Contacts of the helix formed by residues 193 - 208 (chain C) in PDB entry 3RMD
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 ASN 193 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C LEU* 3.6 9.0 - - - -
153C ASN 4.6 2.0 - - - -
191C PHE* 3.3 7.3 - - - +
192C ASP* 1.3 83.3 - - + +
194C GLU* 1.3 64.5 + - - +
195C LYS* 3.3 37.2 - - - +
196C GLU* 2.7 35.8 - - - +
197C LEU* 3.2 13.5 + - - +
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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
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132C PRO* 2.9 22.2 - - + +
133C ILE* 3.4 22.2 + - - +
151C LEU* 3.5 17.5 - - + +
153C ASN 4.7 1.0 + - - -
193C ASN* 1.3 70.6 - - - +
195C LYS* 1.3 61.0 + - + +
197C LEU* 2.6 28.7 + - + +
198C LEU* 2.9 32.1 + - + +
229C ARG* 2.5 50.1 + - - +
233C ILE* 3.8 10.9 - - + +
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Residues in contact with LYS 195 (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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193C ASN* 3.3 15.8 - - - +
194C GLU* 1.3 76.8 - - + +
196C GLU* 1.3 64.7 + - - +
198C LEU* 4.7 2.2 - - - +
199C MET* 3.0 33.6 + - - +
233C ILE* 3.8 44.6 + - + +
234C PHE* 3.6 17.8 - - + -
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Residues in contact with GLU 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C PHE* 3.2 21.2 - - + -
192C ASP 5.7 0.7 - - - +
193C ASN* 2.7 33.6 + - - +
194C GLU 3.1 0.8 - - - -
195C LYS* 1.3 85.1 - - - +
197C LEU* 1.3 63.6 + - - +
199C MET* 4.0 11.9 - - - +
200C GLU* 3.1 17.7 + - - +
234C PHE* 5.6 0.2 - - - -
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Residues in contact with LEU 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ILE 4.4 11.0 - - - +
135C ALA* 5.1 1.8 - - - +
136C ILE* 5.2 9.2 - - + -
149C PHE* 3.1 54.7 - - + +
150C ASP 3.8 2.2 - - - +
151C LEU* 3.8 25.8 - - + +
191C PHE* 3.2 33.6 - - + -
193C ASN 3.2 9.2 + - - +
194C GLU* 2.6 18.0 + - + +
196C GLU* 1.3 69.8 - - - +
198C LEU* 1.3 67.5 + - + +
200C GLU* 3.2 1.6 + - - -
201C TYR* 2.9 22.2 + - - +
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Residues in contact with LEU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ILE* 3.3 35.2 - - + +
136C ILE* 4.9 10.5 - - + -
194C GLU* 2.9 37.7 + - + +
197C LEU* 1.3 78.8 - - + +
199C MET* 1.3 58.8 + - - +
201C TYR* 3.2 6.7 + - + +
202C LEU* 2.9 34.4 + - - +
226C VAL* 5.5 1.6 - - + -
229C ARG* 4.0 11.2 - - + -
230C ILE* 4.3 22.8 - - + +
233C ILE* 3.8 20.6 - - + -
234C PHE* 4.0 20.2 - - + -
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Residues in contact with MET 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 LYS 3.0 14.8 + - - +
196C GLU* 4.2 13.7 - - - +
198C LEU* 1.3 78.4 - - - +
200C GLU* 1.3 60.6 + - - +
202C LEU* 3.6 21.5 + - - +
203C ASN* 3.2 22.2 + - + +
234C PHE* 3.2 40.6 - - + -
238C THR* 5.1 5.6 - - + -
241C ARG* 3.5 23.1 + - - +
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Residues in contact with GLU 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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149C PHE* 4.5 4.9 - - + -
189C MET* 3.6 25.2 - - + +
191C PHE* 3.3 24.2 - - + -
196C GLU 3.1 20.7 + - - +
197C LEU 3.2 0.4 + - - +
199C MET* 1.3 74.7 - - - +
201C TYR* 1.3 59.6 + - - +
203C ASN* 3.7 20.8 - - - +
204C PHE* 3.0 28.1 + - - +
207C GLN* 4.6 4.6 + - - -
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Residues in contact with TYR 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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113C PHE* 4.1 15.1 - + - -
136C ILE* 3.9 38.8 - - + -
138C HIS* 2.7 39.8 + - + +
149C PHE* 3.5 31.8 - + + -
197C LEU 2.9 16.5 + - - +
198C LEU* 3.6 8.7 - - + +
200C GLU* 1.3 74.6 - - - +
202C LEU* 1.3 57.6 + - - +
204C PHE* 2.9 16.2 + + - +
205C TRP* 2.7 68.5 + + - +
226C VAL* 4.9 19.3 - - + -
230C ILE* 5.7 2.9 - - + -
242C LEU* 5.3 2.2 - - + -
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Residues in contact with LEU 202 (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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198C LEU 2.9 20.2 + - - +
199C MET* 3.6 28.5 - - + +
201C TYR* 1.3 77.7 - - - +
203C ASN* 1.3 62.1 + - - +
205C TRP* 3.1 9.4 - - + +
206C GLN* 3.1 27.9 + - - +
230C ILE* 3.5 43.7 - - + -
234C PHE* 4.9 1.3 - - + -
238C THR* 3.9 22.7 - - - +
239C ALA 4.8 0.2 - - - +
241C ARG* 4.1 27.1 - - + +
242C LEU* 4.3 18.2 - - + +
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Residues in contact with ASN 203 (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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199C MET* 3.2 12.0 + - + +
200C GLU* 3.6 22.3 - - - +
201C TYR 3.1 0.4 - - - -
202C LEU* 1.3 76.6 - - - +
204C PHE* 1.3 66.6 + - - +
206C GLN* 2.8 24.7 + - - +
207C GLN* 3.0 38.1 + - - +
241C ARG* 4.9 4.4 - - - +
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Residues in contact with PHE 204 (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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138C HIS* 3.9 29.8 - + - -
140C ASP* 5.2 3.1 - - + -
147C TYR* 3.2 61.2 - + + -
149C PHE* 3.5 20.6 - + + -
200C GLU* 3.0 19.3 + - - +
201C TYR* 2.9 22.2 + + - +
203C ASN* 1.3 74.8 - - - +
205C TRP* 1.3 56.0 + - - +
207C GLN* 3.1 20.9 + - - +
208C LYS* 2.9 54.7 + - + +
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Residues in contact with TRP 205 (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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113C PHE* 5.0 10.5 - + - -
138C HIS* 4.8 5.6 - + - -
201C TYR* 2.7 54.8 + + + +
202C LEU* 3.1 18.2 - - + +
204C PHE* 1.3 74.6 - - - +
206C GLN* 1.3 62.5 + - - +
208C LYS 4.8 3.1 - - - -
209C THR* 2.8 42.4 + - + +
210C PRO* 3.6 26.0 - - + +
213C LEU* 3.6 24.9 - - + -
223C ILE* 6.2 0.7 - - + -
226C VAL* 6.2 0.7 - - + -
241C ARG 4.0 13.9 - - - -
242C LEU* 2.7 50.4 + - + -
243C SER 6.0 0.4 - - - -
244C PRO* 5.2 0.2 - - - +
265C LEU* 4.1 7.6 - - + -
268C ILE* 3.7 19.6 - - + +
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Residues in contact with GLN 206 (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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202C LEU 3.1 17.7 + - - +
203C ASN* 2.8 16.6 + - - +
205C TRP* 1.3 78.9 - - - +
207C GLN* 1.3 62.0 + - + +
209C THR* 3.3 20.8 + - - -
241C ARG* 3.3 59.0 + - - +
243C SER 5.3 1.4 + - - -
244C PRO* 5.5 4.9 - - - +
246C ARG* 3.9 11.9 + - - +
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Residues in contact with GLN 207 (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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109C ARG* 4.3 2.8 + - - -
200C GLU* 4.6 4.6 + - - -
203C ASN* 3.0 51.5 + - - +
204C PHE* 3.3 19.1 - - + +
206C GLN* 1.3 79.9 - - + +
208C LYS* 1.3 75.2 + - + +
209C THR 3.8 0.2 - - - -
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Residues in contact with LYS 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ARG* 2.9 55.0 - - - +
138C HIS* 4.9 5.5 - - - +
140C ASP* 3.5 11.4 - - - +
143C ASP* 2.4 35.2 + - - +
147C TYR* 3.8 7.7 + - - -
204C PHE* 2.9 35.6 + - + +
205C TRP* 3.3 5.5 - - - +
207C GLN* 1.3 88.0 + - + +
209C THR* 1.3 63.9 + - - +
210C PRO* 3.1 8.3 - - - +
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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