Contacts of the helix formed by residues 184 - 201 (chain A) in PDB entry 1NR5
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 PRO 184 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A THR 3.5 7.4 - - - +
183A LEU* 1.3 100.2 - - + +
185A VAL* 1.3 66.0 + - - +
186A ARG* 4.5 4.7 - - + +
187A GLU* 3.1 22.2 + - + +
188A PHE* 3.0 19.2 + - - +
400A NAD 3.7 15.9 - - + +
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU 3.6 1.2 + - - -
184A PRO* 1.3 71.3 - - - +
186A ARG* 1.3 62.5 + - - +
188A PHE* 3.2 2.8 + - - +
189A ILE* 3.0 40.1 + - + +
221A VAL* 3.5 44.6 - - + +
222A ARG* 4.0 24.9 - - + +
231A ARG* 3.5 7.2 - - - +
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Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A PRO* 3.3 3.9 - - + +
185A VAL* 1.3 79.7 - - - +
187A GLU* 1.3 61.4 + - + +
189A ILE* 3.5 6.7 + - - +
190A ASN* 2.9 26.5 + - - +
284A GLN 3.0 26.9 + - - -
285A ILE* 4.0 1.0 - - - +
286A LEU* 3.6 22.1 - - + +
289A GLU* 2.9 41.4 + - - +
333A ARG* 3.6 10.8 - - - +
337A LEU* 3.6 27.9 - - - +
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Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A THR* 5.5 3.0 - - + +
141A LEU* 5.1 0.7 - - - +
142A LEU* 5.5 1.6 + - - +
183A LEU* 3.6 20.2 - - + +
184A PRO* 3.1 25.8 + - + +
186A ARG* 1.3 76.7 - - + +
188A PHE* 1.3 65.4 + - - +
190A ASN* 3.1 15.8 + - - +
191A GLY* 3.0 19.8 + - - -
286A LEU* 3.7 30.0 - - - +
400A NAD 3.5 47.4 + - - +
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Residues in contact with PHE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 3.4 28.4 - - + +
180A LEU* 4.8 6.5 - - + -
183A LEU* 3.7 23.7 - - + +
184A PRO 3.0 12.9 + - - +
185A VAL* 3.6 11.4 - - - +
187A GLU* 1.3 77.2 - - - +
189A ILE* 1.3 69.8 + - + +
191A GLY 3.1 9.5 + - - -
192A MET* 3.3 26.4 + - + +
217A ILE* 3.8 22.7 - - + -
218A LEU* 5.9 2.0 - - + -
221A VAL* 3.6 34.1 - - + -
231A ARG* 5.4 2.0 - - - +
232A PHE* 3.8 28.0 - + - -
239A LEU* 4.1 20.2 - - + -
323A TYR* 5.9 0.4 - + - -
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Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A VAL* 3.0 30.9 + - + +
186A ARG* 3.9 6.3 - - - +
188A PHE* 1.3 82.7 - - + +
190A ASN* 1.3 63.2 + - - +
192A MET* 3.1 20.2 + - + +
218A LEU* 4.0 13.5 - - + -
221A VAL* 5.2 0.2 - - + -
222A ARG* 3.6 28.0 - - - +
323A TYR* 3.1 28.3 - - + +
324A GLY* 4.1 10.8 - - - +
325A LEU* 3.3 30.3 - - + +
333A ARG* 5.7 6.1 - - - +
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Residues in contact with ASN 190 (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 LEU* 3.7 15.0 - - - +
186A ARG 2.9 15.3 + - - +
187A GLU* 3.1 18.4 + - - +
189A ILE* 1.3 78.5 - - - +
191A GLY* 1.3 61.0 + - - +
193A ALA* 3.4 9.9 + - - +
194A GLU 4.5 0.7 + - - -
286A LEU* 3.2 27.3 - - + +
287A HIS* 4.6 1.4 - - - +
288A GLY* 2.7 44.0 + - - +
289A GLU* 3.2 10.5 + - + +
325A LEU* 4.3 8.3 - - - -
400A NAD 3.4 23.4 + - - -
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Residues in contact with GLY 191 (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 LEU* 4.0 8.1 - - - -
142A LEU* 3.8 32.8 - - - -
145A VAL* 4.4 2.9 - - - +
187A GLU 3.0 12.0 + - - -
188A PHE 3.1 5.7 + - - -
190A ASN* 1.3 73.9 - - - +
192A MET* 1.3 64.7 + - - +
193A ALA 3.1 3.4 + - - -
194A GLU* 3.2 15.1 + - - +
195A VAL* 3.5 12.0 + - - +
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Residues in contact with MET 192 (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 LEU* 3.8 16.4 - - - -
188A PHE* 3.3 31.9 + - + +
189A ILE* 3.1 15.2 + - + +
191A GLY* 1.3 76.9 - - - +
193A ALA* 1.3 56.5 + - - +
195A VAL* 3.0 19.8 + - + +
196A ILE* 2.8 40.6 + - + +
210A LEU* 3.9 21.5 - - + -
217A ILE* 5.0 7.4 - - + -
239A LEU* 5.9 2.7 - - - -
242A ARG* 6.0 2.5 - - + -
323A TYR* 3.5 48.7 - - + +
325A LEU* 4.6 3.1 - - + -
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Residues in contact with ALA 193 (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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190A ASN 3.4 11.5 + - - +
191A GLY 3.1 0.6 - - - -
192A MET* 1.3 78.3 - - - +
194A GLU* 1.3 58.3 + - - +
196A ILE* 3.6 1.9 + - - +
197A LYS* 3.0 27.5 + - - +
288A GLY* 3.2 32.5 - - - +
291A VAL* 4.7 2.7 - - + -
292A ALA 4.6 0.4 - - - +
295A MET* 3.3 20.5 - - + +
325A LEU* 3.7 23.8 - - + +
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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
----------------------------------------------------------
142A LEU* 4.0 24.5 - - + -
145A VAL* 4.3 4.0 - - + -
146A ASP* 3.1 27.3 - - + +
190A ASN 5.1 1.1 - - - +
191A GLY 3.2 8.8 + - - +
193A ALA* 1.3 76.6 - - + +
195A VAL* 1.3 60.0 + - - +
197A LYS* 3.0 32.2 + - - +
198A THR* 2.8 34.6 + - - -
246A SER* 4.9 1.3 - - - -
271A HIS* 3.6 3.9 + - - -
287A HIS* 3.2 11.3 + - + -
288A GLY* 5.4 0.7 - - - -
291A VAL* 4.3 6.2 - - - +
400A NAD 3.8 1.2 - - - -
600A ZN 2.0 34.8 - - - -
1500A CRB 3.0 0.3 + - - -
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 4.9 3.8 - - + -
145A VAL* 3.8 28.3 - - + -
191A GLY 3.7 14.1 - - - +
192A MET* 3.0 25.0 + - + +
194A GLU* 1.3 75.1 - - - +
196A ILE* 1.3 64.3 + - - +
198A THR* 3.3 3.8 + - - -
199A ALA* 3.0 22.2 + - - +
206A GLU* 5.8 1.6 - - + +
210A LEU* 3.8 28.9 - - + -
242A ARG* 4.4 21.1 - - + +
243A ILE* 5.9 0.4 - - + -
246A SER* 4.2 10.4 - - - +
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Residues in contact with ILE 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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192A MET* 2.8 23.1 + - + +
193A ALA 3.9 3.6 - - - +
195A VAL* 1.3 73.5 - - - +
197A LYS* 1.3 64.2 + - - +
199A ALA* 3.3 3.1 + - - +
200A ALA* 2.9 23.4 + - + +
207A PHE* 3.9 23.0 - - + -
210A LEU* 3.9 19.5 - - + -
269A TRP* 5.8 0.2 - - + -
295A MET* 4.6 6.3 - - - -
316A ILE* 5.7 2.2 - - + -
319A CYS* 4.2 15.9 - - + +
320A LEU* 3.9 33.4 - - + -
323A TYR* 3.7 32.1 - - + -
325A LEU* 4.2 9.9 - - + -
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Residues in contact with LYS 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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146A ASP* 3.8 7.3 + - - -
193A ALA 3.0 19.6 + - - +
194A GLU* 3.0 26.8 + - - +
196A ILE* 1.3 77.3 - - - +
198A THR* 1.3 81.4 + - - +
200A ALA* 3.3 2.8 + - - +
201A ILE* 3.3 26.1 + - + +
267A LEU* 2.7 42.5 + - - +
269A TRP* 3.5 39.2 - - + +
271A HIS* 3.8 4.3 - - + -
291A VAL* 4.8 0.9 - - + -
295A MET* 3.7 17.2 - - + -
1500A CRB 3.2 15.6 + - - +
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Residues in contact with THR 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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145A VAL 5.2 1.6 + - - -
146A ASP* 5.9 2.1 - - - +
194A GLU* 2.8 21.7 + - - +
195A VAL 3.6 4.5 - - - -
197A LYS* 1.3 88.4 + - - +
199A ALA* 1.3 60.4 + - - +
201A ILE* 3.3 18.6 - - + +
202A SER* 2.8 19.0 + - - +
245A ALA 4.8 0.4 - - - +
246A SER* 3.5 40.1 + - - +
249A HIS* 3.9 24.5 - - + -
250A LYS* 5.0 2.8 - - + +
267A LEU* 5.1 5.5 - - + +
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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 VAL* 3.0 6.7 + - + +
196A ILE 3.3 4.2 + - - +
198A THR* 1.3 76.5 - - - +
200A ALA* 1.3 60.8 + - - +
202A SER* 3.1 5.5 + - - -
203A SER 2.9 35.3 + - - +
206A GLU* 4.0 13.7 - - + -
207A PHE* 3.8 22.9 - - + +
210A LEU* 3.6 30.7 - - + -
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Residues in contact with ALA 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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196A ILE 2.9 17.7 + - - +
197A LYS 3.3 1.3 + - - +
199A ALA* 1.3 78.2 - - - +
201A ILE* 1.3 56.3 + - - +
202A SER 3.4 0.2 - - - -
207A PHE* 4.0 22.4 - - + -
269A TRP* 3.6 29.4 - - + -
316A ILE* 5.5 0.7 - - + -
368A LEU* 3.7 16.2 - - + +
371A ILE* 3.7 5.0 - - + -
372A GLY 2.6 28.3 + - - +
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Residues in contact with ILE 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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197A LYS* 3.3 15.2 + - - +
198A THR* 3.3 17.7 - - - +
200A ALA* 1.3 77.4 - - - +
202A SER* 1.3 57.2 + - - +
249A HIS* 4.2 16.8 + - + +
253A VAL* 5.8 0.2 - - + -
266A LEU* 3.4 37.4 - - + +
267A LEU* 4.0 21.8 - - + -
269A TRP* 3.9 27.8 - - + -
366A VAL* 5.1 2.0 - - + -
368A LEU* 4.2 18.8 - - + -
372A GLY* 4.0 4.9 - - - +
374A PRO* 3.6 27.2 - - + +
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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
------------------------------------------------------------
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