Contacts of the helix formed by residues 221 - 232 (chain D) in PDB entry 5XVO
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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183D LEU* 3.6 22.9 - - + +
187D PHE* 3.5 32.5 - + + -
217D LEU 4.0 4.7 - - - -
218D MET 2.9 13.4 + - - +
220D PRO* 1.3 80.9 - - + +
222D ARG* 1.3 65.2 + - - +
223D PRO* 3.3 3.1 - - - -
224D LEU* 2.9 26.2 + - + +
261D LEU* 3.9 23.1 - - + -
264D ILE* 3.9 17.7 - - + -
265D ALA* 5.2 0.4 - - - -
268D TYR* 3.9 35.4 - + + -
286D PHE* 3.5 51.4 - + + -
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Residues in contact with ARG 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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112D LYS* 3.9 26.7 - - - +
116D GLN* 6.3 0.7 - - - +
166D ARG* 5.8 0.4 - - - +
180D TYR* 3.4 52.7 - - + +
183D LEU* 4.1 4.7 - - - -
215D SER* 4.1 4.2 + - - +
218D MET* 3.5 40.1 + - + +
219D GLU* 2.6 46.6 + - - +
221D PHE* 1.3 77.2 - - - +
223D PRO* 1.3 70.3 - - + +
225D VAL* 2.9 17.3 + - - +
226D ASP* 3.1 15.7 + - - +
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Residues in contact with PRO 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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112D LYS* 4.3 3.4 - - + +
115D ASN* 3.7 39.7 - - + +
116D GLN* 3.9 13.2 - - + +
119D HIS* 4.7 1.7 + - + -
155D TYR* 4.3 5.4 - - - +
219D GLU 4.0 2.5 - - - +
220D PRO 3.4 11.9 - - - +
221D PHE 3.4 4.3 - - - -
222D ARG* 1.3 95.4 - - + +
224D LEU* 1.3 53.0 + - - +
226D ASP* 3.4 16.2 - - + +
227D GLN* 2.7 39.1 + - - +
288D ILE* 4.2 14.4 - - + -
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Residues in contact with LEU 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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183D LEU* 5.5 0.9 - - + -
221D PHE* 2.9 19.8 + - + +
223D PRO* 1.3 77.9 - - - +
225D VAL* 1.3 62.7 + - + +
227D GLN* 3.7 17.1 - - - +
228D ILE* 3.5 25.6 + - - +
247D LEU* 3.9 16.6 - - + -
252D TYR* 3.5 37.0 - - + -
261D LEU* 3.9 25.8 - - + -
286D PHE* 3.8 27.1 - - + -
288D ILE* 3.6 24.0 - - + -
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Residues in contact with VAL 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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176D LEU* 3.9 22.0 - - + +
179D GLY* 4.1 11.9 - - - +
180D TYR* 3.6 27.4 - - + -
183D LEU* 3.2 39.7 - - + -
221D PHE 4.2 0.2 - - - +
222D ARG 2.9 5.6 + - - +
224D LEU* 1.3 74.5 - - + +
226D ASP* 1.3 68.3 + - - +
228D ILE* 3.1 4.5 + - - +
229D ILE* 3.0 26.6 + - + +
244D LEU* 4.1 18.3 - - + +
247D LEU* 4.6 7.4 - - + -
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Residues in contact with ASP 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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116D GLN* 4.9 2.8 + - - -
119D HIS* 3.8 6.2 - - + -
155D TYR* 2.8 42.2 + - + +
156D PHE* 4.3 2.8 - - + -
159D LEU* 5.1 2.5 - - + -
160D PHE* 5.1 3.8 - - + -
176D LEU* 3.2 20.0 - - + +
180D TYR* 2.5 29.2 + - - -
222D ARG* 3.1 10.6 + - - +
223D PRO* 3.0 18.3 + - - +
225D VAL* 1.3 75.4 - - - +
227D GLN* 1.3 56.4 + - - +
229D ILE* 3.3 0.9 + - - +
230D TYR* 2.8 32.9 + - - +
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Residues in contact with GLN 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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119D HIS* 3.5 27.0 - - + -
122D GLN* 3.0 30.8 + - - +
123D ARG* 3.5 8.3 + - - +
223D PRO 2.7 22.0 + - - +
224D LEU* 3.7 27.5 - - - +
226D ASP* 1.3 72.5 - - - +
228D ILE* 1.3 65.0 + - + +
230D TYR* 3.3 0.3 + - - +
231D GLU* 2.9 35.0 + - - +
252D TYR* 5.4 1.7 - - - -
288D ILE* 3.7 25.8 + - + +
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Residues in contact with ILE 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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224D LEU 3.5 14.3 + - - +
225D VAL 3.1 7.9 + - - +
227D GLN* 1.3 80.1 - - + +
229D ILE* 1.3 63.7 + - + +
231D GLU* 3.3 6.6 + - - +
232D ASN* 2.9 32.2 + - - +
240D MET* 4.9 1.3 - - - +
243D LYS* 3.8 41.5 - - + +
244D LEU* 3.9 20.9 - - + +
246D ALA* 4.1 15.3 - - + -
247D LEU* 4.2 22.2 - - + -
250D ASN* 5.7 2.0 - - - +
252D TYR* 5.0 4.0 - - - +
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Residues in contact with ILE 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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160D PHE* 4.5 6.3 - - + -
172D ILE* 3.9 36.1 - - + +
175D GLY* 2.8 47.1 - - - +
176D LEU* 2.9 21.5 - - + +
225D VAL* 3.0 19.0 + - + +
226D ASP 4.0 2.2 - - - +
228D ILE* 1.3 74.0 - - + +
230D TYR* 1.3 61.2 + - - +
232D ASN* 3.1 6.3 + - - -
233D ARG* 2.9 26.7 + - - -
240D MET* 4.7 15.7 - - + -
244D LEU* 4.3 14.8 - - + -
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Residues in contact with TYR 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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119D HIS* 4.3 10.3 - - + -
123D ARG* 3.2 53.0 - - + +
125D TYR* 4.3 12.8 + - - -
159D LEU* 3.4 35.7 + - + -
160D PHE* 3.9 22.4 - + + -
226D ASP 2.8 18.5 + - - +
227D GLN 3.5 4.0 - - - +
229D ILE* 1.3 77.4 - - - +
231D GLU* 1.3 59.6 + - - +
233D ARG* 2.4 74.6 + - - +
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Residues in contact with GLU 231 (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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122D GLN* 4.5 2.8 - - - +
123D ARG* 3.1 34.4 + - - +
227D GLN* 2.9 26.5 + - - +
228D ILE* 3.7 7.6 - - - +
229D ILE 3.3 0.4 - - - -
230D TYR* 1.3 76.6 - - + +
232D ASN* 1.3 67.6 + - - +
233D ARG* 3.6 4.4 + - - +
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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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228D ILE* 2.9 27.9 + - + +
229D ILE* 3.1 7.5 + - - +
231D GLU* 1.3 86.2 - - - +
233D ARG* 1.3 63.9 + - - +
234D LYS 3.1 3.1 - - - -
235D GLU* 3.0 39.1 + - + +
240D MET* 3.7 24.0 - - + +
243D LYS* 3.4 50.2 + - - +
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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