Contacts of the helix formed by residues 221 - 234 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115D ILE* 4.2 26.0 - - + -
117D VAL* 4.4 11.0 - - + -
123D PHE* 3.4 31.4 - + - -
124D PRO* 3.8 10.5 - - + -
126D PRO* 4.2 8.1 - - + -
217D ASN 3.0 14.9 + - - +
220D SER* 1.3 77.9 - - - +
222D ALA* 1.3 74.1 + - - +
223D ILE 3.3 1.6 - - - -
224D PRO* 2.9 5.3 - - - +
225D TYR* 2.8 58.4 + + + +
115L A 2.9 54.5 - - + +
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Residues in contact with ALA 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D PHE* 3.4 27.6 - - + -
114D ASP* 5.1 1.6 - - - +
115D ILE* 3.9 26.2 - - + +
218D VAL* 3.5 24.0 + - + +
221D PHE* 1.3 83.0 - - + +
223D ILE* 1.3 68.4 + - - +
225D TYR* 3.4 1.6 + - - +
226D VAL* 3.1 23.0 + - - +
115L A 5.2 3.4 - - - +
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Residues in contact with ILE 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D PHE* 3.9 20.6 - - + -
213D LEU* 4.1 17.9 - - + -
218D VAL* 2.9 22.2 + - + +
219D GLU* 4.0 10.1 - - + +
222D ALA* 1.3 79.8 - - - +
224D PRO* 1.3 74.2 - - + +
226D VAL* 3.0 11.7 + - - +
227D TYR* 3.1 12.6 + - + +
263D ILE* 4.4 24.2 - - + +
265D LEU* 4.4 19.3 - - + -
270D VAL* 3.7 35.7 - - + -
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Residues in contact with PRO 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PRO* 3.5 18.4 - - + -
218D VAL 3.2 10.1 - - - +
219D GLU 3.2 18.2 - - - +
220D SER 3.4 11.2 - - - +
221D PHE 2.9 16.4 - - - +
223D ILE* 1.3 89.3 - - + +
225D TYR* 1.3 62.5 + - - +
227D TYR* 3.3 0.9 + - - +
228D ASN* 2.9 32.5 + - - +
261D GLU* 4.0 16.6 - - + +
262D ILE* 4.6 4.0 - - - -
263D ILE* 3.3 20.4 - - + +
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Residues in contact with TYR 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ILE* 3.9 12.6 - - + -
117D VAL* 4.3 6.3 - - + -
124D PRO* 3.4 33.0 - - + +
126D PRO* 3.2 20.5 - - + +
129D ALA* 3.4 24.4 - - + +
130D LYS 3.1 5.0 + - - -
131D HIS* 2.4 50.8 + - - +
133D ILE* 3.6 24.9 - - + -
221D PHE* 2.8 44.0 + + + +
222D ALA 3.7 3.4 - - - +
224D PRO* 1.3 72.7 - - - +
226D VAL* 1.3 52.3 + - - +
228D ASN* 4.8 0.2 - - - -
229D ARG* 2.7 34.3 + - + +
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Residues in contact with VAL 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D PHE* 4.5 7.0 - - + -
115D ILE* 3.9 29.6 - - + -
133D ILE* 5.0 7.0 - - + -
136D ILE* 5.8 1.6 - - + -
198D LEU* 5.5 4.3 - - + -
201D TYR* 4.6 19.3 - - + -
222D ALA 3.1 16.6 - - - +
223D ILE* 3.0 7.5 + - - +
225D TYR* 1.3 75.6 - - - +
227D TYR* 1.3 61.9 + - - +
229D ARG* 4.3 4.3 - - - -
230D ILE* 2.8 54.3 + - + +
242D LEU* 4.4 10.1 - - + -
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Residues in contact with TYR 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D ILE* 3.1 8.1 + - + +
226D VAL* 1.3 78.1 - - - +
228D ASN* 1.3 66.8 + - - +
230D ILE* 3.5 1.9 + - - -
231D LYS* 2.9 42.5 + - + +
236D GLU* 3.8 29.5 + - + +
239D ALA* 3.6 37.0 - - + +
240D LYS* 3.9 6.2 - - - -
242D LEU* 4.4 18.0 - - + +
248D THR* 3.3 28.8 + - + -
250D VAL* 4.8 13.0 - - + -
263D ILE* 3.2 46.7 - - + -
265D LEU* 5.0 5.4 - - + -
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Residues in contact with ASN 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PRO 2.7 27.5 + - - +
127D SER 4.2 6.6 - - - +
128D GLN* 5.2 0.2 - - - -
129D ALA* 3.8 10.5 - - + +
224D PRO 2.9 21.2 + - - +
227D TYR* 1.3 81.4 - - - +
229D ARG* 1.3 66.5 + - - +
231D LYS* 3.0 28.5 + - - +
232D ASN* 2.9 24.6 + - - +
261D GLU* 2.7 35.5 + - - +
263D ILE* 4.0 4.2 - - - +
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Residues in contact with ARG 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ALA* 3.3 13.4 + - + +
130D LYS* 2.7 36.6 + - - +
132D PRO* 3.1 22.3 - - - +
133D ILE* 3.3 31.2 - - + -
194D GLU* 2.5 33.2 + - - +
198D LEU* 5.4 3.4 - - + -
225D TYR* 2.7 31.7 + - - +
226D VAL* 3.7 3.8 - - - +
228D ASN* 1.3 72.6 - - - +
230D ILE* 1.3 62.0 + - + +
232D ASN* 2.9 21.2 + - - +
233D ILE* 2.9 44.2 + - + +
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Residues in contact with ILE 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D LEU* 4.3 24.7 - - + -
201D TYR* 5.5 3.1 - - + -
202D LEU* 4.1 32.1 - - + -
226D VAL* 2.8 40.3 + - + +
227D TYR 4.0 2.0 - - - +
229D ARG* 1.3 74.6 - - + +
231D LYS* 1.3 61.4 + - - +
233D ILE* 3.9 7.6 - - - -
234D PHE* 3.4 27.6 + - + +
235D GLY 3.3 15.6 + - - -
238D THR 4.3 6.3 - - - +
239D ALA* 3.7 9.3 - - + +
242D LEU* 4.2 18.2 - - + -
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Residues in contact with LYS 231 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227D TYR* 2.9 33.6 + - + +
228D ASN* 3.2 25.6 - - - +
229D ARG 3.0 0.2 - - - -
230D ILE* 1.3 78.3 - - - +
232D ASN* 1.3 76.8 + - - +
235D GLY* 3.1 5.8 - - - -
236D GLU* 2.8 58.6 + - + +
239D ALA* 3.5 12.1 - - + -
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Residues in contact with ASN 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D GLN* 5.7 1.0 - - - +
129D ALA* 3.7 25.6 + - - +
228D ASN* 2.9 22.0 + - - +
229D ARG 2.9 3.9 + - - +
231D LYS* 1.3 103.7 + - - +
233D ILE* 1.3 71.0 + - + +
234D PHE 4.7 0.2 - - - -
235D GLY* 4.3 1.7 + - - -
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Residues in contact with ILE 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D GLU* 4.6 6.3 - - + +
195D LYS* 4.8 14.6 - - + +
198D LEU* 5.7 4.3 - - + -
229D ARG* 2.9 63.1 + - + +
230D ILE* 3.8 3.6 + - - -
232D ASN* 1.3 83.8 - - + +
234D PHE* 1.3 88.7 + - + +
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Residues in contact with PHE 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LYS* 3.5 26.9 - - + -
198D LEU* 3.8 18.2 - - + -
199D MET* 3.4 43.7 - - + -
202D LEU* 5.5 1.8 - - + -
230D ILE* 3.4 18.2 + - + +
233D ILE* 1.3 103.4 - - + +
235D GLY* 1.3 59.9 + - - +
238D THR* 3.4 41.6 + - + +
241D ARG* 5.7 0.2 - - - -
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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
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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