Contacts of the strand formed by residues 227 - 234 (chain C) in PDB entry 1IAS
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 GLU 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176C THR* 3.4 15.6 - - - +
177C LEU* 2.5 47.2 + - + +
178C LYS* 2.9 52.0 + - - +
223C LYS* 3.1 3.0 - - - -
224C TRP* 2.8 41.8 + - - +
225C ARG* 3.1 8.1 + - - +
226C GLY* 1.3 74.5 - - - +
228C GLU* 1.3 62.8 + - - +
229C VAL* 4.5 0.2 - - - +
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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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4C SO4 4.8 1.5 + - - -
177C LEU* 3.8 10.4 - - - +
221C ARG* 2.7 36.7 + - + +
222C GLY 3.4 5.6 - - - +
223C LYS* 4.1 21.1 - - + -
226C GLY 3.6 1.3 + - - +
227C GLU* 1.3 72.9 - - - +
229C VAL* 1.3 69.3 + - - +
282C TYR* 3.5 39.5 + - + +
284C GLU* 5.5 2.1 - - - +
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Residues in contact with VAL 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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177C LEU* 4.1 12.6 - - + -
201C ILE* 6.4 0.9 - - + -
205C ILE* 4.0 19.1 - - + -
221C ARG* 3.6 3.1 - - - -
222C GLY 2.6 50.0 + - - +
223C LYS* 4.6 1.3 - - - +
224C TRP* 4.9 5.4 - - + +
227C GLU 4.5 2.7 - - - +
228C GLU* 1.3 79.1 - - - +
230C ALA* 1.3 55.9 + - - +
231C VAL* 4.1 5.4 - - + -
263C ILE* 3.6 23.6 - - + -
279C VAL* 3.6 20.2 - - + -
280C SER 3.0 20.4 - - - +
281C ASP* 4.7 1.1 - - - -
282C TYR* 3.7 12.0 - - - +
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Residues in contact with ALA 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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211C ILE* 5.4 1.1 - - + -
219C VAL* 4.6 12.6 - - + -
220C TRP 3.4 8.1 - - - +
229C VAL* 1.3 73.9 - - - +
231C VAL* 1.3 60.2 + - - +
232C LYS 4.2 0.4 - - - -
260C LEU* 6.1 0.2 - - + -
278C LEU 3.9 0.3 - - - +
279C VAL* 3.4 7.3 - - - +
280C SER* 2.8 43.0 + - - +
281C ASP 3.5 19.3 - - - +
282C TYR* 3.9 13.1 - - + +
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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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205C ILE* 3.9 27.8 - - + -
207C LEU* 4.0 20.9 - - + -
218C GLU 3.7 0.2 - - - +
219C VAL* 3.4 3.3 - - - -
220C TRP* 2.7 44.0 + - + +
222C GLY 4.7 1.8 - - - +
229C VAL* 4.1 8.7 - - + +
230C ALA* 1.3 78.0 - - - +
232C LYS* 1.3 60.7 + - - +
233C ILE* 3.6 15.6 + - + -
277C TRP* 3.5 36.6 - - + -
278C LEU 3.4 8.5 - - - +
279C VAL* 4.5 2.5 - - + -
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Residues in contact with LYS 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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216C PHE* 3.7 37.7 - - + +
218C GLU 3.4 5.8 - - - +
219C VAL* 4.3 12.3 - - + +
230C ALA 4.2 0.6 - - - -
231C VAL* 1.3 69.9 - - - +
233C ILE* 1.3 59.9 + - - +
234C PHE* 3.2 39.4 - - + -
245C GLU* 2.8 31.6 + - - +
277C TRP* 3.5 1.6 - - - -
278C LEU* 2.9 38.9 + - + +
351C ASP* 3.6 26.3 + - - +
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Residues in contact with ILE 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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207C LEU* 3.6 31.4 - - + -
217C GLY* 3.6 2.0 - - - -
218C GLU* 2.8 34.4 + - + +
220C TRP* 3.8 22.9 - - + +
231C VAL* 3.8 15.5 - - + +
232C LYS* 1.3 75.2 - - - +
234C PHE* 1.3 70.2 + - - +
275C GLN* 5.8 3.1 - - + +
276C LEU 3.7 3.4 - - - +
277C TRP* 3.6 34.5 - - + +
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Residues in contact with PHE 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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216C PHE* 3.7 31.2 - - + -
217C GLY* 4.5 0.2 - - - -
232C LYS* 3.2 42.4 - - + -
233C ILE* 1.3 83.6 - - - +
235C SER* 1.3 69.2 + - - +
236C SER 3.8 1.2 + - - -
238C GLU 3.9 9.0 - - - +
241C SER* 3.7 8.7 - - - -
242C TRP* 3.3 47.6 - + + -
245C GLU* 4.1 6.5 - - - -
274C THR 5.1 1.7 - - - +
275C GLN* 5.2 0.7 - - - -
276C LEU* 2.9 38.4 + - + +
278C LEU* 3.5 23.8 - - + -
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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