Contacts of the helix formed by residues 132 - 155 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ARG* 3.7 40.9 + - + +
122A ARG* 3.2 32.0 + - + +
131A ARG* 1.3 89.0 + - - +
133A ALA* 1.3 70.4 + - - +
134A ASN* 3.0 13.2 + - - +
135A SER* 3.4 13.2 + - - -
136A LEU* 3.4 35.4 + - + +
253A ILE* 4.7 3.4 - - + -
257A PHE* 4.5 1.3 - - + -
304A VAL* 5.0 3.4 - - + -
307A ALA 5.4 1.6 + - - -
308A LEU* 3.6 38.2 - - + +
311A PHE* 4.1 10.3 - + - -
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A HIS* 1.3 76.5 - - - +
134A ASN* 1.3 54.3 + - - +
136A LEU 3.2 0.9 + - - -
137A LEU* 2.6 53.1 + - + +
253A ILE* 3.7 31.0 - - + +
254A PRO* 4.4 9.2 - - + -
257A PHE* 4.1 23.3 - - + +
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Residues in contact with ASN 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PRO* 3.9 29.7 + - - +
122A ARG* 5.6 0.4 - - - +
124A LEU* 5.2 5.9 - - + +
125A TYR* 5.6 1.4 - - - +
130A LEU* 4.0 26.1 - - + +
131A ARG 4.0 8.0 + - - -
132A HIS* 3.2 25.0 + - - +
133A ALA* 1.3 75.6 + - - +
135A SER* 1.3 69.9 + - - +
137A LEU* 3.2 10.3 + - - +
138A ASN* 3.2 17.5 + - - +
257A PHE* 5.4 1.2 - - - -
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Residues in contact with SER 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 5.1 1.4 - - - +
117A ALA* 3.5 24.4 + - - +
118A ARG* 4.2 12.6 - - - -
121A PRO* 3.8 25.8 - - - +
132A HIS 3.4 4.2 + - - -
134A ASN* 1.3 83.2 - - - +
136A LEU* 1.3 63.3 + - - +
138A ASN* 3.0 30.2 + - - +
139A MET* 3.2 17.7 + - - +
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ARG* 4.9 16.6 - - + +
132A HIS* 3.4 27.0 + - + +
133A ALA 3.2 3.2 + - - +
135A SER* 1.3 79.7 - - - +
137A LEU* 1.3 57.4 + - - +
139A MET* 3.5 25.3 + - + +
140A GLY* 2.8 27.9 + - - -
250A ILE* 4.5 1.0 - - - +
253A ILE* 3.5 40.5 - - + +
300A TRP* 4.6 15.9 - - + -
304A VAL* 3.6 25.1 - - + -
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ALA* 2.6 41.2 + - + +
134A ASN* 3.4 8.7 - - - +
136A LEU* 1.3 69.6 - - - +
138A ASN* 1.3 69.3 + - - +
141A ILE* 2.9 30.3 + - + +
250A ILE* 3.8 27.3 - - + +
253A ILE* 3.8 15.9 - - + +
254A PRO* 4.3 13.9 - - + -
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Residues in contact with ASN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.7 6.4 - - - +
14A VAL* 3.4 39.3 - - + +
17A VAL* 3.3 24.4 - - - +
134A ASN 3.2 8.0 + - - +
135A SER* 3.0 23.7 + - - +
137A LEU* 1.3 80.9 - - - +
139A MET* 1.3 76.8 + - - +
141A ILE* 4.2 2.3 - - - +
142A LEU* 3.4 23.0 + - - +
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Residues in contact with MET 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 3.5 15.5 - - + -
21A GLN* 3.2 20.1 - - - +
114A GLY* 3.7 39.5 - - - +
117A ALA* 4.1 3.4 - - + -
118A ARG* 4.6 4.9 - - + +
135A SER* 3.2 29.9 + - - +
136A LEU* 3.9 27.1 - - + +
138A ASN* 1.3 95.8 - - - +
140A GLY* 1.3 67.0 + - - +
142A LEU 3.0 7.6 + - - -
143A VAL* 2.8 18.4 + - + +
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Residues in contact with GLY 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LEU 2.8 21.7 + - - -
139A MET* 1.3 71.7 - - - +
141A ILE* 1.3 61.6 + - - +
143A VAL* 3.2 12.7 - - - +
144A SER* 3.0 22.9 + - - -
246A SER 4.3 3.8 - - - +
249A PHE* 4.9 14.8 - - - -
250A ILE* 3.6 13.2 - - - -
300A TRP* 6.2 2.0 - - - -
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Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A LEU* 2.9 22.0 + - + +
138A ASN* 4.2 3.1 - - - +
140A GLY* 1.3 67.8 - - - +
142A LEU* 1.3 71.1 + - + +
143A VAL 3.0 0.7 + - - -
144A SER* 3.0 8.8 + - - +
145A PRO* 2.7 42.9 - - + +
250A ILE* 3.3 27.9 - - + +
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.4 32.1 - - + +
17A VAL* 4.3 0.2 - - + -
18A ALA* 3.7 8.7 - - + -
21A GLN* 2.9 23.3 - - - +
22A MET* 3.8 7.2 - - + -
138A ASN* 3.4 24.4 + - - +
139A MET 3.0 2.7 + - - +
141A ILE* 1.3 85.7 - - + +
143A VAL* 1.3 64.3 + - - +
146A LEU* 3.1 45.3 + - + +
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Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLN* 3.3 29.1 - - + +
24A GLN* 5.4 0.7 - - - +
25A THR* 2.9 30.5 - - + +
139A MET* 2.8 26.0 + - + +
140A GLY* 3.2 12.6 - - - +
141A ILE 3.0 1.0 + - - -
142A LEU* 1.3 78.4 - - - +
144A SER* 1.3 68.8 + - - +
147A LEU* 2.9 29.1 + - + +
246A SER* 2.9 26.5 - - - +
249A PHE* 5.2 6.3 - - + -
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Residues in contact with SER 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLY 3.0 8.5 + - - -
141A ILE* 3.0 15.2 + - - +
143A VAL* 1.3 77.7 - - - +
145A PRO* 1.3 77.0 - - - +
147A LEU* 4.0 1.0 - - - +
148A ALA* 3.2 19.8 + - - +
243A MET* 4.0 9.3 - - - +
246A SER* 3.3 12.4 + - - -
247A ILE* 3.7 36.8 - - - -
250A ILE* 5.0 2.4 - - - +
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Residues in contact with PRO 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ILE* 2.7 39.0 - - + +
142A LEU* 4.8 0.2 - - - -
144A SER* 1.3 81.4 - - - +
146A LEU* 1.3 80.2 + - + +
148A ALA* 2.8 5.9 + - + -
149A PRO* 2.7 30.8 - - + +
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A MET* 3.5 28.0 - - + -
142A LEU* 3.1 45.2 + - + +
145A PRO* 1.3 84.9 - - + +
147A LEU* 1.3 56.6 + - - +
149A PRO* 4.0 2.5 - - - +
150A LEU* 3.0 31.2 + - + +
164A CYS* 5.5 6.3 - - - -
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A MET* 3.0 56.1 - - + +
25A THR* 3.0 14.8 - - - +
26A ILE* 3.2 35.9 - - + +
143A VAL* 2.9 39.4 + - + +
144A SER 4.0 2.0 - - - +
145A PRO 2.8 3.0 + - - -
146A LEU* 1.3 71.9 - - - +
148A ALA* 1.3 69.2 + - - +
150A LEU* 2.9 19.8 - - + +
151A ILE 3.5 3.6 + - - -
152A GLY 4.5 0.2 + - - -
239A GLY 4.4 4.3 - - - +
242A SER* 3.1 15.5 - - - +
243A MET 4.7 2.7 - - - +
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A SER 3.2 6.2 + - - +
145A PRO* 2.8 10.1 + - + +
147A LEU* 1.3 76.4 - - - +
149A PRO* 1.4 69.9 - - + +
150A LEU 2.8 6.6 + - - -
152A GLY* 2.9 24.0 + - - -
239A GLY 4.6 0.9 - - - -
240A LEU* 4.0 14.2 - - + +
243A MET* 3.4 37.8 - - + +
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Residues in contact with PRO 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A PRO* 2.7 29.4 - - + +
146A LEU* 4.0 2.7 - - - +
148A ALA* 1.4 83.3 - - + +
150A LEU* 1.3 57.5 + - - +
152A GLY 4.3 0.9 - - - -
153A GLY* 2.9 29.5 - - - +
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Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A MET* 4.0 8.1 - - + -
26A ILE* 3.9 13.9 - - + -
146A LEU 3.0 16.9 + - - +
147A LEU* 2.9 33.7 - - + +
148A ALA 2.8 6.3 + - - -
149A PRO* 1.3 78.7 - - - +
151A ILE* 1.3 65.8 + - - +
153A GLY 3.0 3.8 + - - -
154A LEU 3.4 5.4 + - - -
157A THR* 3.1 53.4 - - + +
160A ASN* 4.2 13.4 + - + +
161A TRP* 4.6 8.5 - - - +
164A CYS* 4.0 27.4 - - + -
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Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 3.5 24.0 - - + +
29A PRO* 3.7 31.0 - - + -
30A ALA* 4.3 5.8 - - + +
33A ASP* 4.2 16.2 - - - +
147A LEU 3.5 2.0 + - - -
150A LEU* 1.3 78.6 - - - +
152A GLY* 1.3 63.7 + - - +
153A GLY 3.1 0.2 + - - -
155A LEU* 3.0 39.3 + - + +
156A ASP* 5.5 1.8 - - - +
157A THR* 3.0 28.9 - - + +
234A MET 5.9 1.6 - - - +
235A GLY 4.8 7.2 - - - +
236A ALA* 6.0 0.7 - - - -
239A GLY* 4.0 18.2 - - - +
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Residues in contact with GLY 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ALA 2.9 16.7 + - - -
149A PRO* 4.3 1.3 - - - -
151A ILE* 1.3 81.2 - - - +
153A GLY* 1.3 63.0 + - - +
155A LEU 4.7 0.9 + - - -
236A ALA* 5.2 11.7 - - - -
239A GLY* 4.9 0.8 - - - -
240A LEU* 4.2 16.8 - - - +
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Residues in contact with GLY 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PRO* 2.9 30.7 + - - -
150A LEU 3.0 6.1 + - - -
152A GLY* 1.3 80.7 - - - +
154A LEU* 1.3 76.8 + - - +
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU 3.4 7.5 + - - -
153A GLY* 1.3 92.7 - - - +
155A LEU* 1.3 72.9 + - - +
156A ASP 3.7 5.2 + - - +
157A THR* 4.7 2.2 - - - +
160A ASN* 4.8 13.2 + - - +
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 3.0 33.3 + - + +
152A GLY 4.7 0.8 + - - -
153A GLY 3.9 0.6 - - - -
154A LEU* 1.3 78.0 - - - +
156A ASP* 1.3 66.1 + - + +
157A THR* 2.7 25.1 + - - +
234A MET* 4.9 15.5 - - + -
235A GLY* 5.9 4.0 - - - +
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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
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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