Contacts of the helix formed by residues 129 - 154 (chain G) in PDB entry 1FSK
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 129 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G THR* 6.4 0.7 - - + -
126G HIS* 3.8 21.2 - - + -
127G GLU* 3.3 37.6 + - - +
128G VAL* 1.3 72.9 - - - +
130G ALA* 1.3 55.4 + - - +
131G GLU* 2.4 33.3 + - + +
132G GLN* 2.8 25.0 + - + +
133G VAL 3.8 1.9 + - - -
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Residues in contact with ALA 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G VAL 2.8 8.9 + - - +
129G LYS* 1.3 69.2 - - - +
131G GLU* 1.3 65.1 + - - +
133G VAL* 3.6 13.3 + - + +
134G LYS* 3.1 22.3 + - - +
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Residues in contact with GLU 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G LYS* 2.4 30.6 + - + +
130G ALA* 1.3 68.3 - - - +
132G GLN* 1.3 61.9 + - + +
134G LYS* 2.9 37.0 - - - +
135G ALA* 3.2 8.1 + - - +
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Residues in contact with GLN 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G PHE* 3.8 21.0 - - - -
90G PRO* 3.7 35.1 - - + +
95G LEU* 5.5 2.9 - - + -
98G ILE* 5.5 0.8 - - - +
120G TYR* 4.0 19.1 + - + -
128G VAL* 5.0 2.0 - - + -
129G LYS* 2.8 16.6 + - + +
131G GLU* 1.3 73.4 - - + +
133G VAL* 1.3 56.9 + - + +
134G LYS 2.6 17.1 + - - -
135G ALA* 2.8 22.5 + - - +
136G SER* 2.9 30.2 + - - +
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Residues in contact with VAL 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G TYR* 3.6 42.8 - - + +
120G TYR* 3.8 10.9 + - + +
128G VAL* 3.3 31.9 - - + +
130G ALA* 4.0 17.7 - - + +
131G GLU 3.5 0.4 - - - -
132G GLN* 1.3 74.3 - - - +
134G LYS* 1.3 60.4 + - - +
136G SER* 4.3 3.0 - - - -
137G LYS* 3.6 25.0 + - + +
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Residues in contact with LYS 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G ALA 3.1 11.9 + - - +
131G GLU* 2.9 27.8 + - - +
132G GLN 2.6 4.2 + - - -
133G VAL* 1.3 72.3 - - - +
135G ALA* 1.3 63.1 + - - +
137G LYS* 3.1 19.9 + - - +
138G GLU* 3.0 43.4 + - - +
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Residues in contact with ALA 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131G GLU 3.2 5.9 + - - +
132G GLN* 2.8 21.0 + - - +
134G LYS* 1.3 75.7 - - - +
136G SER* 1.3 55.3 + - - +
138G GLU* 2.8 12.5 + - - +
139G MET* 2.6 42.0 + - + +
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Residues in contact with SER 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G ILE* 5.8 1.7 - - - +
118G ASN* 5.0 12.6 - - - -
120G TYR* 2.9 26.7 + - - -
132G GLN* 2.9 20.7 + - - +
133G VAL* 4.3 4.3 - - - -
135G ALA* 1.3 76.7 - - - +
137G LYS* 1.3 60.1 + - - +
139G MET* 4.0 6.7 - - - +
140G GLY* 3.4 18.0 + - - -
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Residues in contact with LYS 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G THR* 3.6 40.7 - - + +
8G GLU 4.9 4.8 + - - -
133G VAL* 3.6 16.5 + - + +
134G LYS* 3.1 12.7 + - - +
135G ALA 2.9 0.8 - - - -
136G SER* 1.3 79.7 - - - +
138G GLU* 1.3 60.7 + - + +
140G GLY* 3.9 0.9 - - - -
141G GLU* 2.9 51.5 + - - +
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Residues in contact with GLU 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G LYS* 3.0 46.1 + - - +
135G ALA* 2.8 13.7 + - - +
137G LYS* 1.3 74.3 - - + +
139G MET* 1.3 71.8 + - - +
141G GLU* 3.5 7.2 - - + -
142G THR* 2.8 33.3 + - + +
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Residues in contact with MET 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G ALA* 4.3 21.3 - - + +
38G ILE* 5.5 2.5 - - - -
58G PHE* 4.3 29.4 - - + -
62G LEU* 4.9 12.1 - - + -
63G PRO* 6.2 4.0 - - + -
135G ALA* 2.6 26.4 + - + +
136G SER* 4.0 6.5 - - - +
138G GLU* 1.3 77.3 - - - +
140G GLY* 1.3 63.7 + - - +
141G GLU 3.0 0.2 + - - -
142G THR* 3.3 10.8 + - - -
143G LEU* 3.3 28.0 - - + +
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Residues in contact with GLY 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G PHE* 4.5 6.4 - - - -
116G ILE* 6.3 4.0 - - - -
136G SER 3.4 13.6 + - - -
137G LYS 3.9 0.9 - - - -
139G MET* 1.3 80.7 - - - +
141G GLU* 1.3 62.9 + - - +
143G LEU* 3.9 12.6 - - - +
144G LEU* 3.2 21.5 + - - +
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Residues in contact with GLU 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G THR* 4.1 10.3 + - - +
137G LYS* 2.9 46.5 + - - +
138G GLU* 2.9 15.2 + - + +
140G GLY* 1.3 75.2 - - - +
142G THR* 1.3 69.1 + - + +
144G LEU* 3.1 6.2 + - - +
145G ARG* 2.9 61.5 + - + -
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Residues in contact with THR 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G ALA* 5.1 1.0 - - - +
36G GLN* 5.0 8.8 + - - -
37G ALA* 4.8 7.3 - - - +
138G GLU* 2.8 23.7 + - + +
139G MET* 3.3 7.6 + - - +
141G GLU* 1.3 73.2 - - + +
143G LEU* 1.3 69.8 + - - +
145G ARG* 2.7 14.8 + - - +
146G ALA* 2.6 36.6 + - - +
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Residues in contact with LEU 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G PHE* 3.9 16.4 - - + -
30G PHE* 4.4 22.2 - - + -
34G ALA* 3.7 25.8 - - + -
37G ALA* 4.1 14.8 - - + -
38G ILE* 4.1 25.1 - - + -
139G MET* 3.3 26.0 - - + +
140G GLY* 3.9 9.6 - - - +
141G GLU 3.2 0.4 - - - -
142G THR* 1.3 86.4 + - - +
144G LEU* 1.3 64.6 + - - +
145G ARG 3.1 0.2 + - - -
146G ALA* 3.2 5.1 + - - +
147G VAL* 3.0 27.4 + - - +
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Residues in contact with LEU 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G THR* 3.7 17.9 - - + +
10G THR 4.4 1.6 - - - +
11G SER* 4.7 0.9 - - - +
18G LEU* 4.0 26.5 - - + -
22G PHE* 3.7 18.9 - - + -
114G LEU* 3.6 39.3 - - + -
140G GLY 3.2 10.8 + - - +
141G GLU* 3.1 10.9 + - - +
143G LEU* 1.3 78.8 - - - +
145G ARG* 1.3 83.6 + - - +
147G VAL* 3.4 1.3 + - + +
148G GLU* 2.9 37.6 + - + +
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Residues in contact with ARG 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G THR* 3.2 16.3 + - - -
10G THR 2.7 27.1 + - - -
141G GLU* 2.9 43.3 + - + +
142G THR* 2.7 17.1 + - - +
144G LEU* 1.3 82.9 - - - +
146G ALA* 1.3 63.2 + - - +
148G GLU* 2.6 51.4 + - - +
149G SER* 3.0 14.5 + - - -
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Residues in contact with ALA 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G VAL* 3.8 36.5 - - + +
34G ALA* 4.1 13.7 - - + -
36G GLN* 5.9 0.9 - - - +
142G THR* 2.6 17.0 + - - +
143G LEU* 3.7 5.4 - - - +
145G ARG* 1.3 71.2 - - - +
147G VAL* 1.3 58.0 + - - +
149G SER* 2.6 22.0 + - - -
150G TYR* 3.3 11.3 + - - +
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Residues in contact with VAL 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G LEU* 4.3 12.6 - - + -
21G ALA* 4.5 2.5 - - + -
22G PHE* 3.9 19.7 - - + +
29G LEU* 4.5 15.5 - - + -
30G PHE* 3.8 25.8 - - + -
33G VAL* 4.2 12.3 - - + -
143G LEU 3.0 18.1 + - - +
144G LEU* 3.8 3.1 - - - +
145G ARG 3.0 1.0 - - - -
146G ALA* 1.3 76.3 - - - +
148G GLU* 1.3 56.3 + - - +
149G SER 3.2 0.2 - - - -
150G TYR* 3.7 4.4 - - - +
151G LEU* 2.7 63.1 + - + +
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Residues in contact with GLU 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G SER* 2.6 41.7 + - - +
12G VAL* 3.8 8.0 + - - +
13G ILE* 3.8 16.5 - - + +
18G LEU* 5.3 0.2 - - + -
144G LEU* 2.9 21.1 + - + +
145G ARG* 2.6 53.6 + - - +
147G VAL* 1.3 76.7 - - - +
149G SER* 1.3 64.8 + - - +
151G LEU* 3.5 1.7 - - - +
152G LEU* 2.9 34.9 + - + +
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Residues in contact with SER 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G ARG 3.0 5.9 + - - -
146G ALA* 2.6 23.3 + - - -
148G GLU* 1.3 77.6 - - - +
150G TYR* 1.3 72.9 + - - +
152G LEU* 2.7 23.0 + - - +
153G ALA* 2.9 15.2 + - - +
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Residues in contact with TYR 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G LEU* 4.6 10.5 - - + -
32G LYS* 3.9 27.2 - - + +
33G VAL* 3.4 25.6 - - + -
146G ALA 3.3 14.1 + - - +
147G VAL* 3.7 4.7 - - + +
149G SER* 1.3 80.9 + - - +
151G LEU* 1.3 74.5 + - + +
152G LEU 3.0 0.3 + - - -
153G ALA* 4.5 2.5 - - - +
154G HIS* 3.0 72.6 + + + +
157G ALA* 4.6 5.1 - - + +
158G TYR* 4.4 20.5 + + - -
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Residues in contact with LEU 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G ILE* 3.7 32.1 - - + -
17G ARG* 2.5 49.7 + - - +
18G LEU* 4.0 10.1 - - + -
21G ALA* 3.6 17.7 - - + -
29G LEU* 5.9 0.4 - - + -
147G VAL* 2.7 43.9 + - + +
148G GLU 3.5 4.0 - - - +
150G TYR* 1.3 78.1 - - + +
152G LEU* 1.3 62.7 + - - +
154G HIS 3.5 9.0 - - - -
157G ALA* 4.8 2.7 - - + -
158G TYR* 3.8 30.5 - - + -
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Residues in contact with LEU 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G VAL* 4.3 25.4 - - + -
13G ILE* 4.5 6.5 - - + -
17G ARG* 6.0 0.7 - - - +
148G GLU* 2.9 26.6 + - + +
149G SER* 2.7 19.0 + - - +
151G LEU* 1.3 70.8 - - - +
153G ALA* 1.3 63.9 + - - +
154G HIS 3.1 2.4 + - - -
155G SER* 3.5 14.3 + - - +
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Residues in contact with ALA 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149G SER 2.9 11.0 + - - +
150G TYR* 3.8 4.3 - - - +
152G LEU* 1.3 76.5 - - - +
154G HIS* 1.3 82.2 + - + +
155G SER* 3.6 2.9 + - - -
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Residues in contact with HIS 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G ARG* 4.0 0.2 + - - -
150G TYR* 3.0 64.5 + + + +
151G LEU 3.5 7.3 - - - +
152G LEU 3.1 0.2 - - - -
153G ALA* 1.3 96.7 - - + +
155G SER* 1.3 50.4 + - - +
156G ASP* 2.8 13.4 + - - +
157G ALA* 2.8 36.4 + - + +
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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