Contacts of the helix formed by residues 184 - 203 (chain C) in PDB entry 1NVE
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C THR 3.3 8.3 - - - +
183C LEU* 1.3 91.8 - - + +
185C VAL* 1.3 67.0 + - - +
186C ARG* 4.5 4.0 - - + +
187C GLU* 2.8 32.0 + - + +
188C PHE 3.0 10.7 + - - -
402C NAD 3.7 22.9 - - + +
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Residues in contact with VAL 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C LEU 3.3 3.7 + - - +
184C PRO* 1.3 70.6 - - - +
186C ARG* 1.3 64.7 + - - +
188C PHE* 3.4 2.6 + - - +
189C ILE* 3.0 39.1 + - + +
221C VAL* 3.6 42.0 - - + +
222C ARG* 4.3 26.0 - - + +
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Residues in contact with ARG 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C PRO* 3.1 4.3 - - + +
185C VAL* 1.3 80.2 - - - +
187C GLU* 1.3 60.9 + - + +
189C ILE* 3.4 8.2 + - + +
190C ASN* 2.9 28.6 + - - +
284C GLN 2.8 29.3 + - - -
285C ILE* 3.9 0.2 - - - +
286C LEU* 3.6 24.3 - - + +
289C GLU* 2.9 40.6 + - - +
337C LEU* 3.5 33.1 - - - +
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Residues in contact with GLU 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C THR* 5.6 3.4 - - - +
141C LEU* 4.9 1.4 + - - +
142C LEU* 5.4 0.7 + - - +
183C LEU* 3.5 21.1 - - + +
184C PRO* 2.8 23.3 + - + +
186C ARG* 1.3 74.6 - - + +
188C PHE* 1.3 67.0 + - - +
190C ASN* 3.1 14.8 + - - +
191C GLY* 2.9 19.6 + - - -
286C LEU* 3.9 25.6 - - - +
402C NAD 3.4 48.6 + - - +
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Residues in contact with PHE 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LEU* 3.2 23.2 - - + +
180C LEU* 3.9 46.2 - - + -
183C LEU* 3.4 17.8 - - + +
184C PRO 3.0 9.4 + - - +
185C VAL* 3.6 8.1 - - - +
187C GLU* 1.3 76.5 - - - +
189C ILE* 1.3 69.9 + - + +
191C GLY 3.1 10.4 + - - -
192C MET* 3.2 26.6 + - + -
217C ILE* 3.9 20.2 - - + -
218C LEU* 5.1 3.1 - - + -
221C VAL* 3.5 42.0 - - + -
232C PHE* 4.3 9.0 - + - -
239C LEU* 4.3 9.4 - - + -
243C ILE* 5.2 1.8 - - + -
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Residues in contact with ILE 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C VAL* 3.0 29.4 + - + +
186C ARG* 3.6 7.6 - - + +
188C PHE* 1.3 82.5 - - + +
190C ASN* 1.3 65.2 + - - +
192C MET* 3.0 21.4 + - + +
218C LEU* 3.5 31.0 - - + -
221C VAL* 4.9 1.8 - - + -
222C ARG* 5.2 2.9 - - - +
289C GLU* 6.1 1.8 - - + +
323C TYR 2.9 37.0 - - - +
324C GLY* 3.3 26.5 - - - +
325C LEU* 3.4 18.2 - - + +
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Residues in contact with ASN 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LEU* 4.2 12.4 - - - +
186C ARG 2.9 15.8 + - - +
187C GLU* 3.1 20.5 + - - +
189C ILE* 1.3 75.9 - - - +
191C GLY* 1.3 61.9 + - - +
193C ALA* 3.2 22.0 + - - +
194C GLU* 4.6 0.3 + - - +
286C LEU* 3.2 29.6 - - + +
287C HIS* 4.5 3.4 - - - +
288C GLY* 2.7 37.9 + - - +
289C GLU* 3.2 6.8 + - + +
325C LEU* 4.3 7.2 - - - -
402C NAD 4.1 18.0 + - - -
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Residues in contact with GLY 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LEU* 3.6 18.4 - - - +
142C LEU* 3.8 24.2 - - - -
145C VAL* 4.6 1.7 - - - +
187C GLU 2.9 12.2 + - - -
188C PHE 3.1 4.6 + - - -
190C ASN* 1.3 77.1 - - - +
192C MET* 1.3 61.0 + - - +
193C ALA 3.0 2.0 + - - -
194C GLU* 3.2 16.9 + - - +
195C VAL* 3.6 11.1 + - - +
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Residues in contact with MET 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C LEU* 3.6 15.3 - - + -
188C PHE* 3.2 34.3 + - + +
189C ILE* 3.0 15.0 + - + +
191C GLY* 1.3 76.4 - - - +
193C ALA* 1.3 55.5 + - - +
194C GLU 3.2 0.2 - - - -
195C VAL* 3.2 25.3 + - + +
196C ILE* 2.9 39.7 + - + +
210C LEU* 4.0 13.0 - - + -
217C ILE* 5.3 4.3 - - + -
242C ARG* 6.2 0.7 - - + -
243C ILE* 5.8 3.4 - - - -
323C TYR* 3.4 55.4 - - + +
325C LEU* 4.3 2.2 - - + -
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Residues in contact with ALA 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C ASN 3.2 13.5 + - - +
191C GLY 3.0 0.6 - - - -
192C MET* 1.3 79.8 - - - +
194C GLU* 1.3 60.0 + - + +
196C ILE* 4.1 0.6 - - - +
197C LYS* 3.0 15.9 + - - +
288C GLY* 3.3 33.0 - - - +
291C VAL* 4.6 3.6 - - + -
295C MET* 3.0 30.5 - - + +
325C LEU* 3.6 19.7 - - + +
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Residues in contact with GLU 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LEU* 4.4 16.8 - - + -
145C VAL* 4.1 15.3 - - + +
146C ASP* 4.0 22.2 - - + +
191C GLY 3.2 9.9 + - - +
193C ALA* 1.3 76.4 - - + +
195C VAL* 1.3 61.8 + - - +
197C LYS* 2.6 37.1 + - - +
198C THR* 2.9 35.6 + - - +
246C SER* 4.0 2.7 - - - +
271C HIS* 3.3 11.3 + - - -
287C HIS* 4.3 1.7 + - - -
288C GLY* 5.5 0.7 - - - -
291C VAL* 4.0 11.6 - - - +
602C ZN 2.8 29.7 - - - -
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Residues in contact with VAL 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LEU* 4.1 17.5 - - + -
145C VAL* 4.2 11.4 - - + -
191C GLY 3.7 14.6 - - - +
192C MET* 3.2 26.4 + - + +
194C GLU* 1.3 77.9 - - - +
196C ILE* 1.3 61.4 + - - +
198C THR* 3.4 2.6 + - - -
199C ALA* 3.1 22.9 + - - +
206C GLU* 5.9 0.4 - - + +
210C LEU* 3.9 24.0 - - + -
242C ARG* 3.9 24.0 - - + +
243C ILE* 5.1 3.6 - - + -
246C SER* 3.5 16.8 + - - -
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Residues in contact with ILE 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C MET* 2.9 33.4 + - + +
193C ALA 4.1 3.1 - - - +
195C VAL* 1.3 73.0 - - - +
197C LYS* 1.3 59.8 + - - +
199C ALA* 3.5 1.9 + - - +
200C ALA* 2.9 31.9 + - + +
207C PHE* 4.1 21.7 - - + -
210C LEU* 3.9 14.1 - - + -
295C MET* 4.9 3.8 - - - -
316C ILE* 5.4 3.1 - - + +
319C CYS* 4.0 11.4 - - + +
320C LEU* 3.6 43.1 - - + -
323C TYR* 3.8 32.1 - - + -
325C LEU* 4.3 1.6 - - + -
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Residues in contact with LYS 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C ASP* 5.4 2.8 + - - -
193C ALA 3.0 20.5 + - - +
194C GLU* 2.6 26.5 + - - +
195C VAL 3.3 0.2 - - - -
196C ILE* 1.3 76.8 - - - +
198C THR* 1.3 81.4 + - - +
200C ALA* 3.1 15.0 + - - +
201C ILE* 3.1 20.5 + - + +
267C LEU* 2.9 48.3 + - - +
269C TRP* 3.5 35.7 - - + +
271C HIS* 3.7 14.5 - - + -
295C MET* 3.8 15.0 - - + -
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Residues in contact with THR 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C VAL 5.7 0.3 + - - -
194C GLU* 2.9 13.0 + - - +
195C VAL 3.6 2.7 - - - -
197C LYS* 1.3 86.8 + - - +
199C ALA* 1.3 58.3 + - - +
201C ILE* 3.2 13.5 + - - +
202C SER* 2.7 31.9 + - - +
206C GLU* 6.5 0.4 - - + -
245C ALA 4.6 1.1 - - - +
246C SER* 2.8 36.7 + - - +
249C HIS* 3.4 40.5 + - + +
250C LYS* 5.6 1.9 + - - +
267C LEU* 5.2 3.3 - - - +
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Residues in contact with ALA 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C VAL 3.1 5.6 + - - +
196C ILE 3.9 1.1 - - - +
198C THR* 1.3 79.7 - - - +
200C ALA* 1.3 66.1 + - - +
202C SER* 3.0 17.6 + - - -
203C SER 3.0 20.6 + - - +
206C GLU* 3.8 22.0 - - + -
207C PHE* 3.8 13.7 - - + +
210C LEU* 3.5 32.5 - - + -
372C GLY* 3.9 0.7 + - - -
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Residues in contact with ALA 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C ILE* 2.9 20.4 + - + +
197C LYS 3.1 6.7 + - - +
199C ALA* 1.3 76.7 - - - +
201C ILE* 1.3 56.6 + - - +
207C PHE* 3.8 21.9 - - + -
269C TRP* 3.5 28.5 - - + -
316C ILE* 4.9 3.4 - - + -
368C LEU* 3.9 13.6 - - + +
371C ILE* 3.7 2.1 - - + -
372C GLY 2.6 25.9 + - - +
373C THR 4.1 0.5 + - - -
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Residues in contact with ILE 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C LYS* 3.1 16.6 + - - +
198C THR* 3.3 18.8 - - - +
200C ALA* 1.3 76.9 - - - +
202C SER* 1.3 61.3 + - - +
249C HIS* 4.6 7.0 + - + -
266C LEU* 3.3 36.4 - - + +
267C LEU* 4.2 16.2 - - + -
269C TRP* 3.8 24.5 - - + -
366C VAL* 5.2 1.1 - - + -
368C LEU* 3.5 27.8 - - + -
372C GLY* 3.8 6.1 - - - +
374C PRO* 3.4 29.7 - - + +
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Residues in contact with SER 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C THR* 2.7 23.7 + - - +
199C ALA* 3.0 3.2 + - - -
201C ILE* 1.3 80.4 - - - +
203C SER* 1.3 66.8 + - - +
206C GLU* 5.7 0.5 - - - +
249C HIS* 3.1 40.3 - - - -
372C GLY* 3.5 13.9 - - - +
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Residues in contact with SER 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C ALA 3.0 15.3 + - - +
202C SER* 1.3 85.9 + - - +
204C GLU* 1.3 59.2 + - - +
205C GLU* 3.4 14.0 + - - +
206C GLU* 3.1 29.5 + - - +
207C PHE* 2.9 23.7 + - - +
372C GLY* 3.9 2.6 - - - -
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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