Contacts of the helix formed by residues 132 - 155 (chain B) in PDB entry 2GFP
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 HIS 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ARG* 3.7 41.0 + - + +
122B ARG* 3.2 31.8 + - + +
131B ARG* 1.3 89.6 + - + +
133B ALA* 1.3 70.8 + - - +
134B ASN* 3.0 13.6 + - - +
135B SER* 3.4 12.6 + - - -
136B LEU* 3.4 36.9 + - + +
253B ILE* 4.7 3.8 - - + -
257B PHE* 4.5 1.2 - - + -
304B VAL* 5.1 4.3 - - + -
307B ALA 5.4 1.4 + - - -
308B LEU* 3.6 37.5 - - + +
311B PHE* 4.1 10.7 - + - -
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B HIS* 1.3 76.1 - - - +
134B ASN* 1.3 54.5 + - - +
136B LEU 3.2 0.9 + - - -
137B LEU* 2.6 52.5 + - + +
253B ILE* 3.7 33.0 - - + +
254B PRO* 4.4 8.7 - - + -
257B PHE* 4.1 23.0 - - + +
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Residues in contact with ASN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PRO* 3.9 29.9 + - - +
122B ARG* 5.6 0.4 - - - +
124B LEU* 5.2 5.7 - - + +
125B TYR* 5.6 0.8 - - - +
130B LEU* 4.0 26.5 - - + +
131B ARG 4.0 8.0 + - - -
132B HIS* 3.2 26.2 + - - +
133B ALA* 1.3 75.0 + - - +
135B SER* 1.3 69.2 + - - +
137B LEU* 3.2 11.0 + - - +
138B ASN* 3.2 17.8 + - - +
257B PHE* 5.4 1.0 - - - -
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Residues in contact with SER 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 5.1 1.2 - - - +
117B ALA* 3.5 24.6 + - - +
118B ARG* 4.2 11.4 - - - -
121B PRO* 3.8 27.4 - - - +
132B HIS 3.4 4.4 + - - -
134B ASN* 1.3 81.4 - - - +
136B LEU* 1.3 63.5 + - - +
138B ASN* 3.0 30.1 + - - +
139B MET* 3.2 17.2 + - - +
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ARG* 4.9 17.0 - - + +
132B HIS* 3.4 26.9 + - + +
133B ALA 3.2 2.5 + - - +
135B SER* 1.3 79.5 - - - +
137B LEU* 1.3 57.2 + - - +
139B MET* 3.9 24.9 - - + +
140B GLY* 2.8 28.6 + - - -
250B ILE* 4.5 0.9 - - - +
253B ILE* 3.5 40.7 - - + +
300B TRP* 4.6 16.2 - - + -
304B VAL* 3.6 24.2 - - + -
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Residues in contact with LEU 137 (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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133B ALA* 2.6 40.9 + - + +
134B ASN* 3.4 8.5 - - - +
136B LEU* 1.3 70.1 - - - +
138B ASN* 1.3 71.1 + - - +
141B ILE* 2.9 29.9 + - + +
250B ILE* 3.8 25.6 - - + -
253B ILE* 3.8 15.0 - - + -
254B PRO* 4.3 14.4 - - + -
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Residues in contact with ASN 138 (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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13B LEU* 4.7 6.4 - - - +
14B VAL* 3.4 37.8 - - + +
17B VAL* 3.3 25.8 - - - +
117B ALA* 5.3 0.6 - - - +
134B ASN 3.2 9.1 + - - +
135B SER* 3.0 22.0 + - - +
137B LEU* 1.3 79.9 - - - +
139B MET* 1.3 76.2 + - - +
141B ILE* 4.2 2.8 - - - +
142B LEU* 3.4 21.8 + - - +
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Residues in contact with MET 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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17B VAL* 3.5 15.7 - - + -
21B GLN* 3.2 21.4 - - - +
114B GLY* 3.7 37.9 - - - +
117B ALA* 4.1 4.0 - - + -
118B ARG* 4.6 4.5 - - + +
135B SER* 3.2 29.4 + - - +
136B LEU* 3.9 27.4 - - + +
138B ASN* 1.3 95.9 - - - +
140B GLY* 1.3 66.7 + - - +
142B LEU 3.0 7.4 + - - -
143B VAL* 2.8 18.4 + - + +
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Residues in contact with GLY 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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136B LEU 2.8 21.1 + - - -
139B MET* 1.3 72.9 - - - +
141B ILE* 1.3 59.9 + - - +
143B VAL* 3.2 12.9 - - - +
144B SER* 3.0 23.2 + - - -
246B SER 4.3 4.8 - - - +
249B PHE* 4.9 14.1 - - - -
250B ILE* 3.6 13.7 - - - -
253B ILE* 6.2 0.2 - - - -
300B TRP* 6.2 2.5 - - - -
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Residues in contact with ILE 141 (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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137B LEU* 2.9 21.8 + - + +
138B ASN 4.2 2.0 - - - +
140B GLY* 1.3 67.5 - - - +
142B LEU* 1.3 69.6 + - + +
143B VAL 3.0 0.9 + - - -
144B SER* 3.0 8.8 + - - +
145B PRO* 2.7 43.6 - - + +
250B ILE* 3.3 29.5 - - + +
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Residues in contact with LEU 142 (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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14B VAL* 3.4 31.6 - - + +
17B VAL* 4.3 0.4 - - + -
18B ALA* 3.7 9.6 - - + -
21B GLN* 2.9 22.9 - - - +
22B MET* 3.8 7.4 - - + -
138B ASN* 3.4 25.2 + - - +
139B MET 3.0 2.5 + - - +
141B ILE* 1.3 85.6 - - + +
143B VAL* 1.3 64.7 + - - +
146B LEU* 3.1 46.3 + - + +
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Residues in contact with VAL 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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21B GLN* 3.3 28.9 - - + +
24B GLN* 5.4 0.4 - - - +
25B THR* 2.9 31.6 - - + +
139B MET* 2.8 25.5 + - + +
140B GLY* 3.2 11.7 - - - +
141B ILE 3.0 0.6 + - - -
142B LEU* 1.3 77.2 - - - +
144B SER* 1.3 68.4 + - - +
147B LEU* 2.9 29.3 + - + +
246B SER* 2.9 25.6 - - - +
249B PHE* 5.2 6.3 - - + -
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Residues in contact with SER 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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140B GLY 3.0 8.5 + - - -
141B ILE* 3.0 14.9 + - - +
143B VAL* 1.3 78.3 - - - +
145B PRO* 1.3 77.0 - - - +
147B LEU* 4.0 1.2 - - - +
148B ALA* 3.2 18.4 + - - +
243B MET* 4.0 10.0 - - - +
246B SER* 3.3 13.0 + - - -
247B ILE* 3.7 36.4 - - - -
250B ILE* 5.0 2.9 - - - +
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Residues in contact with PRO 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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141B ILE* 2.7 39.0 - - + +
144B SER* 1.3 81.8 - - - +
146B LEU* 1.3 79.4 + - + +
148B ALA* 2.8 6.4 + - + -
149B PRO* 2.7 31.0 - - + +
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Residues in contact with LEU 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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22B MET* 3.5 28.5 - - + -
141B ILE* 6.3 0.2 - - + -
142B LEU* 3.1 44.5 + - + +
145B PRO* 1.3 85.0 - - + +
147B LEU* 1.3 58.2 + - - +
149B PRO* 4.0 2.9 - - - +
150B LEU* 3.0 29.3 + - - +
164B CYS* 5.5 5.8 - - - -
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Residues in contact with LEU 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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22B MET* 3.0 56.3 - - + +
25B THR* 3.0 15.3 - - - +
26B ILE* 3.2 35.8 - - + +
143B VAL* 2.9 39.2 + - + +
144B SER 4.0 1.6 - - - +
145B PRO 2.8 2.8 + - - -
146B LEU* 1.3 72.2 - - - +
148B ALA* 1.3 68.5 + - - +
150B LEU* 2.9 19.3 - - + +
151B ILE 3.5 4.0 + - - -
152B GLY 4.5 0.2 + - - -
239B GLY 4.4 4.5 - - - +
242B SER* 3.1 16.4 - - - +
243B MET 4.7 2.2 - - - +
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Residues in contact with ALA 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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144B SER 3.2 5.9 + - - +
145B PRO* 2.8 11.2 + - + +
147B LEU* 1.3 73.4 - - - +
149B PRO* 1.4 69.4 - - + +
150B LEU 2.8 6.8 + - - -
152B GLY* 2.9 24.5 + - - -
239B GLY 4.6 0.7 - - - -
240B LEU* 4.0 15.3 - - + +
243B MET* 3.4 37.5 - - + +
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Residues in contact with PRO 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 PRO* 2.7 29.4 - - + +
146B LEU* 4.0 3.1 - - - +
148B ALA* 1.4 83.7 - - + +
150B LEU* 1.3 57.2 + - - +
152B GLY 4.3 0.9 - - - -
153B GLY* 2.9 28.8 - - - +
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Residues in contact with LEU 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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22B MET* 4.0 7.6 - - + -
26B ILE* 3.9 13.7 - - + -
146B LEU 3.0 17.0 + - - +
147B LEU* 2.9 34.1 - - + +
148B ALA 2.8 6.1 + - - -
149B PRO* 1.3 78.4 - - - +
151B ILE* 1.3 66.7 + - - +
153B GLY 3.0 3.5 + - - -
154B LEU 3.4 5.4 + - - -
157B THR* 3.1 53.7 - - + +
160B ASN* 4.2 13.7 + - + +
161B TRP* 4.6 7.9 - - - +
164B CYS* 4.0 26.9 - - + -
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Residues in contact with ILE 151 (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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26B ILE* 3.5 22.9 - - + +
29B PRO* 3.7 31.2 - - + -
30B ALA* 4.3 6.5 - - + +
33B ASP* 4.2 16.6 - - - +
147B LEU 3.5 2.2 + - - +
150B LEU* 1.3 79.1 - - - +
152B GLY* 1.3 65.4 + - - +
153B GLY 3.1 0.2 + - - -
155B LEU* 3.0 38.2 + - + +
156B ASP* 5.1 1.3 - - - +
157B THR* 3.0 30.7 - - - +
234B MET 5.9 1.8 - - - +
235B GLY 4.8 8.1 - - - +
236B ALA* 6.0 0.2 - - - -
239B GLY* 4.0 17.0 - - - +
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Residues in contact with GLY 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 ALA 2.9 15.6 + - - -
149B PRO* 4.3 1.8 - - - -
151B ILE* 1.3 81.0 - - - +
153B GLY* 1.3 62.7 + - - +
155B LEU 4.7 0.9 + - - -
236B ALA* 5.2 10.3 - - - -
239B GLY* 4.9 1.2 - - - -
240B LEU* 4.2 17.5 - - - +
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Residues in contact with GLY 153 (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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149B PRO* 2.9 31.0 + - - -
150B LEU 3.0 6.1 + - - -
152B GLY* 1.3 80.5 - - - +
154B LEU* 1.3 76.6 + - - +
155B LEU 3.9 0.4 - - - -
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Residues in contact with LEU 154 (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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150B LEU 3.4 7.9 + - - -
153B GLY* 1.3 93.6 - - - +
155B LEU* 1.3 71.3 + - - +
156B ASP 3.7 5.0 + - - +
157B THR* 4.7 2.5 - - - +
160B ASN* 4.8 13.7 + - - +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ILE* 3.0 33.7 + - + +
152B GLY 4.7 1.0 + - - -
153B GLY 3.9 0.6 - - - -
154B LEU* 1.3 77.3 - - - +
156B ASP* 1.3 66.7 + - + +
157B THR* 2.7 24.1 + - - +
234B MET* 4.9 15.9 - - + -
235B GLY* 5.9 3.8 - - - +
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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