Contacts of the helix formed by residues 223 - 235 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192C GLN* 3.8 6.9 + - - +
221C PRO 4.0 0.6 + - - -
222C LEU* 1.3 76.5 - - - +
224C THR* 1.3 64.7 + - - +
225C SER* 2.7 17.1 + - - -
226C VAL* 2.7 33.5 + - - +
227C LYS* 3.3 19.1 + - - +
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Residues in contact with THR 224 (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 ASP* 1.3 74.6 + - - +
225C SER* 1.3 65.5 + - - +
227C LYS* 2.9 13.7 + - + +
228C GLU* 2.8 43.3 + - + +
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Residues in contact with SER 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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223C ASP* 2.7 28.6 + - - -
224C THR* 1.3 75.4 - - - +
226C VAL* 1.3 58.8 + - - +
228C GLU* 3.3 9.9 + - - +
229C LYS* 2.9 45.8 + - - +
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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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192C GLN* 3.4 31.2 - - + +
194C THR* 3.6 25.6 - - + -
222C LEU* 3.9 19.7 - - + -
223C ASP* 2.7 29.6 + - - +
225C SER* 1.3 80.8 + - - +
227C LYS* 1.3 57.2 + - - +
229C LYS* 3.1 14.8 + - + +
230C ILE* 2.9 37.9 + - + +
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Residues in contact with LYS 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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221C PRO* 6.1 1.2 - - - +
222C LEU* 3.7 41.4 + - + +
223C ASP 3.3 11.9 + - - +
224C THR* 2.9 11.8 + - + +
226C VAL* 1.3 77.9 - - - +
228C GLU* 1.3 59.4 + - - +
230C ILE* 3.3 4.2 + - - +
231C SER* 2.8 28.9 + - - -
238C PRO* 4.9 14.0 - - + +
241C VAL* 3.9 31.7 + - + +
243C CYS* 4.3 16.0 - - - +
260C GLN* 5.3 10.5 + - - +
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Residues in contact with GLU 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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224C THR* 2.8 39.5 + - + +
225C SER* 3.6 8.3 - - - +
227C LYS* 1.3 76.2 - - - +
229C LYS* 1.3 65.8 + - + +
231C SER* 3.3 8.3 + - - -
232C MET* 3.0 21.7 + - - +
238C PRO* 4.0 22.9 - - - +
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Residues in contact with LYS 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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194C THR* 5.3 7.4 - - + +
225C SER* 2.9 31.5 + - - +
226C VAL* 3.4 14.2 - - + +
228C GLU* 1.3 73.9 - - - +
230C ILE* 1.3 60.4 + - + +
232C MET* 3.1 8.8 + - + +
233C PHE* 2.8 53.7 + - + -
54D GLU* 5.3 7.5 + - - -
602D UTP 5.2 17.9 + - - +
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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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183C VAL* 5.1 4.3 - - + -
194C THR* 3.7 24.0 - - + -
197C THR* 5.3 10.8 - - + -
198C GLN* 6.2 0.7 - - + -
214C VAL* 5.9 3.4 - - + -
216C CYS* 4.6 11.9 - - - -
222C LEU* 3.7 28.9 - - + -
226C VAL* 2.9 25.7 + - + +
227C LYS 3.6 5.4 - - - +
228C GLU 3.3 0.2 - - - -
229C LYS* 1.3 74.4 - - - +
231C SER* 1.3 65.2 + - - +
233C PHE* 3.0 7.7 + - - +
234C CYS* 2.8 43.5 + - + +
236C VAL* 5.0 0.4 - - + -
241C VAL* 3.7 27.4 - - + -
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Residues in contact with SER 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 LYS 2.8 15.2 + - - -
228C GLU* 3.3 16.9 + - - -
230C ILE* 1.3 75.5 - - - +
232C MET* 1.3 53.2 + - - -
235C HIS* 2.6 32.1 + - - -
236C VAL* 2.6 39.0 + - - +
238C PRO* 3.9 21.6 - - - +
241C VAL* 4.0 1.5 - - - +
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Residues in contact with MET 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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114B VAL* 5.4 3.4 - - - -
115B PRO* 4.2 35.9 - - + -
228C GLU 3.0 13.6 + - - +
229C LYS* 3.5 8.3 - - + +
231C SER* 1.3 76.3 + - - +
233C PHE* 1.3 103.8 + - + +
235C HIS* 3.1 27.7 + - + +
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Residues in contact with PHE 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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112B GLN* 5.1 11.2 - - - -
114B VAL* 5.3 14.5 - - + +
115B PRO* 5.4 1.3 - - + -
194C THR* 4.4 5.4 - - - -
198C GLN* 3.4 47.6 - - + -
205C ARG* 3.1 17.1 + - - -
229C LYS* 2.8 51.5 + - + +
230C ILE* 3.6 7.4 - - - +
232C MET* 1.3 99.5 - - + +
234C CYS* 1.3 59.4 + - - +
235C HIS* 3.3 11.7 - - - -
602D UTP 3.3 24.7 - - - -
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Residues in contact with CYS 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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197C THR* 4.8 6.3 - - - -
198C GLN* 5.3 6.3 - - - -
201C VAL* 4.1 34.5 - - + +
205C ARG* 2.9 24.7 + - - +
214C VAL* 5.3 7.4 - - + -
230C ILE* 2.8 32.9 + - - +
233C PHE* 1.3 75.8 - - - +
235C HIS* 1.3 71.5 + - - +
236C VAL* 3.4 26.3 - - + +
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Residues in contact with HIS 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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114B VAL* 5.1 14.0 - - + +
115B PRO* 6.3 0.6 - - - +
161B GLU* 4.1 8.6 + - - -
164B ARG* 3.7 15.9 + - - -
165B GLN* 3.3 39.9 + - + +
169B LYS* 6.3 0.7 - - - -
205C ARG* 3.0 24.4 + - - +
231C SER 2.6 18.1 + - - -
232C MET* 3.1 15.9 + - + +
233C PHE* 3.3 17.0 - - - -
234C CYS* 1.3 74.1 - - - +
236C VAL* 1.3 57.8 + - - +
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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