Contacts of the helix formed by residues 223 - 235 (chain D) in PDB entry 5U03
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 ASP 223 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192D GLN* 3.8 6.5 + - - +
221D PRO 4.0 0.6 + - - -
222D LEU* 1.3 77.5 - - - +
224D THR* 1.3 63.3 + - - +
225D SER* 2.7 17.4 + - - -
226D VAL* 2.7 35.3 + - - +
227D LYS* 3.3 18.9 + - - +
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Residues in contact with THR 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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223D ASP* 1.3 75.1 + - - +
225D SER* 1.3 65.2 + - - +
227D LYS* 2.9 13.7 + - + +
228D GLU* 2.8 43.4 + - + +
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Residues in contact with SER 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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223D ASP* 2.7 27.7 + - - -
224D THR* 1.3 76.5 - - - +
226D VAL* 1.3 59.5 + - - +
228D GLU* 3.3 9.0 + - - +
229D LYS* 2.9 44.9 + - - +
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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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192D GLN* 3.4 30.3 - - + +
194D THR* 3.6 26.0 - - + -
222D LEU* 3.9 19.3 - - + -
223D ASP* 2.7 29.6 + - - +
225D SER* 1.3 81.3 + - - +
227D LYS* 1.3 57.1 + - - +
229D LYS* 3.1 13.2 + - + +
230D ILE* 2.9 38.8 + - + +
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Residues in contact with LYS 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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221D PRO* 6.1 1.0 - - - +
222D LEU* 3.7 39.9 + - + +
223D ASP 3.3 11.4 + - - +
224D THR* 2.9 11.8 + - + +
226D VAL* 1.3 77.7 - - - +
228D GLU* 1.3 61.0 + - - +
230D ILE* 3.3 4.3 + - - +
231D SER* 2.8 29.7 + - - -
238D PRO* 4.9 13.4 - - + +
241D VAL* 3.9 30.4 - - + +
243D CYS* 4.3 16.4 - - - +
260D GLN* 5.3 10.7 + - - +
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Residues in contact with GLU 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 THR* 2.8 37.6 + - + +
225D SER* 3.6 8.3 - - - +
227D LYS* 1.3 76.1 - - - +
229D LYS* 1.3 64.6 + - + +
231D SER* 3.3 9.6 + - - -
232D MET* 3.0 22.3 + - - +
238D PRO* 4.0 24.5 - - - +
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Residues in contact with LYS 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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54C GLU* 5.3 7.5 + - - -
602C UTP 5.2 18.2 + - - +
194D THR* 5.3 7.0 - - + +
225D SER* 2.9 30.0 + - - +
226D VAL* 3.4 14.4 - - + +
228D GLU* 1.3 73.5 - - + +
230D ILE* 1.3 60.3 + - + +
232D MET* 3.1 9.8 + - + +
233D PHE* 2.8 54.8 + - + -
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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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183D VAL* 5.1 4.5 - - + -
194D THR* 3.7 24.2 - - + -
197D THR* 5.3 10.8 - - + -
198D GLN* 6.2 0.7 - - + -
214D VAL* 5.9 3.6 - - + -
216D CYS* 4.6 11.7 - - - -
222D LEU* 3.7 28.9 - - + -
226D VAL* 2.9 25.5 + - + +
227D LYS 3.6 5.6 - - - +
229D LYS* 1.3 74.7 - - - +
231D SER* 1.3 65.0 + - - +
233D PHE* 3.0 8.2 + - - +
234D CYS* 2.8 43.6 + - + +
236D VAL* 5.0 0.4 - - + -
241D VAL* 3.7 27.4 - - + -
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Residues in contact with SER 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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227D LYS 2.8 13.9 + - - -
228D GLU* 3.3 17.7 + - - -
230D ILE* 1.3 76.0 - - - +
232D MET* 1.3 53.3 + - - +
235D HIS* 2.6 32.1 + - - -
236D VAL* 2.6 39.3 + - - +
238D PRO* 3.9 21.4 - - - +
241D VAL* 4.0 1.3 - - - +
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Residues in contact with MET 232 (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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114A VAL* 5.5 3.1 - - - -
115A PRO* 4.2 35.9 - - + -
228D GLU 3.0 12.9 + - - +
229D LYS* 3.1 8.9 + - + +
231D SER* 1.3 77.0 + - - +
233D PHE* 1.3 104.0 + - + +
235D HIS* 3.1 29.4 + - + +
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Residues in contact with PHE 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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112A GLN* 5.1 11.0 - - - -
114A VAL* 5.3 15.6 - - + +
115A PRO* 5.3 0.9 - - + -
602C UTP 3.3 24.7 - - - -
194D THR* 4.4 5.2 - - - -
198D GLN* 3.4 48.0 - - + -
205D ARG* 3.1 17.0 + - - -
229D LYS* 2.8 50.7 + - + +
230D ILE* 3.6 7.2 - - - +
232D MET* 1.3 100.2 - - + +
234D CYS* 1.3 59.6 + - - +
235D HIS* 3.3 11.1 - - - -
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Residues in contact with CYS 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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197D THR* 4.8 6.5 - - - -
198D GLN* 5.3 6.1 - - - -
201D VAL* 4.1 34.5 - - + +
205D ARG* 2.9 24.2 + - - +
214D VAL* 5.3 6.3 - - + -
230D ILE* 2.8 33.9 + - - +
233D PHE* 1.3 75.9 - - - +
235D HIS* 1.3 71.9 + - - +
236D VAL* 3.4 27.2 - - + +
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Residues in contact with HIS 235 (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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114A VAL* 5.1 13.6 - - + +
115A PRO* 6.3 0.8 - - - +
161A GLU* 4.1 8.1 + - - -
164A ARG* 3.7 16.2 - - - -
165A GLN* 3.3 38.6 + - + +
169A LYS* 6.2 0.7 - - - -
205D ARG* 3.0 23.8 + - - +
231D SER 2.6 18.1 + - - -
232D MET* 3.1 16.2 + - + +
233D PHE* 3.3 17.3 - - - -
234D CYS* 1.3 73.6 - - - +
236D VAL* 1.3 56.8 + - - +
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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