Contacts of the helix formed by residues 227 - 237 (chain A) in PDB entry 5IWM
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 LYS 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A MET* 5.1 8.2 - - + +
214A GLU 5.8 3.4 - - - +
226A GLY* 1.3 77.7 - - - +
228A SER* 1.3 63.4 + - - +
229A GLY 3.3 2.2 - - - -
230A ILE* 3.2 13.6 + - + +
231A ARG* 2.8 53.0 + - - +
488A ILE* 4.3 20.6 - - + -
490A LEU* 3.5 38.9 - - + +
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Residues in contact with SER 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A GLY* 5.3 2.3 - - - -
227A LYS* 1.3 78.8 + - - +
229A GLY* 1.3 58.7 + - - +
231A ARG* 3.3 18.9 + - - +
232A ARG* 3.0 30.1 + - - +
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Residues in contact with GLY 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A LEU 5.9 0.8 + - - -
226A GLY 5.3 1.0 - - - -
227A LYS 3.3 1.2 - - - +
228A SER* 1.3 81.6 + - - +
230A ILE* 1.3 61.1 + - - +
232A ARG* 3.5 7.8 + - - +
233A ALA* 3.1 23.6 + - - +
239A GLY* 4.0 4.2 - - - -
240A SER 3.5 23.8 - - - -
241A ILE* 3.9 10.2 - - - +
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Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A MET* 4.0 11.4 - - + -
214A GLU 4.1 2.7 - - - +
215A GLY* 4.0 7.9 - - - -
216A PRO* 3.9 15.0 - - + -
224A ILE* 3.9 23.6 - - + -
226A GLY 4.0 10.7 + - - +
227A LYS* 3.2 11.3 + - + +
229A GLY* 1.3 75.4 - - - +
231A ARG* 1.3 63.5 + - - +
233A ALA* 3.4 2.5 + - - +
234A TYR* 3.1 52.7 + - + -
241A ILE* 3.7 28.9 - - + +
488A ILE* 4.1 20.9 - - + -
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Residues in contact with ARG 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ILE* 5.0 0.4 - - + +
210A MET* 4.3 28.1 - - + +
227A LYS* 2.8 43.9 + - - +
228A SER* 3.6 27.5 - - - +
230A ILE* 1.3 71.8 - - - +
232A ARG* 1.3 65.6 + - - +
234A TYR* 3.4 1.4 + - - +
235A GLU* 3.0 53.8 + - - +
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Residues in contact with ARG 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A SER 3.0 16.8 + - - +
229A GLY* 3.7 8.1 - - - +
231A ARG* 1.3 75.9 - - - +
233A ALA* 1.3 63.2 + - - +
235A GLU* 3.5 9.6 + - - +
236A THR* 2.8 40.0 + - + +
238A ARG 3.3 12.3 + - - +
239A GLY* 4.6 6.1 - - - -
240A SER 5.7 0.7 - - - +
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A GLY 3.1 18.2 + - - +
230A ILE* 3.7 6.5 - - - +
231A ARG 3.3 0.2 - - - -
232A ARG* 1.3 77.6 - - - +
234A TYR* 1.3 63.5 + - + +
237A GLY* 2.6 32.1 + - - -
238A ARG 3.3 11.4 + - - -
239A GLY* 4.0 4.5 - - - -
241A ILE* 4.7 2.7 - - + -
333A VAL* 3.8 35.9 - - + -
335A MET* 3.8 4.7 - - - +
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Residues in contact with TYR 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A PRO* 5.9 2.2 - - + -
186A HIS* 3.0 39.1 + + - -
206A ILE* 3.8 18.2 - - + +
210A MET* 3.7 19.3 - - + -
213A ILE* 3.8 23.2 - - + +
215A GLY* 3.2 17.8 - - - -
216A PRO* 3.3 5.3 - - + +
230A ILE* 3.1 38.7 + - + +
231A ARG 4.0 2.2 - - - +
233A ALA* 1.3 82.5 - - + +
235A GLU* 1.3 57.2 + - - +
241A ILE* 6.2 0.9 - - + -
333A VAL* 6.5 0.4 - - + -
335A MET* 4.6 10.3 - - + -
347A ASN* 3.0 9.0 - - - +
348A LEU* 3.0 60.5 + - + +
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Residues in contact with GLU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ILE* 4.0 28.7 - - + +
207A ALA* 5.9 1.2 + - - +
231A ARG* 3.0 44.2 + - - +
232A ARG* 3.9 6.5 - - - +
233A ALA 3.3 0.2 - - - -
234A TYR* 1.3 78.5 - - - +
236A THR* 1.3 67.1 + - + +
347A ASN* 3.6 16.0 + - - +
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Residues in contact with THR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ARG* 2.8 28.7 + - + +
235A GLU* 1.3 86.6 - - + +
237A GLY* 1.3 58.5 + - - +
238A ARG* 3.1 19.5 + - - +
345A LEU* 4.0 19.6 - - - +
346A ILE 4.6 2.6 - - - +
347A ASN* 4.4 5.6 - - - -
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Residues in contact with GLY 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ALA* 2.6 25.0 + - - -
235A GLU 3.8 0.4 - - - -
236A THR* 1.3 71.9 - - - +
238A ARG* 1.3 62.9 + - - +
333A VAL* 3.6 5.4 - - - +
334A ASN* 3.5 2.6 + - - -
335A MET* 3.0 31.2 + - - -
345A LEU* 3.8 4.4 - - - +
346A ILE 3.4 23.5 + - - -
347A ASN* 4.2 1.4 - - - +
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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