Contacts of the helix formed by residues 221 - 235 (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 PHE 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C ASP* 5.7 4.0 - - - -
115C ILE* 3.8 31.0 - - + -
117C VAL* 4.2 11.9 - - + -
123C PHE* 3.7 31.9 - + + -
124C PRO* 3.6 21.5 - - + -
126C PRO* 4.1 8.2 - - + +
217C ASN* 3.2 17.4 + - + +
219C GLU 3.6 0.6 - - - -
220C SER* 1.3 80.9 - - - +
222C ALA* 1.3 70.0 + - + +
223C ILE 3.4 1.6 - - - -
224C PRO* 3.0 2.6 - - - +
225C TYR* 2.7 66.8 + + - +
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Residues in contact with ALA 222 (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* 3.7 20.4 - - + +
114C ASP* 5.2 3.1 - - - +
115C ILE* 4.3 17.3 - - + +
217C ASN 4.2 0.4 + - - -
218C VAL* 3.4 33.1 + - + +
221C PHE* 1.3 89.6 - - + +
223C ILE* 1.3 63.1 + - - +
225C TYR* 3.6 1.2 - - - +
226C VAL* 3.1 27.4 + - - +
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Residues in contact with ILE 223 (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* 3.9 11.2 - - + -
205C TRP* 6.2 0.9 - - + -
213C LEU* 3.8 13.5 - - + -
218C VAL* 2.9 31.5 + - + +
219C GLU* 4.1 14.4 - - + +
222C ALA* 1.3 72.2 - - - +
224C PRO* 1.3 71.2 - - + +
225C TYR 3.0 0.5 + - - -
226C VAL* 3.9 2.0 - - - +
227C TYR* 2.9 26.7 + - + +
242C LEU* 5.2 4.4 - - + +
263C ILE* 4.4 22.4 - - + +
265C LEU* 4.3 24.2 - - + -
270C VAL* 3.7 32.8 - - + -
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Residues in contact with PRO 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C PRO* 3.6 21.3 - - + +
218C VAL 3.6 2.5 - - - +
219C GLU 3.4 18.4 - - - +
220C SER* 3.7 10.3 - - - +
221C PHE 3.0 17.9 - - - +
223C ILE* 1.3 96.5 - - + +
225C TYR* 1.3 59.7 - - - +
227C TYR* 3.8 0.2 - - - +
228C ASN* 3.1 30.7 + - - +
261C GLU* 5.0 10.3 - - + +
262C ILE* 4.6 5.8 - - - -
263C ILE* 4.0 28.9 - - + +
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Residues in contact with TYR 225 (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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115C ILE* 3.7 21.3 - - + -
117C VAL* 3.2 23.4 - - + +
124C PRO* 3.5 28.8 - - + +
126C PRO* 3.8 14.1 - - + +
129C ALA* 3.7 24.9 - - + +
131C HIS* 2.6 40.6 + - - +
133C ILE* 3.7 21.3 - - + -
221C PHE* 2.7 41.4 + + + +
222C ALA 3.6 3.6 - - - +
223C ILE 3.0 0.8 + - - -
224C PRO* 1.3 72.7 - - - +
226C VAL* 1.3 57.5 + - - +
228C ASN 3.6 0.2 - - - -
229C ARG* 2.7 39.5 + - + +
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Residues in contact with VAL 226 (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* 4.9 6.7 - - + -
115C ILE* 3.9 23.3 - - + -
133C ILE* 3.7 26.2 - - + -
136C ILE* 4.6 9.2 - - + -
198C LEU* 5.5 1.1 - - + -
201C TYR* 4.9 13.7 - - + -
205C TRP* 6.2 0.4 - - + -
222C ALA 3.1 14.8 + - - +
223C ILE* 4.1 2.7 - - - +
225C TYR* 1.3 78.5 - - - +
227C TYR* 1.3 62.6 + - - +
230C ILE* 2.9 45.7 + - + +
242C LEU* 4.1 17.0 - - + -
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Residues in contact with TYR 227 (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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223C ILE* 2.9 18.8 + - + +
224C PRO 3.8 2.7 - - - +
226C VAL* 1.3 78.6 - - - +
228C ASN* 1.3 80.4 + - - +
230C ILE* 3.7 3.3 - - - +
231C LYS* 2.8 40.7 + - + +
236C GLU* 4.3 9.4 - - - +
239C ALA* 3.6 32.7 - - + +
240C LYS* 3.7 20.7 - - - +
242C LEU* 3.9 23.1 - - + +
248C THR* 3.2 27.7 + - + -
250C VAL* 5.1 5.8 - - + +
263C ILE* 3.7 39.7 - - + -
265C LEU* 4.9 2.2 - - + -
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Residues in contact with ASN 228 (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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126C PRO 2.9 24.2 + - - +
127C SER* 3.2 23.9 + - - +
128C GLN 4.9 0.7 - - - -
129C ALA* 4.2 5.2 - - + -
224C PRO* 3.1 15.5 + - - +
225C TYR 4.0 0.7 - - - +
227C TYR* 1.3 99.2 - - - +
229C ARG* 1.3 57.9 + - - +
231C LYS* 3.4 13.8 - - + +
232C ASN* 2.6 43.4 + - - +
261C GLU* 3.7 13.1 + - - -
263C ILE* 4.6 4.4 - - - +
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Residues in contact with ARG 229 (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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129C ALA* 2.9 16.2 + - + +
130C LYS* 2.8 28.7 + - - +
131C HIS 2.6 29.4 + - - -
132C PRO* 3.1 12.9 - - - +
133C ILE* 3.4 28.3 - - + -
194C GLU* 2.5 38.3 + - - +
198C LEU* 4.0 5.2 - - + -
225C TYR* 2.7 26.8 + - + +
226C VAL 3.6 3.8 - - - +
228C ASN* 1.3 72.1 - - - +
230C ILE* 1.3 66.8 + - - +
232C ASN* 2.9 20.0 + - - +
233C ILE* 3.0 29.1 + - + +
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Residues in contact with ILE 230 (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* 4.3 27.4 - - + +
201C TYR* 5.7 3.1 - - + -
202C LEU* 3.5 44.6 - - + -
226C VAL* 2.9 35.2 + - + +
227C TYR* 3.8 2.9 - - - +
229C ARG* 1.3 74.1 - - - +
231C LYS* 1.3 55.2 + - - +
234C PHE* 2.7 57.4 + - + -
235C GLY 3.3 2.8 + - - -
238C THR 4.5 0.2 - - - -
239C ALA* 4.1 18.8 - - - +
242C LEU* 4.9 5.8 - - + -
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Residues in contact with LYS 231 (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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227C TYR* 2.8 29.8 + - + +
228C ASN* 3.4 22.2 - - - +
229C ARG 3.0 0.2 - - - -
230C ILE* 1.3 76.7 - - - +
232C ASN* 1.3 65.7 + - - +
235C GLY* 2.6 31.8 + - - +
236C GLU* 3.9 39.9 + - + +
239C ALA* 3.9 15.4 - - + +
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Residues in contact with ASN 232 (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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128C GLN 3.3 25.4 + - - +
129C ALA 3.4 13.3 + - - -
130C LYS* 5.4 0.2 - - - +
228C ASN* 2.6 26.8 + - - +
229C ARG* 2.9 7.0 + - - +
231C LYS* 1.3 87.7 - - - +
233C ILE* 1.3 65.0 + - + +
234C PHE 3.5 0.7 + - - -
235C GLY* 4.3 1.2 + - - -
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Residues in contact with ILE 233 (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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194C GLU* 3.6 33.7 - - - +
195C LYS* 3.8 43.3 + - + +
198C LEU* 3.8 12.3 - - + -
229C ARG* 3.0 24.8 + - - +
232C ASN* 1.3 82.7 - - + +
234C PHE* 1.3 93.5 + - + +
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Residues in contact with PHE 234 (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* 3.6 21.8 - - + -
198C LEU* 4.0 22.4 - - + -
199C MET* 3.2 41.7 - - + -
202C LEU* 4.9 0.9 - - + -
230C ILE* 2.7 34.8 + - + +
232C ASN 4.6 0.9 - - - -
233C ILE* 1.3 105.9 - - + +
235C GLY* 1.3 56.4 + - - +
237C SER* 4.6 3.5 + - - -
238C THR* 2.9 31.0 + - + +
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Residues in contact with GLY 235 (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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230C ILE 3.3 0.8 + - - -
231C LYS* 2.6 25.9 + - - -
232C ASN 4.3 0.8 + - - -
234C PHE* 1.3 74.0 - - - +
236C GLU* 1.3 68.2 + - - -
237C SER* 2.7 8.7 + - - -
238C THR* 2.9 16.5 + - - -
239C ALA* 3.1 6.9 + - - +
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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