Contacts of the helix formed by residues 140 - 158 (chain A) in PDB entry 2NUP
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 GLU 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A MET* 1.3 79.9 - - - +
141A ASP* 1.3 58.5 + - - +
142A GLU* 3.4 4.5 - - + +
143A ASP* 2.9 25.2 + - + +
144A LEU* 2.7 32.3 + - - +
249A ARG* 5.9 0.7 + - - -
130C ARG* 4.6 16.5 - - - +
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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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139A MET 4.6 0.3 - - - +
140A GLU* 1.3 75.5 + - - +
142A GLU* 1.3 58.7 + - + +
144A LEU* 3.0 8.7 + - - +
145A GLN* 2.7 37.6 + - - +
249A ARG* 3.4 40.8 + - - +
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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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140A GLU* 3.4 3.4 - - + +
141A ASP* 1.3 79.1 - - + +
143A ASP* 1.3 64.3 + - - +
145A GLN* 4.0 6.3 - - - +
146A ALA* 3.2 23.6 + - - +
378A ASN* 3.6 26.0 + - - +
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Residues in contact with ASP 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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139A MET* 4.0 17.3 - - + +
140A GLU* 2.9 28.1 + - - +
142A GLU* 1.3 80.3 - - - +
144A LEU* 1.3 62.0 + - - +
146A ALA 3.6 0.3 + - - -
147A LEU* 3.1 23.4 + - - +
350A CYS 5.2 4.0 - - - +
351A ALA* 5.8 1.6 - - - -
375A ASP 4.9 1.9 - - - +
376A SER* 2.4 37.5 + - - -
377A PHE* 3.6 15.7 - - + +
378A ASN* 3.7 8.1 - - - +
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Residues in contact with LEU 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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135A VAL* 4.8 5.8 - - + -
136A ASP 3.9 21.3 - - - +
137A THR* 4.5 8.7 - - + +
139A MET* 3.9 17.0 - - + +
140A GLU 2.7 19.1 + - - +
141A ASP* 3.7 9.0 - - - +
143A ASP* 1.3 72.7 - - - +
145A GLN* 1.3 59.6 + - - +
147A LEU* 3.3 10.2 + - + +
148A LYS* 2.8 47.1 + - + +
247A LEU* 4.2 10.8 - - + +
248A GLN* 3.8 6.3 - - - +
249A ARG* 3.4 40.8 - - + +
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Residues in contact with GLN 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 2.7 21.1 + - - +
142A GLU* 4.0 6.1 - - - +
144A LEU* 1.3 68.2 - - - +
146A ALA* 1.3 67.6 + - - +
148A LYS* 3.2 18.8 + - + +
149A GLU* 2.8 55.9 + - + +
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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 GLU 3.2 13.5 + - - +
143A ASP 3.7 2.0 - - - +
145A GLN* 1.3 78.4 + - - +
147A LEU* 1.3 64.8 + - - +
149A GLU* 2.9 13.4 + - - +
150A SER* 2.9 26.0 + - - -
377A PHE* 3.5 9.2 - - - +
378A ASN* 3.4 41.7 - - + +
383A LYS* 3.7 10.0 - - - +
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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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135A VAL* 4.1 11.9 - - + -
139A MET* 3.8 17.3 - - + -
143A ASP 3.1 13.9 + - - +
144A LEU* 3.5 8.5 - - + +
146A ALA* 1.3 79.0 - - - +
148A LYS* 1.3 60.7 + - - +
150A SER* 3.3 5.4 + - - -
151A MET* 3.1 42.9 + - + +
289A PHE* 3.3 49.1 - - + -
377A PHE* 3.7 39.8 - - + +
382A PHE* 4.5 4.5 - - + -
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Residues in contact with LYS 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 LEU* 2.8 37.7 + - + +
145A GLN* 3.5 15.2 - - + +
147A LEU* 1.3 73.2 - - - +
149A GLU* 1.3 63.7 + - + +
151A MET* 3.3 17.6 + - + +
152A GLN* 2.9 31.4 + - - +
244A LEU* 3.1 22.1 - - - +
245A GLY* 2.9 31.7 + - - -
246A GLU 4.0 1.6 - - - -
247A LEU* 2.9 36.1 + - + +
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Residues in contact with GLU 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 GLN* 2.8 44.6 + - + +
146A ALA* 2.9 8.5 + - - +
148A LYS* 1.3 76.3 - - + +
150A SER* 1.3 64.2 + - - +
152A GLN* 3.0 20.0 + - - +
153A MET* 2.9 22.1 + - - +
383A LYS* 4.3 18.1 - - - -
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Residues in contact with SER 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 2.9 14.7 + - - -
147A LEU* 3.5 9.6 - - - -
149A GLU* 1.3 76.5 - - - +
151A MET* 1.3 56.3 + - - +
153A MET* 3.4 10.0 + - - +
154A SER 3.2 16.1 + - - -
382A PHE* 3.4 24.4 - - - -
383A LYS* 3.9 19.6 - - - +
386A PHE* 3.0 36.8 - - - -
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Residues in contact with MET 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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133A TYR* 3.8 28.1 + - + -
135A VAL* 3.4 38.8 - - + -
147A LEU* 3.1 46.8 + - + +
148A LYS* 3.7 20.2 - - + +
150A SER* 1.3 73.0 - - - +
152A GLN* 1.3 64.9 + - - +
153A MET 3.1 1.8 - - - -
154A SER* 2.5 22.6 + - - -
155A LEU* 3.2 11.3 + - - +
244A LEU* 4.1 24.1 - - + +
247A LEU* 4.8 1.6 - - + -
289A PHE* 4.3 13.5 - - + -
386A PHE* 4.2 1.3 - - - -
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Residues in contact with GLN 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 LYS* 2.9 21.0 + - - +
149A GLU* 3.0 26.0 + - - +
151A MET* 1.3 76.9 - - - +
153A MET* 1.3 62.4 + - - +
155A LEU* 3.5 17.0 + - - +
156A SER* 3.6 8.0 + - - -
241A THR* 2.8 41.0 + - - +
244A LEU* 4.0 19.5 - - + -
245A GLY* 3.5 20.4 - - - -
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Residues in contact with MET 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 GLU 2.9 11.6 + - - +
150A SER* 3.4 15.7 - - - +
151A MET 3.1 0.2 - - - -
152A GLN* 1.3 74.6 - - - +
154A SER* 1.3 75.4 + - - +
155A LEU 3.1 1.1 - - - -
156A SER* 2.9 27.6 + - - +
157A LEU* 3.0 40.8 + - + -
383A LYS 5.8 0.7 - - - +
386A PHE* 5.0 3.8 - - - -
387A GLN* 3.7 35.0 - - + +
390A PHE* 4.8 2.0 - - + -
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Residues in contact with SER 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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133A TYR* 2.9 21.4 + - - -
150A SER 3.2 2.2 + - - -
151A MET* 2.5 30.8 + - - -
153A MET* 1.3 91.2 - - - +
155A LEU* 1.3 60.1 + - - +
157A LEU* 3.1 14.5 + - - +
158A LEU* 3.2 16.5 + - - +
386A PHE* 3.7 25.2 - - - -
390A PHE* 3.9 19.6 - - - -
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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
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133A TYR* 3.9 7.4 - - + +
151A MET 3.2 8.7 + - - +
152A GLN* 3.5 11.9 - - - +
153A MET 3.1 0.4 - - - -
154A SER* 1.3 83.2 + - - +
156A SER* 1.3 59.8 + - - +
157A LEU 3.4 0.5 + - - -
158A LEU* 3.7 23.3 + - + +
164A VAL* 4.6 2.5 - - + -
233A VAL* 3.9 29.3 - - + +
237A ASP* 3.8 31.7 - - + +
240A LEU* 3.5 34.1 - - + -
241A THR* 3.8 19.7 - - - +
244A LEU* 4.6 4.9 - - + -
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Residues in contact with SER 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 GLN 3.6 7.2 + - - -
153A MET* 2.9 21.5 + - - +
155A LEU* 1.3 78.7 - - - +
157A LEU* 1.3 70.2 + - - +
158A LEU 4.7 2.4 - - - +
392A LYS* 5.3 0.3 + - - -
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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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153A MET* 3.0 36.8 - - + +
154A SER 3.1 6.2 + - - +
156A SER* 1.3 90.8 - - - +
158A LEU* 1.3 66.4 + - - +
159A PRO* 3.8 0.9 - - - +
387A GLN* 4.7 4.3 - - + +
390A PHE* 3.4 32.3 - - + +
392A LYS* 3.0 34.7 + - - +
398A PHE* 3.5 16.1 - - + -
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Residues in contact with LEU 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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131A PHE* 3.5 45.8 - - + -
133A TYR* 3.5 22.9 - - - +
154A SER 3.2 13.2 - - - +
155A LEU* 3.9 17.4 - - + +
156A SER 3.6 3.1 - - - +
157A LEU* 1.3 81.1 - - - +
159A PRO* 1.3 71.5 - - + +
160A PRO* 3.6 4.0 - - - +
162A ALA* 4.8 0.9 - - + -
164A VAL* 3.8 27.1 - - + -
233A VAL* 4.2 18.3 - - + +
390A PHE* 4.1 7.0 - - + -
398A PHE* 3.8 11.0 - - + -
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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
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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