Contacts of the helix formed by residues 139 - 160 (chain A) in PDB entry 3R1N
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 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ALA* 3.7 3.6 + - - -
138A PHE* 1.3 75.9 - - - +
140A GLU* 1.3 71.8 + - - +
141A ARG* 3.4 7.7 + - + +
142A GLU* 3.1 48.7 + - + +
143A ALA* 3.0 18.5 + - - +
312A GLN* 2.9 15.6 - - + -
313A THR 2.9 30.4 + - - -
314A PRO* 5.0 1.1 - - - -
315A LEU* 3.3 10.7 - - - +
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Residues in contact with GLU 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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139A THR* 1.3 77.3 + - - +
141A ARG* 1.3 59.3 + - - +
143A ALA* 3.3 4.8 + - - +
144A ALA 3.1 16.8 + - - -
236A LEU* 4.9 4.5 - - + -
272A GLU 4.0 3.5 - - - +
273A VAL* 3.4 17.7 - - - +
274A SER* 2.4 52.6 + - - -
277A ALA* 3.7 0.5 - - - +
303A TRP* 3.0 25.4 + - + +
310A VAL* 3.5 14.3 - - + +
311A PRO* 3.6 11.4 - - - +
313A THR* 3.2 19.5 + - + +
315A LEU* 3.4 20.6 - - + +
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Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A THR* 3.2 9.0 + - + +
140A GLU* 1.3 78.6 - - - +
142A GLU* 1.3 59.1 + - + +
144A ALA* 3.0 3.8 + - - +
145A GLU* 3.0 44.7 + - - +
307A SER 3.5 10.1 - - - +
308A MET* 2.7 45.2 + - - +
309A VAL* 4.6 2.6 - - - +
310A VAL* 3.4 29.3 + - - +
311A PRO 3.3 8.0 + - - +
312A GLN* 3.3 37.6 + - - +
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Residues in contact with GLU 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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133A ARG* 2.9 30.2 + - - +
137A ALA 3.5 9.7 - - - +
138A PHE* 3.9 13.2 - - + -
139A THR* 3.1 34.8 + - + +
141A ARG* 1.3 78.1 - - + +
143A ALA* 1.3 56.5 + - - +
145A GLU* 3.4 17.8 + - - +
146A ILE* 3.0 33.6 + - + +
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Residues in contact with ALA 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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138A PHE* 3.9 20.3 - - + -
139A THR 3.0 11.2 + - - +
140A GLU* 3.6 8.5 - - - +
141A ARG 3.2 0.2 - - - -
142A GLU* 1.3 76.2 - - - +
144A ALA* 1.3 57.2 + - - +
146A ILE* 3.3 6.1 + - - +
147A MET* 3.0 31.4 + - - +
235A LEU* 4.4 8.0 - - + +
236A LEU* 3.4 32.8 - - + -
303A TRP* 3.7 2.5 - - + -
315A LEU* 4.6 0.4 - - + -
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLU 3.1 7.7 + - - +
141A ARG 3.0 8.5 + - - +
143A ALA* 1.3 72.2 - - - +
145A GLU* 1.3 60.1 + - - +
147A MET* 3.8 1.0 - - - +
148A ARG* 2.9 32.1 + - - +
303A TRP* 3.3 55.1 - - + +
304A ILE* 4.3 2.3 - - - +
307A SER* 3.9 12.3 - - - -
310A VAL* 3.9 9.2 - - + -
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Residues in contact with GLU 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 ARG* 3.0 36.0 + - - +
142A GLU* 3.7 22.3 - - - +
144A ALA* 1.3 78.3 - - - +
146A ILE* 1.3 62.2 + - + +
148A ARG* 3.4 7.5 + - - +
149A ASP* 3.1 30.7 + - - +
307A SER* 4.3 15.5 - - - +
308A MET* 4.5 17.3 - - - +
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Residues in contact with ILE 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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126A LEU* 4.1 9.9 - - + -
130A ILE* 4.1 13.5 - - + -
138A PHE* 4.0 26.2 - - + -
142A GLU* 3.0 22.5 + - + +
143A ALA 3.3 3.6 + - - +
145A GLU* 1.3 76.0 - - + +
147A MET* 1.3 63.5 + - - +
149A ASP* 3.1 19.0 + - - +
150A ILE* 3.1 21.1 + - + +
174A TYR* 3.8 22.4 - - - +
183A LEU* 3.7 20.2 - - + -
235A LEU* 3.7 22.4 - - + -
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Residues in contact with MET 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 ALA 3.0 20.5 + - - +
144A ALA 3.3 0.6 + - - +
146A ILE* 1.3 76.4 - - - +
148A ARG* 1.3 51.8 + - - +
150A ILE* 3.5 8.0 + - + +
151A GLY* 2.7 31.9 + - - -
228A LEU* 3.4 48.7 - - + +
231A ILE* 4.0 7.6 - - + -
232A MET* 3.7 23.1 - - + -
235A LEU* 3.6 26.2 - - + -
298A PHE* 3.7 18.6 - - + -
303A TRP* 3.8 15.9 - - + -
304A ILE* 3.7 20.0 - - + -
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Residues in contact with ARG 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 ALA 2.9 19.1 + - - +
145A GLU* 3.7 7.0 - - - +
146A ILE 3.3 0.2 - - - -
147A MET* 1.3 73.7 - - - +
149A ASP* 1.3 66.2 + - - +
151A GLY* 3.5 1.3 + - - -
152A THR* 2.8 35.7 + - + +
299A MET* 4.2 14.0 - - + +
304A ILE* 3.9 34.2 + - + +
305A ASN* 3.8 30.1 + - - +
307A SER* 3.3 24.6 + - - +
308A MET* 4.8 11.3 - - - -
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Residues in contact with ASP 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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96A HIS* 3.4 44.5 + - + +
145A GLU* 3.1 20.6 + - - +
146A ILE* 3.1 13.3 + - - +
148A ARG* 1.3 81.2 - - - +
150A ILE* 1.3 61.1 + - - +
152A THR* 2.7 25.8 + - - +
153A ALA 3.2 4.3 + - - -
183A LEU* 4.6 16.8 + - + +
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Residues in contact with ILE 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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96A HIS* 5.4 0.9 - - - -
126A LEU* 4.4 0.7 - - + -
146A ILE* 3.1 29.9 + - + +
147A MET* 3.9 21.8 - - + +
149A ASP* 1.3 73.0 - - - +
151A GLY* 1.3 63.8 + - - +
153A ALA* 3.2 11.2 + - + +
154A ILE* 3.0 27.0 + - + +
167A VAL* 4.8 9.0 - - + -
172A LEU* 3.9 39.9 - - + -
183A LEU* 3.8 17.5 - - + -
185A LEU* 5.4 2.0 - - + -
228A LEU* 3.5 21.1 - - + -
231A ILE* 4.2 8.3 - - + -
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Residues in contact with GLY 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 MET 2.7 22.6 + - - -
148A ARG 3.8 2.2 - - - -
149A ASP 3.3 0.2 - - - -
150A ILE* 1.3 72.7 - - - +
152A THR* 1.3 51.4 + - - +
154A ILE 3.3 0.7 + - - -
155A GLN* 2.7 35.3 + - - +
228A LEU* 4.3 5.1 - - - +
295A ILE* 3.4 12.9 - - - +
298A PHE* 3.7 20.8 - - - -
299A MET* 3.6 7.8 - - - +
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Residues in contact with THR 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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95A PRO* 3.9 15.9 - - - +
96A HIS* 3.2 19.5 - - + +
148A ARG* 2.8 30.5 + - + +
149A ASP* 2.7 18.9 + - - +
151A GLY* 1.3 72.2 - - - +
153A ALA* 1.3 64.3 + - - +
155A GLN* 3.5 12.7 - - - +
156A PHE* 2.9 24.3 + - - +
299A MET* 3.7 17.7 - - + -
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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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95A PRO 3.4 11.4 + - - +
96A HIS* 3.5 24.9 - - + +
97A ILE* 4.2 8.9 - - + +
149A ASP 3.2 4.8 + - - +
150A ILE* 3.2 12.7 + - - +
152A THR* 1.3 81.1 + - - +
154A ILE* 1.3 61.9 + - - +
156A PHE* 3.1 5.9 + - - +
157A LEU* 3.0 26.8 + - - +
185A LEU* 4.4 17.5 - - + -
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Residues in contact with ILE 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 ILE* 3.0 14.5 + - + +
151A GLY 3.8 6.1 - - - +
153A ALA* 1.3 75.5 - - - +
155A GLN* 1.3 60.8 + - - +
157A LEU* 3.8 12.3 - - + -
158A HIS* 2.9 58.6 + - + +
164A HIS* 4.6 0.4 - - + -
167A VAL* 3.9 19.7 - - + -
185A LEU* 3.7 27.6 - - + -
224A ASP* 4.3 13.7 - - + +
225A MET* 4.2 6.1 - - - -
228A LEU* 4.3 17.7 - - + -
295A ILE* 3.6 18.6 - - + -
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Residues in contact with GLN 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 GLY 2.7 21.3 + - - +
152A THR* 3.5 10.7 - - - +
153A ALA 3.2 0.2 - - - -
154A ILE* 1.3 74.3 - - - +
156A PHE* 1.3 64.3 + - - +
158A HIS* 4.2 0.2 - - - +
159A SER* 3.0 30.7 + - - +
295A ILE* 3.7 21.3 - - + +
296A THR* 5.0 11.8 - - + +
299A MET* 3.7 35.6 - - + +
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Residues in contact with PHE 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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90A GLN 4.1 9.9 - - - -
91A ALA* 3.7 26.9 - - - -
93A GLY* 4.7 3.4 - - - -
94A GLY* 3.7 15.7 - - - -
95A PRO* 3.5 26.0 - - + -
97A ILE* 3.7 18.8 - - + -
152A THR 2.9 13.5 + - - +
153A ALA 3.5 8.1 - - - +
155A GLN* 1.3 76.5 - - - +
157A LEU* 1.3 64.5 + - + +
159A SER* 2.9 10.7 + - - -
160A HIS* 2.9 59.1 + + + -
162A ILE* 6.2 0.7 - - + -
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Residues in contact with LEU 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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91A ALA* 3.5 31.4 - - + -
97A ILE* 4.0 12.1 - - + -
153A ALA 3.0 19.0 + - - +
154A ILE* 4.0 8.7 - - + +
156A PHE* 1.3 79.8 - - + +
158A HIS* 1.3 60.7 + - + +
160A HIS* 3.0 16.9 + - - +
161A ASN 3.0 0.2 + - - -
162A ILE* 2.9 48.9 + - + +
164A HIS* 4.1 15.9 - - + +
185A LEU* 4.1 23.1 - - + -
188A PHE* 3.7 23.1 - - + -
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Residues in contact with HIS 158 (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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154A ILE* 2.9 41.3 + - + +
155A GLN 4.2 0.2 - - - +
157A LEU* 1.3 80.3 - - + +
159A SER* 1.3 55.4 + - - +
161A ASN* 3.0 15.9 + - - +
162A ILE 3.2 18.4 - - - -
221A LYS* 3.0 76.8 + - + +
224A ASP* 2.6 26.4 + - + -
225A MET* 4.3 6.7 - - + -
295A ILE* 4.0 24.2 + - + +
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Residues in contact with SER 159 (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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155A GLN* 3.0 16.0 + - - -
156A PHE* 2.9 17.3 + - - -
158A HIS* 1.3 75.6 - - - +
160A HIS* 1.3 67.7 + - - +
161A ASN* 3.4 5.4 + - - +
295A ILE* 5.9 0.2 - - - +
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Residues in contact with HIS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLN* 5.8 7.2 + - + +
156A PHE* 2.9 58.9 + + + +
157A LEU* 3.0 10.7 + - - +
159A SER* 1.3 85.1 + - - +
161A ASN* 1.3 69.5 + - - +
162A ILE* 3.3 13.2 + - + +
193A GLU* 3.7 16.7 - - - +
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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