Contacts of the strand formed by residues 217 - 224 (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 GLY 217 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213C LYS* 3.4 5.5 - - - +
214C GLY 3.3 26.1 + - - +
215C ARG 3.5 1.4 - - - -
216C PHE* 1.3 90.9 - - - +
218C GLU* 1.3 63.9 + - - +
233C ILE 3.6 9.6 - - - -
235C SER* 3.9 10.1 - - - -
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Residues in contact with GLU 218 (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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210C SER* 2.9 24.6 + - - -
212C GLY 3.4 4.9 - - - +
213C LYS* 3.4 41.4 - - + -
216C PHE* 3.7 1.9 - - - -
217C GLY* 1.3 74.2 - - - +
219C VAL* 1.3 63.9 + - - +
220C TRP* 3.4 32.8 + - + +
231C VAL 3.7 0.2 - - - +
232C LYS* 3.4 3.1 - - - +
233C ILE* 2.8 37.2 + - + +
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Residues in contact with VAL 219 (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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210C SER* 3.7 0.9 + - - -
211C ILE* 2.7 47.5 + - + -
212C GLY* 2.8 20.2 + - - +
216C PHE* 3.8 24.0 - - + -
218C GLU* 1.3 76.3 - - - +
220C TRP* 1.3 71.2 + - - +
230C ALA* 4.6 12.3 - - + -
231C VAL 3.4 7.0 - - - +
232C LYS* 4.3 15.7 - - + +
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Residues in contact with TRP 220 (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* 4.0 35.4 - - + -
208C GLN 4.5 3.4 - - - -
209C GLU* 3.4 29.6 - - - -
210C SER* 3.8 17.3 - - - -
211C ILE* 3.8 5.6 - - - +
218C GLU* 3.4 45.3 + - + +
219C VAL* 1.3 85.6 - - - +
221C ARG* 1.3 64.7 + - - +
222C GLY 3.8 0.2 - - - -
230C ALA* 3.4 5.5 - - - +
231C VAL* 2.7 37.5 + - + +
233C ILE* 3.8 26.1 - - + +
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Residues in contact with ARG 221 (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 2.6 43.4 + - - -
207C LEU* 4.1 0.7 - - - -
208C GLN* 2.8 49.2 + - + +
209C GLU* 2.3 51.1 + - - +
211C ILE* 3.3 23.5 - - + +
220C TRP* 1.3 75.4 - - - +
222C GLY* 1.3 62.6 + - - +
223C LYS* 3.4 12.5 - - - +
228C GLU* 2.7 25.2 + - - +
229C VAL 3.7 4.0 - - - +
282C TYR* 3.4 35.0 + - + -
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Residues in contact with GLY 222 (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* 4.4 7.4 - - - -
206C VAL 3.5 11.7 - - - -
207C LEU* 4.1 7.2 - - - -
208C GLN* 3.8 2.7 - - - -
220C TRP 3.8 1.6 + - - -
221C ARG* 1.3 75.7 - - - +
223C LYS* 1.3 62.1 + - - +
228C GLU* 3.4 4.9 - - - +
229C VAL* 2.6 51.1 + - - -
231C VAL* 4.7 2.1 - - - +
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Residues in contact with LYS 223 (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 3.0 36.0 + - - -
205C ILE* 3.5 4.1 - - - +
206C VAL* 2.8 42.4 + - + +
208C GLN* 3.6 23.5 + - + +
221C ARG* 3.4 18.4 - - - +
222C GLY* 1.3 79.7 - - - +
224C TRP* 1.3 60.7 + - - +
225C ARG 3.9 1.3 + - - -
226C GLY* 3.5 30.5 - - - +
227C GLU 3.1 7.4 - - - +
228C GLU* 4.1 14.8 - - + -
229C VAL* 5.0 0.4 - - - -
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Residues in contact with TRP 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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171C ILE* 3.7 31.9 - - + -
175C THR 3.8 8.5 - - - -
176C THR* 3.7 6.3 - - - -
177C LEU* 3.5 48.7 - - + -
180C LEU* 4.1 8.7 - - + -
200C THR* 5.8 0.4 - - + -
201C ILE* 3.6 33.8 - - + +
204C THR* 2.6 40.9 - - + +
205C ILE* 4.0 12.6 - - + +
223C LYS* 1.3 71.6 - - - +
225C ARG* 1.3 113.8 + - + +
227C GLU* 2.8 22.6 + - - +
229C VAL* 4.9 6.9 - - + +
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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