Contacts of the helix formed by residues 77 - 99 (chain F) in PDB entry 5LN3
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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ARG* 5.1 9.2 - - - +
159E SER* 4.2 21.5 - - - +
161E THR* 4.2 13.0 - - - +
76F GLY* 1.3 69.4 - - - +
78F THR* 1.4 70.7 + - - +
79F ALA* 3.4 14.3 + - + +
80F ASP* 3.9 18.0 + - - +
81F ALA* 4.0 3.6 + - - +
128F TYR 6.0 0.4 - - - +
130F VAL* 3.2 23.1 - - + +
436M GLN* 5.3 1.6 - - - +
437M TYR* 3.5 61.0 - - + +
438M TYR* 4.2 8.7 - - - +
439M ALA* 5.2 0.7 - - + +
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Residues in contact with THR 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E THR* 3.6 35.0 - - + +
162E PHE* 5.6 4.7 - - + -
60F GLN* 4.8 16.6 - - + +
61F LYS 5.7 1.5 + - - +
62F LYS* 3.9 19.1 + - - +
74F ILE* 5.7 4.9 - - - -
76F GLY 3.6 2.1 + - - -
77F LEU* 1.4 74.2 - - - +
79F ALA* 1.4 65.9 + - - +
81F ALA* 3.4 20.1 + - - +
82F ARG* 3.5 23.0 - - + +
439M ALA* 4.4 8.3 + - - +
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Residues in contact with ALA 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E LEU* 3.7 26.0 - - + -
159E SER 4.3 9.0 - - - +
160E GLY 3.4 21.1 - - - +
161E THR* 4.1 0.8 + - - +
77F LEU* 3.4 9.4 - - + +
78F THR* 1.4 78.7 - - - +
80F ASP* 1.4 66.5 + - - +
81F ALA 3.3 0.5 + - - -
82F ARG* 3.3 36.0 + - - +
83F LEU* 3.9 6.2 - - - +
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Residues in contact with ASP 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E LEU* 4.4 9.5 - - - +
77F LEU* 3.9 20.2 + - - +
78F THR 3.5 0.4 - - - -
79F ALA* 1.4 80.1 - - - +
81F ALA* 1.3 62.8 + - - +
83F LEU* 3.3 29.0 + - + +
84F LEU* 3.4 13.2 - - + +
126F ARG* 3.3 27.2 + - - -
128F TYR* 3.7 42.1 - - + +
130F VAL* 4.8 4.9 - - + -
437M TYR* 5.2 2.6 + - - -
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Residues in contact with ALA 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F LEU* 6.0 3.8 - - + -
72F ILE* 6.3 1.1 - - + -
74F ILE* 3.8 36.3 - - + -
77F LEU 4.0 5.9 + - - +
78F THR* 3.4 13.5 - - - +
79F ALA 3.2 0.2 - - - -
80F ASP* 1.3 77.7 - - - +
82F ARG* 1.4 62.0 + - + +
84F LEU* 3.3 15.2 + - - +
85F CYS* 3.2 31.2 + - - -
130F VAL* 4.8 1.3 - - + -
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Residues in contact with ARG 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E GLN* 3.8 10.9 + - - +
117E SER* 3.3 41.3 + - - -
118E ASN* 3.1 44.0 + - - +
121E LEU* 4.0 11.3 - - - +
160E GLY 4.4 2.6 + - - -
161E THR* 6.1 0.4 - - - +
162E PHE* 4.9 13.7 - - - -
78F THR* 3.5 24.0 - - + +
79F ALA* 3.3 32.7 + - - +
81F ALA* 1.4 72.1 - - + +
83F LEU* 1.3 63.3 + - - +
85F CYS* 3.4 15.7 + - - +
86F ASN* 2.9 28.9 + - - +
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Residues in contact with LEU 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E ASN* 4.2 30.5 - - + +
121E LEU* 3.8 32.8 - - + +
128E ALA 5.0 10.8 - - - +
129E ASP* 5.2 0.7 - - - +
79F ALA 3.9 6.7 - - - +
80F ASP* 3.4 16.6 - - + +
81F ALA 3.3 0.4 - - - -
82F ARG* 1.3 82.9 - - - +
84F LEU* 1.3 67.3 + - + +
85F CYS 3.5 0.2 + - - -
86F ASN* 3.7 15.6 + - - +
87F PHE* 3.6 26.7 + - + -
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Residues in contact with LEU 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F ILE* 6.0 0.7 - - + -
80F ASP* 3.4 16.8 - - + +
81F ALA* 3.3 9.3 + - - +
83F LEU* 1.3 77.2 - - + +
85F CYS* 1.3 58.7 + - - +
87F PHE* 3.2 28.6 + - + +
88F MET* 3.2 45.7 + - + +
112F ILE* 6.6 0.2 - - + -
116F THR* 5.5 6.5 - - + -
128F TYR* 4.9 29.2 - - + -
130F VAL* 4.1 26.5 - - + -
132F LEU* 5.3 11.2 - - + -
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Residues in contact with CYS 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F LEU* 4.3 13.5 - - - -
66F VAL* 4.8 4.6 - - + +
72F ILE* 4.2 24.5 - - - -
81F ALA* 3.2 23.3 + - - -
82F ARG* 3.6 12.3 - - - +
83F LEU 3.2 0.6 - - - -
84F LEU* 1.3 76.6 - - - +
86F ASN* 1.4 56.7 + - - +
88F MET* 3.4 10.7 + - - +
89F ARG* 2.9 65.7 + - - +
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Residues in contact with ASN 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026 MET* 4.1 23.3 - - + +
118E ASN* 4.4 14.3 - - - +
82F ARG* 2.9 25.0 + - - +
83F LEU* 3.8 11.2 - - - +
84F LEU 3.4 0.2 - - - -
85F CYS* 1.4 70.7 - - - +
87F PHE* 1.4 69.3 + - + +
89F ARG* 3.3 11.0 + - - +
90F GLN* 3.1 24.8 + - - +
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Residues in contact with PHE 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F LEU* 3.6 23.1 + - + -
84F LEU* 3.2 34.0 + - + +
86F ASN* 1.4 80.6 - - + +
88F MET* 1.3 56.6 + - - +
90F GLN* 3.5 5.1 + - - +
91F GLU* 3.0 42.3 + - - +
112F ILE* 4.7 5.6 - - + -
115F LYS* 3.7 21.1 - - - +
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Residues in contact with MET 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F VAL* 4.6 20.4 - - + -
72F ILE* 5.8 6.7 - - + -
84F LEU* 3.2 33.1 + - + +
85F CYS* 3.7 8.7 - - - +
86F ASN 3.3 0.2 - - - -
87F PHE* 1.3 77.8 - - - +
89F ARG* 1.4 64.9 + - - +
91F GLU* 3.3 10.0 + - - +
92F CYS* 3.1 30.2 + - - -
108F LEU* 5.0 11.1 - - + +
109F VAL* 6.5 1.1 - - - -
112F ILE* 3.9 40.8 - - + -
132F LEU* 5.0 16.4 - - + -
134F ILE* 5.5 11.7 - - + -
147F THR* 6.5 1.6 - - + -
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Residues in contact with ARG 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026 MET* 4.6 18.6 - - - -
1056 HIS* 3.6 46.2 + - + +
1066 SER* 5.8 0.2 - - - +
64F LEU* 4.0 15.4 - - - +
65F HIS* 3.1 31.9 + - - +
66F VAL* 3.6 38.7 + - + +
67F ASP* 5.2 0.2 - - - -
85F CYS* 2.9 44.4 + - - +
86F ASN* 3.3 10.7 + - - +
88F MET* 1.4 73.3 - - - +
90F GLN* 1.4 59.1 + - - +
92F CYS* 3.0 12.1 + - - +
93F LEU* 2.8 33.6 + - + +
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Residues in contact with GLN 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026 MET* 5.3 8.0 - - - +
86F ASN 3.1 17.5 + - - +
87F PHE* 3.8 5.2 - - - +
89F ARG* 1.4 74.7 - - - +
91F GLU* 1.4 63.8 + - + +
93F LEU* 2.9 46.2 + - - +
94F ASP* 3.1 23.6 + - - +
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Residues in contact with GLU 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F PHE* 3.0 22.1 + - - +
88F MET 3.7 7.6 - - - +
89F ARG 3.3 0.4 - - - -
90F GLN* 1.4 76.4 - - + +
92F CYS* 1.4 59.3 + - - +
94F ASP* 3.2 31.4 - - - +
95F SER* 3.3 8.3 + - - -
108F LEU* 4.1 22.5 - - + +
111F LEU* 4.5 13.5 - - - +
112F ILE* 3.4 23.0 - - - +
115F LYS* 3.1 29.0 + - - +
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Residues in contact with CYS 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F VAL* 5.1 0.7 - - - -
67F ASP* 3.1 41.1 - - - +
69F HIS* 6.1 2.2 - - + -
70F ILE* 4.4 4.0 - - - -
88F MET 3.1 25.0 + - - -
89F ARG* 3.0 11.5 + - - +
91F GLU* 1.4 72.7 - - - +
93F LEU* 1.3 64.0 - - + +
95F SER* 3.2 10.2 + - - -
96F ARG* 3.1 20.5 + - - +
102F PRO 5.7 5.4 - - - +
108F LEU* 4.1 22.0 - - - -
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Residues in contact with LEU 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986 ALA* 4.1 37.0 - - + +
1016 LYS* 4.4 26.2 - - + -
1026 MET* 4.6 21.5 - - + +
1056 HIS* 6.3 2.2 - - + -
89F ARG* 2.8 20.2 + - + +
90F GLN* 2.9 38.7 + - - +
92F CYS* 1.3 76.3 - - + +
94F ASP* 1.4 56.2 + - - +
96F ARG* 3.0 10.6 + - + +
97F PHE* 2.9 25.8 + - - +
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Residues in contact with ASP 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F GLN* 3.1 24.4 + - - +
91F GLU* 3.2 23.2 - - - +
93F LEU* 1.4 75.3 - - - +
95F SER* 1.4 70.2 + - - +
97F PHE* 4.1 8.3 - - - +
98F VAL* 2.8 45.9 + - + +
99F PHE* 5.5 2.6 - - - -
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Residues in contact with SER 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F GLU 3.6 9.2 - - - -
92F CYS* 3.2 13.9 + - - -
94F ASP* 1.4 83.7 + - - +
96F ARG* 1.4 58.9 + - - +
99F PHE* 3.0 22.4 + - - +
100F ASP 2.9 22.0 + - - -
101F ARG* 3.0 29.2 + - - +
102F PRO 3.6 12.3 + - - -
103F LEU* 3.6 16.6 - - - +
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Residues in contact with ARG 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946 LYS* 5.2 4.1 - - + +
1016 LYS* 5.0 19.3 - - + +
69F HIS* 4.6 9.7 + - - -
92F CYS 3.1 7.5 + - - +
93F LEU* 3.0 14.0 + - + +
95F SER* 1.4 78.6 - - - +
97F PHE* 1.3 65.1 + - - +
100F ASP* 3.0 66.0 + - - +
101F ARG* 3.3 11.0 + - - +
102F PRO* 3.2 38.2 - - - +
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Residues in contact with PHE 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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916 THR* 4.4 20.2 - - + -
946 LYS* 4.2 35.7 - - + +
956 ILE* 4.6 22.2 - - + -
1357 SER* 5.6 0.2 - - - -
1397 ARG* 3.6 43.2 - - + -
93F LEU 2.9 14.1 + - - +
94F ASP* 3.2 9.4 + - - +
96F ARG* 1.3 80.9 - - - +
98F VAL* 1.4 76.3 + - + +
100F ASP* 3.5 8.5 - - - +
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Residues in contact with VAL 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1357 SER* 3.5 24.3 - - - -
1367 TRP* 3.9 21.6 + - + +
1397 ARG* 4.5 17.8 - - + +
94F ASP* 2.8 29.7 + - + +
97F PHE* 1.4 95.3 - - + +
99F PHE* 1.4 84.5 - - + +
100F ASP* 3.6 0.3 - - - +
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Residues in contact with PHE 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157 MET* 6.6 0.2 - - - -
1287 TYR* 3.7 26.7 - + - -
1327 ALA* 3.7 37.1 - - + +
1357 SER* 4.6 1.0 + - - -
1367 TRP* 3.4 35.0 - + + -
94F ASP* 4.8 2.5 - - - -
95F SER* 3.0 19.1 + - - +
98F VAL* 1.4 94.2 - - + +
100F ASP* 1.3 68.9 + - - +
101F ARG* 3.3 55.1 + - - +
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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