAL* 1.3 68.0 + - + +
63t THR* 4.4 14.1 - - + -
66t LYS* 4.0 25.9 - - + +
67t ILE* 3.6 40.4 - - + -
70t ALA* 5.2 9.2 - - + -
90u SER* 4.0 3.3 + - - -
94u ARG* 3.8 39.6 - - + +
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Residues in contact with VAL 98 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94m ASP* 2.9 18.6 + - + +
95m SER* 5.0 0.2 - - - -
97m PHE* 1.3 91.9 - - + +
99m PHE* 1.3 74.8 + - + +
90u SER* 2.8 14.6 + - - +
91u TRP* 3.0 53.0 + - + +
94u ARG* 4.4 10.5 - - + -
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Residues in contact with PHE 99 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95m SER* 3.0 20.7 + - - +
98m VAL* 1.3 88.9 - - + +
100m ASP* 1.3 69.7 + - - +
101m ARG* 3.0 34.6 + - + +
70u MET* 3.0 38.6 - - + -
83u TYR* 3.2 33.9 - + - -
87u ALA* 3.3 39.4 - - + +
88u ILE* 5.4 1.3 - - + -
90u SER* 3.5 5.6 - - - -
91u TRP* 3.9 17.7 - + + -
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Residues in contact with ASP 100 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95m SER 3.6 0.8 + - - -
96m ARG* 2.9 27.7 + - - +
99m PHE* 1.3 78.2 - - - +
101m ARG* 1.3 58.5 + - - +
102m PRO* 4.6 1.6 - - - +
66t LYS* 5.2 11.9 - - - -
86u ARG* 3.9 24.2 + - + +
90u SER* 3.6 16.7 + - - +
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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