Contacts of the helix formed by residues 129 - 154 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J THR* 6.4 0.7 - - + -
126J HIS* 3.8 21.2 - - + -
127J GLU* 3.3 37.1 + - - +
128J VAL* 1.3 72.6 - - - +
130J ALA* 1.3 55.5 + - - +
131J GLU* 2.4 32.5 + - + +
132J GLN* 2.8 24.6 + - + +
133J VAL 3.8 1.4 + - - -
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Residues in contact with ALA 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J VAL 2.8 9.3 + - - +
129J LYS* 1.3 68.6 - - - +
131J GLU* 1.3 66.3 + - - +
132J GLN 3.3 0.2 - - - -
133J VAL* 3.6 13.6 + - + +
134J LYS* 3.1 21.7 + - - +
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Residues in contact with GLU 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J LYS* 2.4 31.3 + - + +
130J ALA* 1.3 67.9 - - - +
132J GLN* 1.3 63.2 + - + +
134J LYS* 2.9 37.9 - - - +
135J ALA* 3.2 8.1 + - - +
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Residues in contact with GLN 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64J PHE* 3.8 20.8 - - - -
90J PRO* 3.7 35.1 - - + +
95J LEU* 5.5 2.5 - - + -
98J ILE* 5.5 1.0 - - - +
120J TYR* 4.0 19.5 + - + -
128J VAL* 5.0 2.0 - - + -
129J LYS* 2.8 17.7 + - + +
131J GLU* 1.3 72.9 - - + +
133J VAL* 1.3 55.4 - - + +
134J LYS 2.6 17.0 + - - -
135J ALA* 2.8 22.7 + - - +
136J SER* 2.9 30.9 + - - -
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Residues in contact with VAL 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J TYR* 3.6 44.4 - - + +
120J TYR* 3.8 11.4 + - - +
128J VAL* 3.3 31.9 - - + -
130J ALA* 4.0 17.7 - - - +
131J GLU 3.5 0.6 - - - -
132J GLN* 1.3 74.1 - - - +
134J LYS* 1.3 60.4 + - - +
136J SER* 4.3 2.8 - - - -
137J LYS* 3.6 24.7 + - + +
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Residues in contact with LYS 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130J ALA 3.1 11.7 + - - +
131J GLU* 2.9 27.5 + - - +
132J GLN 2.6 4.4 + - - -
133J VAL* 1.3 72.6 - - - +
135J ALA* 1.3 63.7 + - - +
137J LYS* 3.1 19.6 + - - +
138J GLU* 3.0 43.7 + - - +
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Residues in contact with ALA 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131J GLU 3.2 6.7 + - - +
132J GLN* 2.8 21.2 + - - +
134J LYS* 1.3 75.1 - - - +
136J SER* 1.3 55.7 + - - +
138J GLU* 2.8 13.1 + - - +
139J MET* 2.6 40.9 + - + +
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Residues in contact with SER 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98J ILE* 5.8 1.6 - - - +
118J ASN* 5.0 12.3 - - - -
120J TYR* 2.9 27.0 + - - -
132J GLN* 2.9 21.2 + - - +
133J VAL* 4.3 4.5 - - - -
135J ALA* 1.3 76.3 - - - +
137J LYS* 1.3 60.0 + - - +
139J MET* 4.0 6.2 - - - +
140J GLY* 3.4 18.5 + - - -
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Residues in contact with LYS 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J THR* 3.6 40.8 - - + +
8J GLU 4.9 4.2 + - - -
133J VAL* 3.6 16.3 + - + +
134J LYS* 3.1 11.8 + - - +
135J ALA 2.9 0.8 - - - -
136J SER* 1.3 79.5 - - - +
138J GLU* 1.3 60.8 + - + +
140J GLY 4.0 0.3 - - - -
141J GLU* 2.9 52.6 + - - +
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Residues in contact with GLU 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J LYS* 3.0 47.8 + - + +
135J ALA* 2.8 14.4 + - - +
137J LYS* 1.3 71.4 - - + +
139J MET* 1.3 72.0 + - - +
141J GLU* 3.5 7.2 - - + -
142J THR* 2.8 31.9 + - + +
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Residues in contact with MET 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J ALA* 4.3 21.1 - - + -
38J ILE* 5.5 2.2 - - - -
58J PHE* 4.3 29.6 - - + -
62J LEU* 4.9 11.9 - - + -
63J PRO* 6.3 4.3 - - + -
135J ALA* 2.6 25.8 + - + +
136J SER* 4.0 7.2 - - - +
138J GLU* 1.3 76.5 - - - +
140J GLY* 1.3 63.1 + - - +
141J GLU 3.0 0.2 + - - -
142J THR* 3.3 10.8 + - - -
143J LEU* 3.3 28.2 - - + +
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Residues in contact with GLY 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J PHE* 4.5 7.6 - - - -
116J ILE* 6.3 4.0 - - - -
136J SER 3.4 13.2 + - - -
137J LYS 4.0 0.9 - - - -
139J MET* 1.3 81.4 - - - +
141J GLU* 1.3 62.4 + - - +
143J LEU* 3.9 11.9 - - - +
144J LEU* 3.2 20.4 + - - +
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Residues in contact with GLU 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J THR* 4.1 10.4 + - - +
137J LYS* 2.9 44.9 + - - +
138J GLU* 2.9 15.4 + - + +
140J GLY* 1.3 75.0 - - - +
142J THR* 1.3 69.6 + - + +
144J LEU* 3.2 6.9 + - - +
145J ARG* 2.9 60.4 + - + -
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Residues in contact with THR 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J ALA* 5.1 0.9 - - - +
36J GLN* 5.0 9.0 + - - -
37J ALA* 4.8 7.3 - - - +
138J GLU* 2.8 22.8 + - + +
139J MET* 3.3 7.9 + - - +
141J GLU* 1.3 74.2 - - + +
143J LEU* 1.3 70.7 + - - +
145J ARG* 2.7 15.1 + - - +
146J ALA* 2.6 36.6 + - - +
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Residues in contact with LEU 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J PHE* 3.9 15.3 - - + -
30J PHE* 4.4 22.0 - - + -
34J ALA* 3.7 26.0 - - + -
37J ALA* 4.1 14.4 - - + -
38J ILE* 4.1 25.8 - - + -
139J MET* 3.3 26.2 - - + +
140J GLY* 3.9 10.3 - - - +
141J GLU 3.2 0.8 - - - -
142J THR* 1.3 86.2 + - - +
144J LEU* 1.3 64.6 + - - +
146J ALA* 3.2 5.1 + - - +
147J VAL* 3.0 27.5 + - - +
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Residues in contact with LEU 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J THR* 3.7 17.5 - - + +
10J THR 4.4 1.3 - - - +
11J SER* 4.7 1.3 - - - +
18J LEU* 4.0 26.7 - - + -
22J PHE* 3.7 18.3 - - + -
114J LEU* 3.6 39.0 - - + -
140J GLY 3.2 11.1 + - - +
141J GLU* 3.2 10.3 + - - +
143J LEU* 1.3 78.0 - - - +
145J ARG* 1.3 81.9 + - - +
147J VAL* 3.4 1.3 + - + +
148J GLU* 2.9 37.3 + - + +
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Residues in contact with ARG 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J THR* 3.2 16.3 + - - -
10J THR 2.7 27.7 + - - -
141J GLU* 2.9 43.7 + - + +
142J THR* 2.7 17.5 + - - +
144J LEU* 1.3 82.6 - - - +
146J ALA* 1.3 63.3 + - - +
148J GLU* 2.6 50.7 + - - +
149J SER* 3.0 14.0 + - - -
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Residues in contact with ALA 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J VAL* 3.8 36.3 - - + +
34J ALA* 4.1 12.8 - - + -
36J GLN* 5.9 0.9 - - - +
142J THR* 2.6 17.7 + - - +
143J LEU* 3.7 4.7 - - - +
145J ARG* 1.3 71.2 - - - +
147J VAL* 1.3 57.6 + - - +
149J SER* 2.6 21.7 + - - -
150J TYR* 3.3 11.6 + - - +
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Residues in contact with VAL 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J LEU* 4.3 12.6 - - + -
21J ALA* 4.5 1.8 - - + -
22J PHE* 3.9 18.6 - - + +
29J LEU* 4.5 15.0 - - + -
30J PHE* 3.8 26.0 - - + -
33J VAL* 4.2 13.2 - - + -
143J LEU 3.0 17.2 + - - +
144J LEU 3.8 3.8 - - - +
145J ARG 3.0 0.8 - - - -
146J ALA* 1.3 75.3 - - - +
148J GLU* 1.3 57.6 + - - +
149J SER 3.2 0.2 - - - -
150J TYR* 3.7 5.3 - - + +
151J LEU* 2.7 63.3 + - + +
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Residues in contact with GLU 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J SER* 2.6 41.2 + - - +
12J VAL* 3.8 8.3 + - - +
13J ILE* 3.8 15.2 - - + +
18J LEU* 5.3 0.2 - - + -
144J LEU* 2.9 21.9 + - + +
145J ARG* 2.6 52.8 + - - +
147J VAL* 1.3 76.5 - - - +
149J SER* 1.3 64.0 + - - +
151J LEU* 3.4 2.3 + - - +
152J LEU* 2.9 34.3 + - + +
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Residues in contact with SER 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J ARG 3.0 6.2 + - - -
146J ALA* 2.6 31.2 + - - -
148J GLU* 1.3 78.9 - - - +
150J TYR* 1.3 65.9 + - - +
152J LEU* 2.7 22.0 + - - +
153J ALA* 2.9 15.3 + - - +
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Residues in contact with TYR 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J LEU* 4.6 10.3 - - + +
32J LYS* 3.9 28.2 - - + +
33J VAL* 3.4 25.8 - - + -
146J ALA 3.3 14.7 + - - +
147J VAL* 3.7 4.5 - - + +
149J SER* 1.3 80.1 + - - +
151J LEU* 1.3 73.2 + - + +
152J LEU 3.0 0.3 + - - -
153J ALA* 4.6 2.5 - - - -
154J HIS* 3.0 74.6 + + + +
157J ALA* 4.6 4.0 - - + -
158J TYR* 4.4 20.1 + + - -
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Residues in contact with LEU 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J ILE* 3.7 31.9 - - + -
17J ARG* 2.5 51.9 + - + +
18J LEU* 4.0 10.3 - - + -
21J ALA* 3.6 17.7 - - + -
29J LEU* 5.9 0.4 - - + -
147J VAL* 2.7 43.8 + - + +
148J GLU 3.5 4.7 - - - +
150J TYR* 1.3 78.2 - - + +
152J LEU* 1.3 61.7 + - - +
154J HIS 3.5 8.9 - - - -
157J ALA* 4.8 2.7 - - + -
158J TYR* 3.8 30.3 - - + -
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Residues in contact with LEU 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J VAL* 4.3 24.9 - - + -
13J ILE* 4.5 6.7 - - + -
17J ARG* 4.8 1.1 - - - +
148J GLU* 2.9 26.0 + - + +
149J SER* 2.7 18.1 + - - +
151J LEU* 1.3 71.4 - - - +
153J ALA* 1.3 63.1 + - - +
154J HIS 3.1 3.4 + - - -
155J SER* 3.5 14.0 + - - -
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Residues in contact with ALA 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149J SER 2.9 10.9 + - - +
150J TYR* 3.8 4.0 - - - +
152J LEU* 1.3 75.9 - - - +
154J HIS* 1.3 83.2 + - + +
155J SER* 3.6 3.1 + - - -
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Residues in contact with HIS 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J ARG* 4.0 0.5 + - - -
150J TYR* 3.0 66.0 + + + +
151J LEU 3.5 7.1 - - - +
153J ALA* 1.3 95.9 - - + +
155J SER* 1.3 51.0 + - - +
156J ASP* 2.8 12.7 + - - +
157J ALA* 2.8 35.9 + - + +
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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