Contacts of the helix formed by residues 151 - 172 (chain A) in PDB entry 2QNJ
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 LYS 151 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ARG* 3.9 6.8 + - - +
150A MET* 1.3 71.6 - - - +
152A GLU* 1.3 57.1 + - - +
153A LYS* 3.2 11.4 - - + +
154A GLU* 2.7 35.7 + - + +
155A ALA 2.8 10.6 + - - -
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Residues in contact with GLU 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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150A MET 3.7 1.6 + - - +
151A LYS* 1.3 71.5 - - - +
153A LYS* 1.3 68.5 + - + +
155A ALA* 3.8 7.4 - - - +
156A ARG* 2.7 41.4 + - - +
247A VAL* 4.2 17.8 - - + +
275A TYR* 4.0 5.1 - - - +
276A MET* 3.7 10.0 - - - +
277A SER* 2.7 51.8 + - - -
280A CYS* 3.9 6.6 - - - +
306A TRP* 3.0 23.5 + - + +
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Residues in contact with LYS 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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151A LYS* 3.2 8.5 - - + -
152A GLU* 1.3 87.3 + - + +
154A GLU* 1.3 61.0 + - - +
156A ARG* 3.2 43.3 - - - +
157A SER* 3.3 19.9 + - - -
309A ALA* 5.7 0.8 - - - +
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Residues in contact with GLU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 3.9 10.0 + - - -
150A MET* 3.6 28.9 - - + +
151A LYS* 2.7 21.4 + - + +
153A LYS* 1.3 72.7 - - - +
155A ALA* 1.3 65.5 + - - +
157A SER* 3.2 14.9 + - - +
158A LYS* 3.2 33.7 + - - +
190A MET* 3.5 27.7 - - - +
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Residues in contact with ALA 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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150A MET* 3.9 19.8 - - + +
151A LYS 2.8 16.1 + - - +
152A GLU* 3.8 2.9 - - - +
154A GLU* 1.3 73.3 - - - +
156A ARG* 1.3 62.6 + - - +
158A LYS* 3.5 3.0 + - - +
159A PHE* 2.9 25.1 + - - +
246A LEU* 3.8 21.1 - - + +
247A VAL* 3.6 30.3 - - + -
306A TRP* 4.1 3.8 - - + -
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Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLU* 2.7 26.5 + - - +
153A LYS* 3.2 61.6 - - - +
155A ALA* 1.3 72.3 - - - +
157A SER* 1.3 60.4 + - - +
159A PHE* 3.0 16.8 + - - +
160A ARG* 3.1 22.7 + - + +
306A TRP* 2.7 71.1 + - + +
307A ILE* 4.1 13.4 - - - +
309A ALA* 3.3 43.6 + - - +
311A HIS* 4.4 5.8 - - - +
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Residues in contact with SER 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 LYS 3.3 9.3 + - - -
154A GLU* 3.2 11.7 + - - +
156A ARG* 1.3 80.6 - - - +
158A LYS* 1.3 75.8 + - - +
160A ARG* 3.8 12.5 + - - +
161A GLN* 3.5 28.0 + - - +
311A HIS* 5.3 8.1 - - - -
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Residues in contact with LYS 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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150A MET* 4.0 22.0 - - + -
154A GLU* 3.2 37.6 - - - +
155A ALA 3.7 4.9 - - - +
157A SER* 1.3 94.1 + - - +
159A PHE* 1.3 59.9 + - - +
161A GLN* 3.2 11.7 + - - +
162A ILE* 3.0 29.6 + - - +
186A LEU* 4.3 4.0 - - + -
190A MET* 3.2 39.1 + - - +
191A ASN* 5.3 2.6 + - - -
192A ILE* 3.4 28.6 - - + +
246A LEU* 4.5 11.7 - - + -
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Residues in contact with PHE 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 ALA 2.9 20.0 + - - +
156A ARG 3.0 5.5 + - - +
158A LYS* 1.3 75.1 - - - +
160A ARG* 1.3 61.4 + - - +
162A ILE* 4.2 13.7 - - + +
163A VAL* 2.8 51.0 + - + +
239A LEU* 3.6 32.5 - - + -
242A ILE* 4.8 2.7 - - + -
243A LEU* 3.6 33.0 - - + -
246A LEU* 3.7 20.4 - - + -
283A LEU* 4.1 4.7 - - + -
287A PHE* 3.9 22.2 - + - -
306A TRP* 4.2 10.5 - + + -
307A ILE* 3.8 17.0 - - + -
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Residues in contact with ARG 160 (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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156A ARG* 3.1 18.0 + - + +
157A SER* 4.0 9.2 - - - +
159A PHE* 1.3 71.8 - - - +
161A GLN* 1.3 69.3 + - + +
163A VAL* 4.1 0.2 - - - +
164A SER* 3.0 27.2 + - - -
307A ILE* 2.8 40.1 + - + +
308A ASN* 2.9 20.8 + - - -
311A HIS* 3.4 41.3 + - - -
314A ASP* 2.9 30.5 + - - -
315A GLU 4.1 0.2 - - - -
316A LEU* 3.6 39.9 - - + +
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Residues in contact with GLN 161 (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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114A ASN* 3.4 41.3 + - - +
157A SER 3.5 17.5 + - - +
158A LYS* 3.2 18.3 + - - +
159A PHE 3.2 0.2 - - - -
160A ARG* 1.3 83.0 - - + +
162A ILE* 1.3 62.2 + - - +
164A SER* 3.4 4.5 + - - -
165A ALA* 3.1 22.0 + - - +
191A ASN* 2.8 33.8 + - - +
192A ILE* 3.6 19.9 + - + +
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Residues in contact with ILE 162 (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 VAL* 5.9 0.4 - - + -
158A LYS 3.0 15.0 + - - +
159A PHE* 3.8 17.7 - - + +
160A ARG 3.3 0.4 - - - -
161A GLN* 1.3 74.8 - - - +
163A VAL* 1.3 65.0 + - - +
165A ALA* 3.3 1.9 + - - +
166A VAL* 3.0 28.1 + - + +
184A LEU* 4.0 21.1 - - + -
192A ILE* 4.0 28.0 - - + -
194A ILE* 4.5 12.1 - - + -
239A LEU* 3.8 26.7 - - + -
242A ILE* 3.9 26.5 - - + -
246A LEU* 4.4 11.0 - - + -
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Residues in contact with VAL 163 (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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159A PHE* 2.8 58.0 + - + +
160A ARG 4.1 1.6 - - - +
162A ILE* 1.3 73.7 - - - +
164A SER* 1.3 64.7 + - - +
166A VAL* 3.9 0.3 - - - -
167A GLN* 2.9 24.4 + - - +
239A LEU* 4.7 14.4 - - + -
287A PHE* 4.7 7.2 - - + -
298A LEU* 4.0 17.5 - - + +
301A ILE* 5.5 3.4 - - + -
302A MET* 3.8 30.1 - - + +
307A ILE* 4.5 6.7 - - + -
316A LEU* 3.9 8.7 - - + -
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Residues in contact with SER 164 (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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112A HIS* 2.8 19.9 + - - -
160A ARG 3.0 18.9 + - - -
161A GLN* 3.5 5.6 - - - -
163A VAL* 1.3 78.3 - - - +
165A ALA* 1.3 63.0 - - - +
167A GLN* 3.4 6.8 + - - +
168A TYR* 3.0 23.6 + - - +
302A MET* 5.3 3.8 - - - -
316A LEU* 4.6 16.1 - - - +
317A LYS 4.9 1.7 + - - -
319A PHE* 3.7 22.0 + - - +
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Residues in contact with ALA 165 (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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112A HIS* 3.3 20.1 + - + +
114A ASN* 4.3 4.3 - - + -
115A ILE* 3.8 19.3 - - + +
161A GLN 3.1 12.8 + - - +
162A ILE 3.8 0.2 - - - +
164A SER* 1.3 78.6 - - - +
166A VAL* 1.3 63.0 + - - +
168A TYR* 3.1 5.5 + - - +
169A CYS* 3.1 26.8 + - - -
194A ILE* 3.5 27.4 - - + -
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Residues in contact with VAL 166 (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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162A ILE* 3.0 19.2 + - + +
163A VAL 4.2 1.8 - - - +
165A ALA* 1.3 72.9 - - - +
167A GLN* 1.3 52.3 + - - +
169A CYS* 3.0 8.6 + - - +
170A HIS* 2.7 61.7 + - + +
179A LEU* 5.3 4.0 - - + -
184A LEU* 6.3 0.4 - - + -
194A ILE* 4.3 13.5 - - + -
197A PHE* 3.7 27.4 - - + -
235A ASP* 4.3 7.9 - - + -
239A LEU* 4.1 25.1 - - + -
298A LEU* 4.2 8.7 - - + -
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Residues in contact with GLN 167 (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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163A VAL* 2.9 19.7 + - + +
164A SER* 3.7 4.5 - - - +
166A VAL* 1.3 75.6 - - - +
168A TYR* 1.3 51.9 + - - +
170A HIS* 3.3 6.1 + - - +
171A GLN* 2.6 56.9 + - - +
298A LEU* 3.5 22.6 - - + +
299A GLU* 3.2 39.0 + - - +
302A MET* 4.5 14.1 - - + -
318A PRO* 3.4 31.7 - - - +
319A PHE 3.9 2.3 + - - -
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Residues in contact with TYR 168 (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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109A ILE 3.4 6.2 + - - -
110A LEU* 3.8 17.3 - - + -
111A ASN 2.8 39.0 + - - -
112A HIS* 3.8 20.0 - + + -
115A ILE* 3.7 20.2 - - + -
164A SER 3.0 14.6 + - - +
165A ALA 3.2 7.2 - - - +
166A VAL 3.1 0.2 - - - -
167A GLN* 1.3 73.3 + - - +
169A CYS* 1.3 55.1 + - - +
171A GLN* 2.9 31.7 - - + +
172A LYS* 2.7 47.6 + - + +
319A PHE* 4.0 20.4 - + + -
321A GLU* 2.7 33.1 + - + -
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Residues in contact with CYS 169 (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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110A LEU* 4.2 16.2 - - - -
115A ILE* 3.7 21.1 - - - -
165A ALA 3.1 21.0 + - - -
166A VAL* 3.0 7.9 + - - +
168A TYR* 1.3 73.2 - - - +
170A HIS* 1.3 68.1 + - - +
172A LYS* 3.0 8.2 + - - +
173A ARG 3.0 6.4 + - - -
174A ILE* 2.7 40.9 + - + +
194A ILE* 6.5 0.2 - - - -
197A PHE* 3.5 31.2 - - + -
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Residues in contact with HIS 170 (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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166A VAL* 2.7 35.6 + - + +
167A GLN* 3.6 8.3 - - - +
169A CYS* 1.3 73.2 - - - +
171A GLN* 1.3 57.5 + - - +
173A ARG* 2.9 20.3 + - - +
174A ILE 3.5 18.4 - - - +
175A VAL* 4.0 9.5 - - + +
197A PHE* 4.4 1.1 - + - -
232A PRO* 3.5 33.4 - - + +
235A ASP* 3.0 38.6 + - + -
236A VAL* 4.7 3.3 - - + +
298A LEU* 4.3 17.6 - - + +
299A GLU* 5.4 7.3 + - - +
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Residues in contact with GLN 171 (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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167A GLN* 2.6 43.9 + - - +
168A TYR* 2.9 38.4 + - + +
170A HIS* 1.3 74.3 - - - +
172A LYS* 1.3 63.3 + - + +
173A ARG* 3.1 5.7 + - - +
318A PRO* 4.3 4.5 - - - +
319A PHE 2.9 29.1 + - - +
320A VAL* 5.6 0.6 - - - +
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Residues in contact with LYS 172 (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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109A ILE* 3.9 31.6 - - + -
110A LEU* 4.4 18.2 - - + -
168A TYR* 2.7 31.7 + - + +
169A CYS 3.0 4.7 + - - +
171A GLN* 1.3 76.7 - - + +
173A ARG* 1.3 69.2 + - - +
174A ILE* 3.3 10.3 + - + +
321A GLU* 3.1 28.4 + - - +
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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