Contacts of the helix formed by residues 81 - 105 (chain B) in PDB entry 1SFX
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 LYS 81 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ASP* 5.3 5.7 + - - -
29B LEU* 5.2 3.4 - - - -
64B ARG* 5.0 1.2 - - - +
79B ALA 3.9 1.0 + - - -
80B GLU* 1.3 75.9 + - - +
82B PRO* 1.3 74.6 - - + +
83B GLU* 4.1 16.5 + - + +
84B LYS* 3.0 36.9 + - + +
85B VAL* 3.1 9.9 + - - +
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Residues in contact with PRO 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 3.9 16.8 - - + -
104A PHE* 3.5 39.5 - - + +
25B TYR* 3.4 19.3 - - - +
29B LEU* 4.3 20.2 - - + -
81B LYS* 1.3 85.8 - - + +
83B GLU* 1.3 57.4 + - - +
85B VAL* 3.2 3.3 + - + +
86B LEU* 2.9 34.6 + - - +
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLU* 5.1 2.6 - - - +
104A PHE* 3.4 25.7 - - + +
105A THR* 3.6 22.2 - - - +
106A ASP* 3.9 24.4 + - - +
81B LYS* 3.2 18.5 + - + +
82B PRO* 1.3 77.3 - - - +
84B LYS* 1.3 57.6 + - - +
86B LEU* 3.6 8.9 + - + +
87B LYS* 3.0 28.9 + - - +
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Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLY* 2.8 36.3 + - - +
80B GLU* 3.3 36.3 + - + +
81B LYS* 3.0 29.4 + - + +
83B GLU* 1.3 75.4 - - - +
85B VAL* 1.3 64.9 + - - +
87B LYS* 3.3 9.6 + - + +
88B GLU* 2.9 48.7 + - + +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 4.1 12.3 - - + -
5A LEU* 3.5 28.9 - - + -
8A LEU* 4.5 8.5 - - + -
25B TYR* 3.7 32.3 - - + +
62B PHE* 3.5 32.7 - - + +
80B GLU* 3.9 4.7 - - + +
81B LYS 3.1 13.6 + - - +
82B PRO* 3.2 9.4 + - + +
84B LYS* 1.3 77.8 - - - +
86B LEU* 1.3 58.1 + - - +
88B GLU 3.4 0.2 + - - -
89B PHE* 2.9 28.2 + - - +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 4.2 10.8 - - + -
8A LEU* 4.1 29.6 - - + -
97A ILE* 4.6 12.4 - - + +
100A ILE* 3.9 18.6 - - + -
101A GLU* 3.9 44.2 - - + +
104A PHE* 4.0 24.0 - - + -
82B PRO 2.9 20.1 + - - +
83B GLU* 4.0 8.1 - - + +
85B VAL* 1.3 75.5 - - - +
87B LYS* 1.3 57.9 + - - +
89B PHE* 3.5 3.7 + - - +
90B LYS* 2.9 32.3 + - - +
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Residues in contact with LYS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLU 3.0 18.4 + - - +
84B LYS* 3.3 9.4 + - + +
86B LEU* 1.3 77.7 - - - +
88B GLU* 1.3 73.6 + - + +
90B LYS* 3.5 8.0 + - - +
91B SER* 3.1 27.8 + - - -
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ARG 3.7 21.0 - - - +
61B GLY* 4.1 6.9 - - - +
62B PHE* 3.9 4.7 - - + -
84B LYS* 2.9 54.8 + - + +
85B VAL 3.9 2.5 - - - +
87B LYS* 1.3 87.5 + - + +
89B PHE* 1.3 60.6 + - - +
91B SER* 3.3 8.9 + - - -
92B SER* 2.9 35.3 + - - +
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Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.8 41.7 - - + -
12A LEU* 4.1 18.8 - - + -
93A ILE* 4.7 4.9 - - + -
97A ILE* 3.9 15.3 - - + -
15B LEU* 3.9 17.7 - - + -
17B PHE* 4.2 8.5 - + - -
60B ARG* 3.5 29.2 - - - -
62B PHE* 4.0 12.2 - + + -
85B VAL 2.9 18.1 + - - +
86B LEU* 3.9 3.6 - - - +
88B GLU* 1.3 75.8 - - - +
90B LYS* 1.3 60.1 + - - +
92B SER* 3.2 5.7 + - - -
93B ILE* 2.9 59.5 + - + +
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Residues in contact with LYS 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 3.7 29.6 - - + +
97A ILE* 3.6 22.4 - - + +
98A GLU* 4.7 12.9 + - - +
101A GLU* 2.7 31.4 + - - -
86B LEU 2.9 17.6 + - - +
87B LYS* 3.7 7.2 - - - +
89B PHE* 1.3 78.4 - - - +
91B SER* 1.3 64.1 + - - +
93B ILE* 3.4 7.8 + - - +
94B LEU* 3.0 38.5 + - + +
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Residues in contact with SER 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LYS* 3.1 19.4 + - - -
88B GLU* 3.6 10.3 - - - -
89B PHE 3.3 0.2 - - - -
90B LYS* 1.3 77.5 - - - +
92B SER* 1.3 56.7 + - - +
94B LEU* 3.8 6.8 - - - +
95B GLY* 2.9 26.5 + - - -
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Residues in contact with SER 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 4.3 18.2 - - - -
60B ARG* 5.2 8.2 + - - +
62B PHE* 6.0 0.6 - - - -
88B GLU* 2.9 21.9 + - - +
89B PHE* 3.6 7.4 - - - -
91B SER* 1.3 77.8 - - - +
93B ILE* 1.3 62.1 + - - +
95B GLY* 3.3 3.2 + - - -
96B GLU* 3.0 27.9 + - - +
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.4 1.3 - - + -
89A PHE* 4.6 2.7 - - + -
93A ILE* 3.9 28.9 - - + -
94A LEU* 5.7 0.7 - - + -
97A ILE* 4.3 8.7 - - + -
12B LEU* 3.9 29.2 - - + -
15B LEU* 3.8 23.1 - - + +
89B PHE* 2.9 42.3 + - + +
90B LYS* 3.4 12.3 - - + +
92B SER* 1.3 76.6 - - - +
94B LEU* 1.3 67.6 + - + +
96B GLU* 3.2 2.6 + - + +
97B ILE* 3.0 38.6 + - + +
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LYS* 3.6 38.1 - - + -
93A ILE* 5.6 0.4 - - + -
94A LEU* 3.9 26.0 - - + -
90B LYS* 3.0 37.4 + - + +
91B SER* 3.8 5.6 - - - +
93B ILE* 1.3 78.9 - - + +
95B GLY* 1.3 56.7 + - - +
97B ILE* 3.3 7.5 + - + +
98B GLU* 2.9 48.1 + - - +
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Residues in contact with GLY 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B SER 2.9 16.4 + - - -
92B SER* 3.3 3.8 + - - -
94B LEU* 1.3 76.4 - - - +
96B GLU* 1.3 59.3 + - - +
98B GLU* 3.4 12.1 + - - +
99B ARG* 3.0 28.1 + - - +
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Residues in contact with GLU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 3.6 24.8 - - + +
14B LYS* 4.9 10.1 - - + +
15B LEU* 4.2 22.7 - - + -
92B SER 3.0 17.0 + - - +
93B ILE* 3.2 8.5 + - + +
95B GLY* 1.3 74.9 - - - +
97B ILE* 1.3 66.5 + - + +
99B ARG* 3.0 47.2 + - - +
100B ILE* 3.1 29.4 + - - +
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 4.1 21.5 - - + +
89A PHE* 3.8 31.9 - - + -
90A LYS* 3.7 44.2 - - + -
93A ILE* 4.1 10.5 - - + -
8B LEU* 4.4 9.0 - - + -
93B ILE* 3.0 27.9 + - + +
94B LEU* 3.8 5.6 - - + +
96B GLU* 1.3 75.7 - - + +
98B GLU* 1.3 58.1 + - - +
100B ILE* 3.2 9.5 + - - +
101B GLU* 2.8 37.1 + - + +
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LYS* 4.2 12.9 + - - +
94B LEU* 2.9 33.6 + - - +
95B GLY* 3.7 11.1 + - - +
97B ILE* 1.3 77.0 - - - +
99B ARG* 1.3 61.9 + - - +
101B GLU* 3.3 20.7 + - - +
102B LYS* 3.0 22.9 + - - +
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Residues in contact with ARG 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLU* 4.6 7.1 + - - -
10B LYS* 6.2 1.0 - - - +
11B ALA* 4.4 5.7 - - - +
14B LYS* 6.2 0.6 - - - +
95B GLY 3.0 13.8 + - - +
96B GLU* 3.0 44.8 + - - +
98B GLU* 1.3 74.2 - - - +
100B ILE* 1.3 81.4 + - - +
102B LYS* 3.2 9.6 + - + +
103B MSE 3.2 47.8 + - + +
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 3.8 20.0 - - + -
4B PRO* 4.6 2.5 - - + +
7B GLU* 3.7 44.6 - - + +
8B LEU* 4.0 15.9 - - + -
11B ALA* 4.0 15.9 - - + -
96B GLU 3.1 16.8 + - - +
97B ILE* 3.2 6.0 + - + +
99B ARG* 1.3 89.6 - - - +
101B GLU* 1.3 65.4 + - - +
103B MSE 3.1 18.0 + - - +
104B PHE* 3.1 33.3 - - + -
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Residues in contact with GLU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 4.9 5.5 - - - +
86A LEU* 3.6 38.9 - - + +
87A LYS* 4.3 4.2 + - - +
90A LYS* 3.2 33.6 + - - -
97B ILE* 2.8 19.6 + - - +
98B GLU* 3.4 22.3 - - - +
100B ILE* 1.3 77.0 - - - +
102B LYS* 1.3 56.3 + - - +
104B PHE* 3.2 6.5 + - - +
105B THR* 3.1 32.9 + - + +
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Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU 3.0 13.0 + - - +
99B ARG* 3.6 11.4 - - - +
100B ILE 3.1 0.4 - - - -
101B GLU* 1.3 74.0 - - - +
103B MSE 1.3 64.6 + - - +
104B PHE 3.1 2.3 + - - -
105B THR* 3.4 26.4 + - - +
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Residues in contact with MSE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B SER* 3.9 15.3 - - - +
7B GLU* 3.6 44.9 - - + +
99B ARG* 3.2 35.0 + - + +
100B ILE* 3.1 16.9 + - - +
102B LYS* 1.3 75.4 - - - +
104B PHE* 1.3 68.5 + - + +
105B THR 4.9 1.0 - - - -
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Residues in contact with PHE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 5.5 1.1 - - + -
82A PRO* 3.7 31.2 - - + -
83A GLU* 5.5 4.3 - - - +
86A LEU* 4.3 4.5 - - + -
2B SER* 3.6 30.7 - - - -
3B ASN* 3.5 7.9 - - - -
4B PRO* 3.3 36.8 - - + -
7B GLU* 4.6 4.3 - - + -
100B ILE* 3.1 41.7 - - + -
101B GLU* 3.2 6.1 + - - +
102B LYS 3.1 0.4 - - - -
103B MSE 1.3 86.2 - - + +
105B THR* 1.3 63.7 + - + +
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Residues in contact with THR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 5.9 7.2 - - + -
101B GLU* 3.1 13.3 + - + +
102B LYS* 3.4 32.2 + - - +
103B MSE 4.9 1.1 - - - -
104B PHE* 1.3 80.8 - - + +
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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