Contacts of the strand formed by residues 227 - 235 (chain C) in PDB entry 1I3O
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 ARG 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156C TYR* 3.9 2.0 - - - -
162C GLU* 3.3 39.5 + - + +
163C GLY* 3.9 16.4 - - - -
164C LEU* 3.3 26.1 - - - +
199C GLU* 3.6 6.9 + - - -
201C ARG* 3.5 6.9 - - - +
221C GLU* 2.8 36.4 + - - +
222C ASP 4.1 9.2 + - - +
224C HIS* 2.8 52.1 + - + +
226C LYS* 1.3 79.2 - - + +
228C SER* 1.3 61.0 + - - +
229C SER 3.4 4.5 - - - +
273C LEU* 5.1 0.2 - - - +
276C LYS* 2.8 32.4 + - - +
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Residues in contact with SER 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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154C LYS 3.9 6.9 - - - +
155C MET* 3.2 46.5 + - - +
156C TYR* 3.1 27.0 + - - +
162C GLU* 3.0 22.1 + - - -
227C ARG* 1.3 73.4 - - - +
229C SER* 1.3 62.0 + - - +
276C LYS* 3.7 9.9 - - - +
277C PRO* 3.7 16.8 - - - +
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Residues in contact with SER 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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155C MET* 4.2 7.2 - - - +
162C MET 3.0 12.0 + - - -
163C GLY* 3.3 18.3 - - - -
164C LEU 3.9 1.6 + - - -
198C TYR* 2.7 31.4 + - - -
224C HIS* 5.1 1.0 + - - -
227C ARG* 3.4 5.4 - - - +
228C SER* 1.3 79.9 - - - +
230C PHE* 1.3 64.9 + - - +
231C VAL* 5.4 0.7 - - - -
273C LEU* 4.2 10.1 - - - +
276C LYS* 4.7 3.8 - - - -
277C PRO* 3.4 27.8 - - - -
279C LEU* 5.9 1.3 - - - -
398D LEU* 5.8 1.1 - - - -
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Residues in contact with PHE 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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164C LEU* 3.8 20.0 - - + -
166C ILE* 3.9 25.6 - - + -
215C MET* 5.0 2.7 - - - -
218C VAL* 4.0 11.2 - - + -
224C HIS* 4.5 7.9 - + - +
229C SER* 1.3 80.8 - - - +
231C VAL* 1.3 78.4 + - - +
232C CYS* 4.0 23.1 - - + -
265C PHE* 3.3 49.4 - + - -
273C LEU* 3.9 20.2 - - + -
277C PRO 3.2 7.1 + - - +
278C LYS* 3.6 9.0 - - + -
279C LEU* 2.8 27.5 + - - +
280C PHE* 4.2 12.1 - + - -
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Residues in contact with VAL 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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164C LEU 2.9 12.5 + - - +
165C CYS* 3.1 17.9 - - + -
166C ILE 2.9 24.0 + - - -
193C PHE* 4.0 23.8 - - + -
198C TYR* 3.8 29.6 - - + +
229C SER* 4.8 0.4 - - - +
230C PHE* 1.3 88.6 - - - +
232C CYS* 1.3 63.7 + - - +
233C VAL* 4.2 4.5 - - + -
279C LEU* 3.3 25.6 - - + +
281C ILE* 4.1 17.9 - - + -
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Residues in contact with CYS 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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166C ILE* 3.2 10.1 - - + -
168C ILE* 4.8 1.8 - - - -
215C MET* 3.9 31.6 - - - -
230C PHE* 4.0 10.5 - - + -
231C VAL* 1.3 76.6 - - - +
233C VAL* 1.3 65.2 + - - +
234C LEU* 4.1 24.0 + - - +
261C ILE* 5.2 0.7 - - - -
279C LEU 2.9 5.9 + - - +
280C PHE* 3.3 31.3 - - + +
281C ILE* 2.8 24.9 + - - +
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Residues in contact with VAL 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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165C CYS* 4.7 4.3 - - - -
166C ILE 2.7 12.6 + - - +
167C ILE* 4.0 17.2 - - + +
168C ILE* 2.8 34.3 + - - +
189C LEU* 3.4 36.1 - - + -
193C PHE* 5.1 0.7 - - + -
231C VAL* 4.2 9.0 - - + -
232C CYS* 1.3 75.9 - - - +
234C LEU* 1.3 61.4 + - - +
235C LEU* 3.7 15.7 - - + -
281C ILE* 3.3 42.2 - - + +
350D ILE* 4.6 0.4 - - + -
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Residues in contact with LEU 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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168C ILE* 3.3 39.5 - - + -
211C ILE* 5.0 0.4 - - + -
232C CYS* 4.3 15.9 - - - +
233C VAL* 1.3 74.1 - - - +
235C LEU* 1.3 64.5 + - - +
236C SER 4.0 0.4 - - - -
243C ILE* 3.4 34.3 - - + -
258C LEU* 3.9 28.5 - - + -
261C ILE* 4.1 16.6 - - + -
280C PHE* 5.4 4.0 - - + -
281C ILE 2.8 13.0 + - - +
282C ILE* 4.2 14.3 - - + +
283C GLN 2.9 28.2 + - - +
284C ALA* 6.0 0.4 - - - -
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Residues in contact with LEU 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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167C ILE* 4.4 4.5 - - + -
168C ILE* 2.9 15.2 + - - +
169C ASN* 3.8 27.6 - - + +
170C ASN* 3.0 21.8 + - - +
179C ARG* 3.5 9.4 + - - +
182C THR* 3.9 14.4 - - - +
185C ASP* 4.2 5.8 - - + +
186C ALA* 4.0 26.5 - - - +
189C LEU* 4.1 5.4 - - + -
233C VAL* 3.7 20.4 - - + -
234C LEU* 1.3 81.1 - - - +
236C SER* 1.3 64.5 + - - +
243C ILE* 5.0 0.4 - - - +
283C GLN* 3.7 24.2 - - + -
350D ILE* 4.1 13.7 - - + -
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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