Contacts of the helix formed by residues 221 - 235 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B ILE* 3.8 29.2 - - + -
117B VAL* 4.4 12.1 - - + -
123B PHE* 3.3 32.5 - + + -
124B PRO* 3.2 31.9 - - + -
126B PRO* 4.0 7.8 - - + +
217B ASN* 3.0 22.9 + - + +
219B GLU 3.6 0.2 - - - -
220B SER* 1.3 79.5 - - - +
222B ALA* 1.3 61.9 + - + +
224B PRO* 3.0 4.9 - - - +
225B TYR* 2.8 60.4 + + - +
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Residues in contact with ALA 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B PHE* 3.8 17.0 - - + -
114B ASP* 5.1 2.0 - - - -
115B ILE* 4.5 19.7 - - + +
217B ASN 4.0 0.2 + - - -
218B VAL* 3.3 32.5 + - + +
221B PHE* 1.3 87.4 - - + +
223B ILE* 1.3 63.8 + - - +
225B TYR* 3.7 0.7 - - - +
226B VAL* 3.0 31.7 + - - +
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Residues in contact with ILE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE* 3.7 20.9 - - + -
205B TRP* 6.3 0.4 - - + -
213B LEU* 4.1 11.4 - - + -
218B VAL* 2.7 31.6 + - + +
219B GLU* 3.9 11.4 - - + +
222B ALA* 1.3 72.7 - - - +
224B PRO* 1.3 70.5 - - + +
226B VAL* 4.0 3.2 - - - +
227B TYR* 2.9 27.8 + - + +
242B LEU* 5.2 4.3 - - + +
263B ILE* 4.7 12.8 - - + +
265B LEU* 3.7 33.9 - - + -
270B VAL* 3.9 33.0 - - + -
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Residues in contact with PRO 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PRO* 3.7 16.8 - - + -
218B VAL 3.4 5.4 - - - +
219B GLU 3.4 19.3 - - - +
220B SER* 3.5 13.9 - - - +
221B PHE 3.0 15.3 - - - +
223B ILE* 1.3 96.8 - - + +
225B TYR* 1.3 55.0 - - - +
227B TYR* 3.7 0.5 - - - +
228B ASN* 2.9 37.4 + - - -
261B GLU* 4.4 21.3 - - + +
263B ILE* 4.1 20.6 - - + +
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Residues in contact with TYR 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ILE* 3.9 15.5 - - + -
117B VAL* 3.6 11.7 - - + +
124B PRO* 3.5 25.2 - - + +
125B GLU 3.9 1.6 - - - -
126B PRO* 3.6 20.6 - - + +
129B ALA* 3.4 26.5 - - + +
130B LYS 3.6 0.3 + - - -
131B HIS* 2.7 50.1 + - - +
133B ILE* 3.8 25.6 - - + -
221B PHE* 2.8 36.7 + + + +
222B ALA 3.7 2.7 - - - +
224B PRO* 1.3 70.4 - - - +
226B VAL* 1.3 56.7 + - - +
227B TYR 3.1 1.1 - - - -
229B ARG* 2.7 41.1 + - + +
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Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE* 4.6 8.7 - - + -
115B ILE* 4.0 26.9 - - + -
133B ILE* 3.9 21.3 - - + -
136B ILE* 5.3 1.6 - - + -
198B LEU* 5.0 2.9 - - + -
201B TYR* 4.5 21.5 - - + -
222B ALA 3.0 19.2 + - - +
223B ILE* 4.1 2.9 - - - +
225B TYR* 1.3 74.5 - - - +
227B TYR* 1.3 66.3 + - - +
230B ILE* 3.0 47.9 + - + +
242B LEU* 4.2 12.8 - - + -
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Residues in contact with TYR 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ILE* 2.9 20.0 + - + +
224B PRO 3.7 3.4 - - - +
226B VAL* 1.3 80.3 - - - +
228B ASN* 1.3 59.1 + - - +
230B ILE* 3.6 2.9 - - - +
231B LYS* 2.7 57.3 + - + +
236B GLU* 2.8 21.5 + - - -
239B ALA* 3.4 39.6 - - + +
240B LYS* 3.6 10.8 + - - +
242B LEU* 4.0 17.6 - - + +
248B THR* 3.2 33.4 + - + -
250B VAL* 5.5 2.0 - - + -
263B ILE* 3.7 39.3 - - + -
265B LEU* 5.4 1.6 - - + -
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Residues in contact with ASN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PRO 3.0 24.5 + - - +
127B SER* 4.1 11.9 - - - +
129B ALA* 3.8 6.7 - - + -
224B PRO* 2.9 23.0 + - - +
227B TYR* 1.3 85.6 - - - +
229B ARG* 1.3 63.5 + - - +
231B LYS* 3.2 31.6 + - - +
232B ASN* 2.9 34.3 + - - +
261B GLU* 3.2 24.9 + - - +
263B ILE* 4.5 6.0 - - - +
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Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ALA* 3.3 30.0 + - + +
130B LYS* 3.6 11.7 + - - +
131B HIS 3.1 16.2 + - - -
132B PRO* 3.3 19.6 - - - +
133B ILE* 3.7 22.2 - - + -
194B GLU* 2.7 44.3 + - - +
198B LEU* 3.9 7.4 - - + -
225B TYR* 2.7 25.6 + - + +
226B VAL 3.7 2.9 - - - +
228B ASN* 1.3 71.5 - - - +
230B ILE* 1.3 63.2 + - - +
232B ASN* 3.0 19.6 + - - +
233B ILE* 3.0 34.1 + - - +
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Residues in contact with ILE 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B LEU* 3.9 33.0 - - + +
201B TYR* 5.7 1.8 - - + -
202B LEU* 3.7 31.4 - - + -
226B VAL* 3.0 37.6 + - + +
227B TYR* 3.7 2.2 - - - +
229B ARG* 1.3 76.8 - - - +
231B LYS* 1.3 57.5 + - - +
233B ILE* 4.8 0.2 - - - -
234B PHE* 2.8 47.8 + - + -
235B GLY 3.4 2.9 + - - -
238B THR* 3.9 21.1 - - + -
239B ALA* 3.9 15.0 - - + +
242B LEU* 4.9 4.7 - - + -
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Residues in contact with LYS 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B TYR* 2.7 34.2 + - + +
228B ASN* 3.3 31.3 + - - +
229B ARG 3.1 0.2 - - - -
230B ILE* 1.3 73.8 - - - +
232B ASN* 1.3 63.5 + - - +
235B GLY* 2.6 31.9 + - - -
236B GLU* 2.9 49.0 + - + +
239B ALA* 3.9 9.4 - - + +
250B VAL* 5.3 8.7 - - - +
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Residues in contact with ASN 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLN* 3.0 34.1 + - - +
129B ALA 3.7 10.3 + - - -
228B ASN* 2.9 25.2 + - - +
229B ARG* 3.5 9.8 - - - +
231B LYS* 1.3 86.3 - - - +
233B ILE* 1.3 64.0 + - + +
234B PHE 3.5 0.5 + - - -
235B GLY* 4.4 1.0 + - - -
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Residues in contact with ILE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B GLU* 3.6 16.2 - - + +
195B LYS* 3.6 45.8 + - + -
198B LEU* 3.6 22.0 - - + -
229B ARG* 3.0 47.8 + - - +
232B ASN* 1.3 76.9 - - + +
234B PHE* 1.3 69.4 + - + +
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Residues in contact with PHE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LYS* 3.5 48.0 - - + -
198B LEU* 4.2 22.4 - - + -
199B MET* 3.6 30.7 - - + -
202B LEU* 6.3 0.2 - - + -
230B ILE* 2.8 33.3 + - + +
232B ASN 4.8 0.7 - - - -
233B ILE* 1.3 92.0 - - + +
235B GLY* 1.3 58.3 + - - +
237B SER* 5.8 1.0 - - - -
238B THR* 3.7 31.0 + - + +
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Residues in contact with GLY 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B ILE 3.4 1.4 + - - +
231B LYS* 2.6 25.5 + - - -
232B ASN 4.4 0.8 + - - -
234B PHE* 1.3 74.8 - - - +
236B GLU* 1.3 66.8 + - - -
237B SER* 2.8 6.5 + - - -
238B THR 2.9 14.2 + - - -
239B ALA* 3.1 9.5 + - - +
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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