Contacts of the helix formed by residues 193 - 213 (chain A) in PDB entry 3NUI
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 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A TYR* 3.5 5.2 - - - -
191A GLY 4.1 7.0 - - - +
192A GLU* 1.3 78.3 - - - +
194A GLU* 1.3 60.1 + - - +
195A GLU* 3.6 8.7 + - - +
196A GLN* 3.1 43.0 + - - +
197A PHE* 2.9 27.2 + - - +
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Residues in contact with GLU 194 (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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184A TYR* 3.4 39.4 + - + +
193A THR* 1.3 74.0 - - - +
195A GLU* 1.3 58.0 + - - +
197A PHE* 3.4 1.7 + - - +
198A VAL* 2.9 28.9 + - - +
235A ALA* 3.3 23.7 - - + +
236A LYS* 2.9 47.6 + - + +
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Residues in contact with GLU 195 (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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193A THR* 3.3 8.1 + - - +
194A GLU* 1.3 79.8 - - - +
196A GLN* 1.4 58.2 + - + +
198A VAL* 3.5 6.5 + - - +
199A ALA* 3.0 27.0 + - + +
236A LYS 5.7 1.8 - - - -
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Residues in contact with GLN 196 (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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191A GLY 3.9 3.3 - - - +
192A GLU* 3.7 19.8 - - + +
193A THR* 3.1 43.5 + - - +
195A GLU* 1.4 77.0 - - + +
197A PHE* 1.3 61.7 + - - +
199A ALA* 3.2 8.1 + - - +
200A ARG* 2.9 28.2 + - - +
203A ARG* 4.8 1.6 + - - -
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Residues in contact with PHE 197 (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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180A THR* 4.5 1.3 - - - -
181A CYS 3.6 22.2 - - - -
182A PRO* 3.6 17.9 - - + -
183A HIS 3.9 9.9 - - - -
184A TYR* 3.6 31.6 - + + -
187A TYR* 3.7 17.3 - - + -
188A GLY* 3.9 4.3 - - - -
192A GLU* 3.5 14.7 - - - +
193A THR 2.9 16.7 + - - +
194A GLU 3.5 3.4 - - - +
196A GLN* 1.3 73.5 - - - +
198A VAL* 1.3 67.3 + - + +
200A ARG* 3.1 31.2 + - - +
201A LEU* 2.9 50.6 + - + +
235A ALA* 3.8 22.0 - - + -
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Residues in contact with VAL 198 (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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194A GLU 2.9 19.0 + - - +
195A GLU* 3.9 6.5 - - - +
196A GLN 3.3 0.2 - - - -
197A PHE* 1.3 76.6 - - + +
199A ALA* 1.3 63.1 + - - +
201A LEU* 3.2 7.6 + - + +
202A ALA* 3.0 21.0 + - - +
235A ALA* 3.6 23.8 - - + -
236A LYS 3.4 22.0 - - - +
237A GLY* 3.9 13.2 - - - +
238A TYR* 4.0 17.3 - - + +
241A ALA* 3.6 27.1 - - + +
242A ILE* 5.8 0.6 - - + +
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Residues in contact with ALA 199 (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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195A GLU* 3.0 16.7 + - + +
196A GLN* 3.2 10.9 + - - +
198A VAL* 1.3 77.8 - - - +
200A ARG* 1.3 58.3 + - - +
202A ALA* 3.3 9.2 + - - +
203A ARG* 2.9 41.4 + - - +
241A ALA* 6.0 0.7 - - - -
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Residues in contact with ARG 200 (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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180A THR* 4.8 12.1 + - - +
187A TYR* 3.1 24.2 + - - +
189A GLU* 3.4 29.4 + - - +
192A GLU* 2.8 38.8 + - - +
196A GLN 2.9 13.6 + - - +
197A PHE* 3.1 23.0 + - - +
199A ALA* 1.3 75.1 - - - +
201A LEU* 1.3 69.4 + - + +
203A ARG* 3.3 33.5 + - - +
204A GLU* 2.7 32.0 + - + +
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Residues in contact with LEU 201 (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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180A THR* 3.7 26.2 - - - +
182A PRO* 3.6 38.6 - - + -
197A PHE* 2.9 48.2 + - + +
198A VAL* 3.2 6.5 + - + +
200A ARG* 1.3 88.5 - - + +
202A ALA* 1.3 59.0 + - - +
204A GLU* 3.5 16.3 - - - +
205A LEU* 2.9 29.1 + - - +
238A TYR* 4.0 20.6 - - + -
242A ILE* 4.8 3.7 - - + +
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Residues in contact with ALA 202 (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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198A VAL 3.0 13.3 + - - +
199A ALA* 3.5 11.9 - - - +
201A LEU* 1.3 77.2 - - - +
203A ARG* 1.4 57.2 + - - +
205A LEU* 3.2 6.8 + - - +
206A GLU* 2.9 32.1 + - - +
241A ALA* 4.4 17.3 - - + +
242A ILE* 4.5 6.1 - - - +
245A ILE* 3.6 22.9 - - + +
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Residues in contact with ARG 203 (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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192A GLU* 5.5 0.2 + - - -
196A GLN 4.8 1.4 + - - -
199A ALA* 2.9 22.2 + - - +
200A ARG* 3.4 53.6 - - + +
202A ALA* 1.4 72.0 - - - +
204A GLU* 1.3 66.7 + - - +
206A GLU* 3.3 7.6 + - - +
207A GLU* 3.0 48.4 + - - +
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Residues in contact with GLU 204 (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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179A LEU* 3.5 17.6 - - + +
180A THR* 2.3 55.3 + - - +
200A ARG* 2.7 26.3 + - + +
201A LEU* 3.5 14.7 - - - +
203A ARG* 1.3 74.8 - - - +
205A LEU* 1.3 56.7 + - - +
207A GLU* 3.8 7.2 - - - +
208A THR* 2.9 41.0 + - - +
211A ARG* 5.3 0.2 + - - -
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Residues in contact with LEU 205 (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* 3.9 23.1 - - + -
179A LEU* 3.9 29.6 - - + -
201A LEU 2.9 13.8 + - - +
202A ALA* 3.2 8.5 + - - +
204A GLU* 1.3 74.8 - - - +
206A GLU* 1.3 63.7 + - - +
208A THR* 3.3 2.1 + - - -
209A ILE* 2.9 43.6 + - + +
220A PHE* 5.7 0.2 - - + -
242A ILE* 3.7 37.9 - - + +
245A ILE* 3.8 19.5 - - + -
246A LEU* 4.0 13.2 - - + -
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Residues in contact with GLU 206 (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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202A ALA 2.9 17.9 + - - +
203A ARG* 3.5 11.4 - - - +
205A LEU* 1.3 78.2 - - - +
207A GLU* 1.3 55.2 + - + +
209A ILE* 3.3 4.4 + - - +
210A GLN* 2.9 55.6 + - - +
245A ILE* 3.9 25.6 - - + +
248A LYS* 2.6 30.6 + - - -
249A TYR* 2.9 24.5 + - - -
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Residues in contact with GLU 207 (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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203A ARG* 3.0 36.8 + - - +
204A GLU* 3.8 6.0 - - - +
206A GLU* 1.3 80.8 - - + +
208A THR* 1.3 60.1 + - - +
210A GLN* 3.8 13.5 - - - +
211A ARG* 2.8 48.6 + - - +
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Residues in contact with THR 208 (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* 4.4 11.7 - - + -
177A VAL* 3.8 28.5 - - + -
179A LEU* 4.0 20.4 - - + +
204A GLU* 2.9 22.8 + - - +
205A LEU* 3.6 4.7 - - - -
207A GLU* 1.3 73.3 - - - +
209A ILE* 1.3 57.0 + - - +
211A ARG* 3.5 21.8 + - - +
212A GLU* 2.8 45.3 + - + +
217A ILE* 5.5 0.4 - - + -
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Residues in contact with ILE 209 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A LEU* 4.5 2.5 - - + -
205A LEU* 2.9 38.9 + - + +
206A GLU 3.6 6.1 - - - +
208A THR* 1.3 75.0 - - - +
210A GLN* 1.4 55.4 + - - +
213A GLY* 2.7 35.9 + - - -
214A ALA* 3.7 16.1 + - + -
217A ILE* 4.0 11.9 - - + -
245A ILE* 3.8 14.8 - - + +
246A LEU* 4.4 3.6 - - + -
249A TYR* 3.5 50.0 - - + -
251A ILE* 3.6 26.5 - - + -
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Residues in contact with GLN 210 (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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206A GLU* 2.9 46.9 + - - +
207A GLU* 4.0 13.7 - - - +
209A ILE* 1.4 73.9 - - - +
211A ARG* 1.3 61.9 + - - +
213A GLY* 3.8 7.0 + - - -
249A TYR* 3.5 19.0 + - + +
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Residues in contact with ARG 211 (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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204A GLU 5.3 0.2 + - - -
207A GLU* 2.8 48.7 + - - +
208A THR* 3.5 29.8 + - - +
210A GLN* 1.3 73.0 - - - +
212A GLU* 1.3 78.5 + - + +
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Residues in contact with GLU 212 (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 LYS* 2.7 48.0 + - + +
177A VAL* 4.3 19.8 - - + +
208A THR* 2.8 36.0 + - + +
211A ARG* 1.3 89.2 + - + +
213A GLY* 1.3 60.5 + - - +
216A THR* 3.1 19.3 + - - +
217A ILE* 4.0 18.2 - - + -
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Residues in contact with GLY 213 (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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209A ILE 2.7 17.8 + - - -
210A GLN* 4.2 6.1 - - - -
211A ARG 3.3 2.0 - - - -
212A GLU* 1.3 72.5 - - - +
214A ALA* 1.3 60.3 + - - +
215A ASP* 3.2 13.2 - - - -
216A THR* 2.9 30.3 + - - -
217A ILE* 3.8 6.1 + - - +
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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