Contacts of the helix formed by residues 130 - 152 (chain B) in PDB entry 3SF4
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 ASP 130 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 5.3 12.3 - - + +
125B SER* 2.7 30.0 + - - +
126B ARG* 5.3 0.2 - - - -
128B LEU* 3.2 12.2 - - + +
129B ASN* 1.3 70.3 - - - +
131B LYS* 1.3 59.2 + - - +
132B VAL* 3.2 23.4 - - - +
133B GLY* 3.3 19.8 - - - -
134B GLU* 3.0 24.8 + - - +
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Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ASN* 3.3 19.2 + - - +
130B ASP* 1.3 70.9 + - - +
132B VAL* 1.3 67.2 + - + +
134B GLU* 3.2 28.6 + - - +
135B ALA* 3.0 18.5 + - - +
184B LEU* 3.5 28.1 - - + +
188B LEU* 4.0 22.4 - - + -
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP* 3.2 15.9 + - - +
131B LYS* 1.3 78.1 - - + +
133B GLY* 1.3 67.0 + - - +
135B ALA* 3.4 3.8 + - - +
136B ARG* 3.1 44.4 + - - +
188B LEU* 4.2 23.8 - - + -
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Residues in contact with GLY 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B HIS* 3.5 18.4 - - - -
125B SER* 3.6 10.7 + - - -
130B ASP* 3.3 21.3 + - - -
131B LYS 3.2 0.4 - - - -
132B VAL* 1.3 82.9 - - - +
134B GLU* 1.3 64.9 + - - +
136B ARG* 3.5 7.8 + - - +
137B ALA* 3.2 16.6 + - - +
48E GLN* 5.4 4.0 - - - -
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 3.7 18.3 - - + +
125B SER* 3.5 14.0 - - - -
126B ARG* 2.7 41.7 + - + +
130B ASP 3.0 16.1 + - - +
131B LYS* 3.3 34.9 + - - +
133B GLY* 1.3 73.8 - - - +
135B ALA* 1.3 67.6 + - - +
137B ALA* 3.0 4.9 + - - +
138B LEU* 3.0 30.2 + - + +
184B LEU* 3.4 16.9 - - + +
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LYS 3.0 11.9 + - - +
132B VAL* 3.5 13.0 - - - +
134B GLU* 1.3 76.0 - - - +
136B ARG* 1.3 63.9 + - + +
138B LEU* 3.0 8.6 + - - +
139B TYR 2.9 18.9 + - - -
181B ASN* 3.0 12.6 - - - +
184B LEU* 3.5 20.1 - - + +
185B VAL* 4.0 26.5 - - + -
188B LEU* 4.5 3.4 - - + -
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B HIS* 4.6 5.2 - - - +
132B VAL* 3.1 31.2 + - - +
133B GLY* 3.8 5.4 - - - +
134B GLU 3.3 0.2 - - - -
135B ALA* 1.3 77.3 - - + +
137B ALA* 1.3 52.7 + - - +
139B TYR* 3.3 9.5 + - - +
140B ASN* 2.7 44.6 + - - +
46E VAL* 5.2 9.9 - - + -
48E GLN* 2.6 53.5 - - - +
62E LEU* 3.7 38.3 - - + +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B CYS* 4.1 3.9 - - - +
121B HIS* 3.8 13.2 + - + -
122B LEU* 3.7 37.7 - - + +
133B GLY 3.2 12.8 + - - +
134B GLU 3.0 9.5 + - - +
136B ARG* 1.3 73.4 - - - +
138B LEU* 1.3 67.0 + - - +
140B ASN* 3.3 11.6 + - - +
141B LEU* 2.9 30.6 + - - +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 3.8 24.7 - - + -
126B ARG* 4.2 1.8 - - - +
134B GLU* 3.0 23.2 + - + +
135B ALA* 3.0 6.8 + - - +
137B ALA* 1.3 77.4 - - - +
139B TYR* 1.3 61.9 + - - +
141B LEU* 3.3 1.9 + - - +
142B GLY* 3.0 18.9 + - - -
177B PHE* 3.5 35.5 - - + +
180B GLU* 3.7 51.6 - - + +
181B ASN* 3.8 15.0 - - + +
184B LEU* 4.2 18.2 - - + -
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Residues in contact with TYR 139 (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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135B ALA 2.9 6.5 + - - +
136B ARG* 3.5 11.9 - - - +
138B LEU* 1.3 77.5 - - - +
140B ASN* 1.3 59.2 + - - +
142B GLY* 3.2 3.6 + - - -
143B ASN* 3.0 57.3 + - - +
178B TYR* 3.9 12.1 - + - -
181B ASN* 3.7 33.1 + - - +
193B ALA 5.2 0.9 - - - -
196B ARG* 3.5 44.6 - - + +
197B ALA* 4.2 3.1 - - - -
200B ASN* 2.9 24.1 + - - -
42E GLU* 3.9 4.0 - - - +
43E CYS 2.9 20.3 + - - -
46E VAL* 3.4 26.5 - - + -
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Residues in contact with ASN 140 (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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99B GLY* 4.8 4.4 - - - -
103B ASN* 3.6 22.0 + - - +
118B CYS* 3.9 19.5 - - - +
121B HIS* 3.8 17.4 + - - -
136B ARG* 2.7 31.9 + - - +
137B ALA* 3.6 9.4 - - - +
139B TYR* 1.3 74.0 - - - +
141B LEU* 1.3 61.1 + - - +
143B ASN* 3.1 10.7 + - - +
144B VAL* 2.8 33.9 + - + +
46E VAL* 3.7 29.7 + - - +
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ILE* 3.9 32.5 - - + +
118B CYS* 3.7 30.7 - - + +
119B GLN* 4.0 8.7 - - - +
122B LEU* 3.9 21.5 - - + -
137B ALA 2.9 20.5 + - - +
138B LEU* 3.3 4.5 + - - +
140B ASN* 1.3 75.5 - - - +
142B GLY* 1.3 63.6 + - - +
144B VAL* 3.1 5.8 + - + +
145B TYR* 3.0 33.6 + - + -
177B PHE* 3.5 42.8 - - + -
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Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU 3.0 11.3 + - - -
139B TYR 3.6 4.0 - - - -
140B ASN 3.2 0.2 - - - -
141B LEU* 1.3 77.9 - - - +
143B ASN* 1.3 55.9 + - - +
145B TYR 3.5 0.3 + - - -
146B HIS* 2.9 25.1 + - - +
174B ALA* 3.5 13.1 - - - +
177B PHE* 3.6 18.3 - - - +
178B TYR* 3.2 24.2 + - - -
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Residues in contact with ASN 143 (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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103B ASN* 5.6 1.1 - - - +
106B LYS* 3.7 7.2 + - + +
139B TYR* 3.0 45.5 + - - -
140B ASN* 3.1 10.9 + - - +
142B GLY* 1.3 74.6 - - - +
144B VAL* 1.3 64.0 + - - +
146B HIS* 3.6 2.3 - - - +
147B ALA* 3.0 25.1 + - - +
178B TYR* 2.5 26.7 + - - -
200B ASN* 3.1 16.5 + - - -
43E CYS 3.6 4.0 + - - -
44E MET* 3.6 41.5 + - + +
46E VAL* 4.8 2.2 - - - +
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Residues in contact with VAL 144 (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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102B GLY 4.9 1.1 - - - +
103B ASN* 5.9 2.2 - - - +
106B LYS* 3.8 19.7 - - + -
111B PHE* 3.9 15.7 - - + +
114B ALA* 3.6 26.9 - - + -
115B ILE* 3.9 22.2 - - + -
118B CYS* 4.0 23.3 - - + -
140B ASN* 2.8 21.8 + - - +
141B LEU* 3.1 8.9 + - + +
143B ASN* 1.3 77.3 - - - +
145B TYR* 1.3 53.3 + - + +
147B ALA* 3.2 4.5 + - - +
148B LYS* 2.7 33.1 + - + +
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Residues in contact with TYR 145 (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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115B ILE* 3.4 48.6 - - + +
141B LEU* 3.0 28.0 + - + +
144B VAL* 1.3 73.9 - - - +
146B HIS* 1.3 55.1 + - - +
148B LYS* 3.4 25.6 - - + +
149B GLY* 2.7 32.6 + - - -
170B ALA* 3.4 27.2 - - - +
173B ALA* 3.7 20.2 - - + -
174B ALA* 3.8 9.9 - - - +
177B PHE* 3.4 33.9 - + - -
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Residues in contact with HIS 146 (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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142B GLY 2.9 19.0 + - - +
143B ASN 3.6 5.4 - - - +
145B TYR* 1.3 76.4 - - - +
147B ALA* 1.3 63.8 + - - +
149B GLY* 2.9 13.2 + - - -
150B LYS* 3.1 49.5 + - - +
171B LEU* 4.1 9.0 - - + +
174B ALA* 3.8 7.8 - - + +
178B TYR* 3.6 13.0 - + - +
200B ASN* 4.3 2.9 - - - -
203B ASN* 4.3 3.2 - - - +
204B THR* 2.8 40.2 + - + -
207B LEU* 3.9 16.2 - - + +
39E THR* 5.1 0.2 - - - -
41E CYS* 4.0 10.7 - - - -
44E MET* 3.6 19.8 - - + +
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Residues in contact with ALA 147 (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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106B LYS* 3.9 18.6 - - + +
111B PHE* 3.8 20.7 - - + -
143B ASN 3.0 17.9 + - - +
144B VAL 3.5 4.0 - - - +
146B HIS* 1.3 78.6 + - - +
148B LYS* 1.3 63.9 + - - +
150B LYS* 2.9 20.6 + - - +
151B SER* 3.0 10.2 + - - -
44E MET* 6.0 2.2 - - + -
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Residues in contact with LYS 148 (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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111B PHE* 3.6 41.7 - - + -
112B ASP* 4.7 11.5 + - - -
115B ILE* 4.7 7.6 - - + +
144B VAL 2.7 18.3 + - - +
145B TYR* 3.4 36.1 - - + +
147B ALA* 1.3 72.4 - - - +
149B GLY* 1.3 62.3 + - - +
151B SER* 2.8 21.1 + - - +
152B PHE* 3.2 34.5 - - + -
170B ALA* 4.4 7.7 - - + +
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Residues in contact with GLY 149 (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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145B TYR 2.7 18.0 + - - -
146B HIS 2.9 6.2 + - - -
148B LYS* 1.3 74.9 - - - +
150B LYS* 1.3 58.8 + - - +
152B PHE* 4.0 10.4 + - - +
153B GLY 5.1 0.7 + - - -
167B VAL* 3.8 22.5 - - - +
170B ALA* 3.7 16.4 - - - +
171B LEU* 4.0 16.2 - - - -
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Residues in contact with LYS 150 (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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146B HIS* 3.1 42.9 + - + +
147B ALA* 2.9 13.0 + - - +
149B GLY* 1.3 79.2 - - - +
151B SER* 1.3 64.7 + - - +
152B PHE 3.5 0.2 - - - -
153B GLY* 3.5 11.6 + - - -
171B LEU* 5.6 0.2 - - + -
207B LEU* 3.6 23.3 - - + -
37E LEU 5.3 3.6 - - - -
39E THR* 3.4 19.4 + - - -
41E CYS* 3.8 7.1 - - - -
44E MET* 5.3 1.8 - - - +
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Residues in contact with SER 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PHE* 3.4 36.4 - - - -
147B ALA 3.0 4.6 + - - -
148B LYS* 2.8 18.6 + - - +
150B LYS* 1.3 73.6 - - - +
152B PHE* 1.3 80.4 + - - +
153B GLY* 2.8 6.2 + - - -
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Residues in contact with PHE 152 (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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148B LYS* 3.2 54.5 - - + -
149B GLY* 4.0 5.8 - - - +
150B LYS 3.5 0.2 - - - -
151B SER* 1.3 85.5 + - - +
153B GLY* 1.3 62.0 + - - +
164B PRO* 5.8 1.1 - - + -
166B GLU* 3.4 59.9 - - + +
167B VAL* 3.8 30.1 - - + -
170B ALA* 4.4 1.3 - - + -
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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