Contacts of the helix formed by residues 136 - 157 (chain A) in PDB entry 3J2I
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 THR 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A GLN* 3.8 13.7 + - + +
135A VAL* 1.3 82.6 - - - +
137A GLY* 1.3 68.3 + - - +
139A LYS* 3.9 8.7 + - - +
140A ALA* 3.5 10.4 + - - -
344A LYS* 3.5 31.0 - - + +
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Residues in contact with GLY 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A THR* 1.3 77.8 - - - +
138A ARG* 1.3 61.2 + - - -
140A ALA* 3.0 4.2 + - - +
141A ASP* 2.9 36.7 + - - +
344A LYS 4.2 2.4 + - - -
345A SER* 5.7 0.6 - - - +
346A GLU* 6.6 0.2 - - - -
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Residues in contact with ARG 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLY* 1.3 70.8 - - - -
139A LYS* 1.3 57.4 + - - +
141A ASP* 2.8 37.0 + - - +
142A VAL* 3.0 33.1 + - - +
177A PHE 3.0 20.2 + - - -
178A ASN* 2.8 32.3 + - - +
179A CYS* 4.0 2.6 - - - -
232A SER* 2.8 43.0 + - - +
314A GLU* 5.0 3.2 + - - +
315A PHE* 4.2 20.4 - - + -
347A MET* 4.1 3.0 - - - +
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Residues in contact with LYS 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLY* 2.7 38.5 + - - +
105A LEU* 4.3 9.6 - - + -
126A VAL* 4.2 19.3 - - + +
135A VAL* 3.8 19.5 - - + -
136A THR 3.9 6.3 + - - +
137A GLY 3.2 0.8 - - - -
138A ARG* 1.3 78.4 - - - +
140A ALA* 1.3 61.5 + - - +
142A VAL* 3.5 6.3 - - - +
143A ILE* 3.1 30.4 + - - +
315A PHE* 3.6 42.3 - - + -
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Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 3.4 23.7 - - + +
136A THR 3.5 6.5 + - - -
137A GLY 3.0 8.8 + - - +
139A LYS* 1.3 76.8 - - - +
141A ASP* 1.3 67.9 + - - +
144A LYS* 2.9 32.4 + - + +
343A TYR* 4.3 9.0 - - + -
344A LYS 3.3 33.9 - - - +
345A SER* 4.5 0.7 - - - +
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Residues in contact with ASP 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 GLY* 2.9 19.7 + - - +
138A ARG* 2.8 48.0 + - - +
140A ALA* 1.3 76.6 - - - +
142A VAL* 1.3 57.0 + - - +
144A LYS 3.9 0.2 - - - -
145A ALA* 2.9 30.7 + - - +
177A PHE* 3.7 16.4 - - + +
179A CYS* 4.0 3.1 - - - -
345A SER* 2.7 34.3 + - - -
346A GLU* 4.3 2.1 + - - +
347A MET* 3.3 18.8 - - - +
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Residues in contact with VAL 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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105A LEU* 4.1 11.0 - - + -
138A ARG 3.0 20.3 + - - +
139A LYS 3.5 6.7 - - - +
141A ASP* 1.3 75.1 - - - +
143A ILE* 1.3 63.5 + - - +
145A ALA* 3.7 0.8 - - - +
146A ALA* 2.9 30.1 + - - +
179A CYS* 3.7 12.1 - - - -
230A VAL* 3.2 39.7 - - + +
231A SER 3.7 16.2 - - - -
232A SER* 4.4 2.5 - - - +
315A PHE* 3.7 27.6 - - + +
317A ALA* 3.9 5.6 - - + +
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Residues in contact with ILE 143 (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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105A LEU* 3.8 21.8 - - + -
124A THR* 3.9 23.6 - - + +
125A PHE 4.8 0.4 - - - -
126A VAL* 3.8 16.8 - - + -
139A LYS 3.1 21.1 + - - +
140A ALA 4.1 1.6 - - - +
142A VAL* 1.3 75.1 - - - +
144A LYS* 1.3 61.0 + - - +
146A ALA 3.3 0.3 + - - -
147A HIS* 2.9 28.2 + - - +
317A ALA* 3.9 7.2 - - + -
319A PHE* 3.7 13.1 - - + -
338A PHE* 3.8 16.2 - - + -
343A TYR* 3.6 46.4 - - + +
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Residues in contact with LYS 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 ALA 2.9 18.9 + - - +
141A ASP 4.0 2.5 - - - +
143A ILE* 1.3 75.2 - - - +
145A ALA* 1.3 62.5 + - - +
147A HIS* 3.3 4.5 + - - +
148A LEU* 2.9 35.4 + - + +
177A PHE* 4.2 19.3 - - + -
338A PHE* 5.1 5.8 - - + -
340A PRO* 4.5 8.3 + - - +
343A TYR* 3.3 37.7 + - + +
345A SER* 3.5 39.7 - - - +
347A MET 4.8 2.9 - - - -
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Residues in contact with ALA 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 ASP 2.9 20.4 + - - +
142A VAL 3.7 3.8 - - - +
144A LYS* 1.3 77.7 - - - +
146A ALA* 1.3 57.3 + - - +
148A LEU 3.3 0.2 + - - -
149A CYS* 2.9 34.8 + - - -
173A VAL* 3.8 3.6 - - - +
174A ALA* 4.2 16.4 - - - -
177A PHE* 3.7 30.8 - - + -
179A CYS* 4.3 3.6 - - + -
230A VAL* 4.2 11.4 - - + -
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Residues in contact with ALA 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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142A VAL 2.9 17.8 + - - +
143A ILE 3.9 1.1 - - - +
145A ALA* 1.3 76.7 - - - +
147A HIS* 1.3 62.2 + - - +
149A CYS* 3.2 4.0 + - - +
150A ALA* 3.0 20.4 + - - +
228A VAL* 3.5 20.9 - - + +
230A VAL* 3.9 8.5 - - + +
317A ALA* 3.8 27.4 - - + +
318A GLN 4.4 0.2 - - - +
319A PHE* 3.7 16.8 - - + -
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Residues in contact with HIS 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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143A ILE 2.9 13.8 + - - +
144A LYS 4.1 1.8 - - - +
146A ALA* 1.3 77.1 - - - +
148A LEU* 1.3 59.2 + - + +
150A ALA* 3.1 9.3 + - + +
151A GLU* 2.8 59.8 + - + +
319A PHE* 3.6 40.1 - + + +
332A ARG* 5.6 9.0 + - - -
336A GLY 5.4 1.8 + - - -
338A PHE* 3.5 55.5 - + + +
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Residues in contact with LEU 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 LYS* 2.9 21.2 + - + +
147A HIS* 1.3 78.1 - - + +
149A CYS* 1.3 55.9 + - - +
151A GLU* 3.3 28.5 - - - +
152A ALA* 2.9 30.7 + - - +
173A VAL* 3.6 16.3 - - + +
177A PHE* 3.6 35.4 - - + -
349A VAL* 4.1 12.8 - - + -
358A LEU* 3.6 25.7 - - + +
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Residues in contact with CYS 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 ALA 2.9 17.8 + - - -
146A ALA 3.4 8.7 - - - +
148A LEU* 1.3 76.4 - - - +
150A ALA* 1.3 55.9 + - - +
152A ALA* 3.3 3.1 + - - +
153A ALA* 2.9 18.4 + - - +
170A TRP* 2.9 67.1 + - + -
173A VAL* 3.9 13.0 - - - +
174A ALA* 4.2 4.3 - - - -
181A PRO* 5.4 0.2 - - - -
228A VAL* 3.6 13.7 - - + -
230A VAL* 4.3 15.5 - - - -
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Residues in contact with ALA 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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146A ALA 3.0 12.2 + - - +
147A HIS* 3.1 17.9 + - + +
149A CYS* 1.3 76.1 - - - +
151A GLU* 1.3 55.9 + - - +
153A ALA* 3.3 1.7 + - - +
154A LEU* 2.9 26.6 + - - +
228A VAL* 3.8 11.8 - - + +
319A PHE* 4.0 23.3 - - + -
321A PHE* 3.6 26.5 - - + -
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Residues in contact with GLU 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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147A HIS* 2.8 47.9 + - + +
148A LEU* 3.3 35.7 + - - +
150A ALA* 1.3 72.5 - - - +
152A ALA* 1.3 67.2 + - - +
154A LEU* 3.3 5.4 + - - +
155A ARG* 3.1 48.3 + - - +
338A PHE* 4.7 4.7 - - - -
358A LEU* 3.9 16.7 - - + +
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Residues in contact with ALA 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 LEU 2.9 17.2 + - - +
149A CYS* 3.6 7.9 - - - +
151A GLU* 1.3 75.3 - - - +
153A ALA* 1.3 59.0 + - - +
155A ARG* 3.1 6.1 + - - +
156A LEU* 2.9 38.8 + - + +
169A ALA* 4.7 7.2 - - + -
170A TRP* 4.8 2.9 - - + -
173A VAL* 4.6 12.1 - - + -
357A LEU* 4.1 22.2 - - + -
358A LEU* 3.9 10.9 - - + +
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Residues in contact with ALA 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 CYS 2.9 17.2 + - - +
150A ALA* 3.6 5.4 - - - +
152A ALA* 1.3 73.8 - - - +
154A LEU* 1.3 60.6 + - - +
156A LEU* 4.3 2.7 - - - +
157A VAL* 2.8 41.1 + - + +
166A VAL* 4.1 10.3 - - + -
170A TRP* 3.7 18.1 - - + +
226A VAL* 3.7 27.6 - - + -
321A PHE* 4.2 1.3 - - - -
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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 ALA 2.9 14.6 + - - +
151A GLU* 3.6 11.2 - - + +
152A ALA 3.3 0.4 - - - -
153A ALA* 1.3 76.4 - - - +
155A ARG* 1.3 65.5 + - - +
157A VAL* 4.3 9.5 - - - +
321A PHE* 3.8 25.9 - - + -
323A VAL* 4.5 10.5 - - + +
330A PRO* 4.3 18.2 - - + +
332A ARG* 4.1 44.2 - - + +
362A ALA* 3.7 28.5 - - + +
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Residues in contact with ARG 155 (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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151A GLU* 3.1 43.5 + - - +
152A ALA* 3.1 7.4 + - - +
154A LEU* 1.3 84.4 - - - +
156A LEU* 1.3 60.5 + - - +
157A VAL 5.1 0.2 - - - -
158A LYS* 3.9 25.8 + - - +
330A PRO* 5.9 0.2 - - - +
357A LEU* 3.2 41.0 + - + +
358A LEU* 3.9 14.1 + - - +
359A GLN 5.3 0.2 - - - -
360A SER* 2.8 33.7 + - - +
361A SER* 4.3 6.4 - - - +
362A ALA* 3.7 34.1 - - + +
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Residues in contact with LEU 156 (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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152A ALA* 2.9 20.6 + - + +
153A ALA* 4.3 0.9 - - - +
155A ARG* 1.3 79.7 - - - +
157A VAL* 1.3 60.8 + - - +
158A LYS* 2.9 6.4 + - - -
161A ASN* 2.9 41.3 + - - +
165A GLN* 4.1 26.2 - - + +
166A VAL* 4.0 18.2 - - + +
169A ALA* 3.7 30.3 - - + -
218A PHE* 3.9 3.1 - - - -
357A LEU* 3.8 29.4 - - + -
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Residues in contact with VAL 157 (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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153A ALA* 2.8 29.9 + - + +
154A LEU* 4.3 3.5 - - - +
155A ARG 3.7 0.2 - - - -
156A LEU* 1.3 67.5 - - - +
158A LYS* 1.3 60.5 + - - +
166A VAL* 3.9 13.2 - - + -
201A ILE* 3.7 25.6 - - + -
218A PHE* 3.8 23.6 - - + -
224A TYR* 4.1 22.0 - - + -
226A VAL* 4.2 12.1 - - + -
321A PHE* 6.1 0.2 - - + -
323A VAL* 4.3 16.5 - - + +
325A LEU* 3.4 15.8 - - + +
330A PRO* 3.6 9.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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