Contacts of the helix formed by residues 221 - 235 (chain A) in PDB entry 5IWS
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 ILE 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A PRO* 1.3 89.0 - - + +
222A VAL* 1.3 67.4 + - + +
224A PRO* 3.2 11.6 - - - +
225A PHE* 3.5 1.9 + - + +
381A ALA* 3.4 36.6 - - + +
384A ASP* 4.1 14.4 - - + +
385A LEU* 3.7 36.6 - - + -
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Residues in contact with VAL 222 (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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219A ALA* 3.6 23.3 - - + -
220A PRO* 4.9 3.6 - - + -
221A ILE* 1.3 82.0 - - + +
223A ALA* 1.3 64.7 + - - +
225A PHE* 3.8 10.3 - - + +
226A VAL* 3.1 34.1 + - + +
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Residues in contact with ALA 223 (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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215A SER 4.3 4.7 - - - +
216A LYS* 3.7 15.0 - - - +
219A ALA* 3.3 33.6 - - + +
220A PRO 3.6 0.8 + - - -
222A VAL* 1.3 81.7 - - - +
224A PRO* 1.3 68.3 - - + +
226A VAL* 4.0 3.5 - - - +
227A TYR* 3.2 16.3 + - - +
305A ARG* 4.2 0.2 - - - +
306A PHE* 3.4 18.6 - - + -
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Residues in contact with PRO 224 (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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220A PRO 3.2 15.9 - - - +
221A ILE 3.2 8.5 - - - +
223A ALA* 1.3 91.4 - - + +
225A PHE* 1.3 54.8 + - - +
227A TYR* 3.8 0.2 - - - +
228A GLY 2.8 26.0 + - - -
305A ARG* 3.6 27.8 - - + +
306A PHE* 3.7 15.7 - - + -
380A PHE* 3.2 40.6 - - + +
381A ALA* 3.8 1.6 - - - +
384A ASP* 3.3 19.1 - - - +
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Residues in contact with PHE 225 (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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221A ILE* 3.5 10.2 + - + +
222A VAL* 3.5 10.1 + - + +
223A ALA 3.2 1.0 - - - -
224A PRO* 1.3 77.3 - - - +
226A VAL* 1.3 69.2 + - + +
228A GLY 3.8 0.2 - - - -
229A THR* 2.7 55.0 + - + -
374A ILE* 3.7 34.5 - - + -
377A GLY* 3.4 29.9 - - - +
378A LEU* 3.9 17.7 - - + -
381A ALA* 3.7 12.4 - - + +
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Residues in contact with VAL 226 (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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208A PHE* 5.7 5.6 - - + -
211A TRP* 5.5 13.7 - - + -
222A VAL* 3.1 23.9 + - + +
223A ALA* 4.0 3.8 - - - +
225A PHE* 1.3 87.5 - - + +
227A TYR* 1.3 59.3 + - - +
229A THR* 4.7 2.2 - - - -
230A LEU* 2.8 46.4 + - + +
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Residues in contact with TYR 227 (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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212A ILE* 5.3 6.1 - - + -
223A ALA 3.2 8.5 + - - +
224A PRO 3.8 1.6 - - - +
226A VAL* 1.3 80.6 - - - +
228A GLY* 1.3 64.6 + - - +
230A LEU* 3.9 1.4 - - - +
231A GLU* 3.0 35.5 + - - +
243A LEU* 3.5 43.8 - - + +
244A THR* 3.3 30.0 - - + +
247A MSE 3.6 31.3 - - + +
248A ASN* 3.9 6.4 + - - -
306A PHE* 3.3 51.3 + + + -
380A PHE* 3.8 20.0 - + - -
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Residues in contact with GLY 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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224A PRO 2.8 17.1 + - - -
225A PHE 3.9 0.7 - - - -
227A TYR* 1.3 74.0 - - - +
229A THR* 1.3 60.8 + - - +
231A GLU* 3.8 4.5 - - - +
232A ARG* 3.5 26.3 + - - +
373A ALA 4.5 0.2 - - - -
376A THR* 4.2 0.7 + - - -
377A GLY* 4.3 6.3 - - - -
380A PHE* 3.5 38.1 - - - -
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Residues in contact with THR 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 PHE* 2.7 37.5 + - + -
226A VAL* 4.1 2.9 - - - -
228A GLY* 1.3 72.7 - - - +
230A LEU* 1.3 65.9 + - - +
232A ARG* 3.2 5.5 + - - +
233A LEU* 3.2 30.9 + - + +
370A VAL* 6.5 0.2 - - + -
373A ALA* 3.3 38.4 + - + +
374A ILE* 4.0 13.9 - - + -
377A GLY* 3.4 9.6 - - - -
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Residues in contact with LEU 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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208A PHE* 4.1 30.3 - - + -
212A ILE* 5.9 0.2 - - + -
226A VAL* 2.8 32.0 + - + +
227A TYR* 4.1 2.7 - - - +
229A THR* 1.3 72.7 - - - +
231A GLU* 1.3 61.3 + - - +
233A LEU* 3.3 16.7 + - + -
234A LEU* 3.1 48.6 + - + +
243A LEU* 4.0 17.7 - - + -
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Residues in contact with GLU 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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227A TYR* 3.0 23.3 + - + +
228A GLY 3.8 2.2 - - - +
229A THR 3.2 0.2 - - - -
230A LEU* 1.3 78.4 - - - +
232A ARG* 1.3 84.1 + - - +
234A LEU* 3.5 1.0 + - - -
235A LEU* 3.1 21.5 + - - +
240A HIS* 3.5 17.3 - - + +
243A LEU* 4.5 9.4 - - + +
244A THR* 3.4 28.1 - - + +
310A GLN* 4.3 2.1 - - - +
380A PHE* 3.6 26.9 - - - -
1B GLC 4.3 1.2 + - - -
2B GLC 2.8 29.8 + - - -
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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 GLY 3.5 9.1 + - - +
229A THR 3.2 7.7 + - - +
231A GLU* 1.3 110.2 + - - +
233A LEU* 1.3 63.0 + - - +
235A LEU* 3.3 16.7 + - - +
236A PRO* 3.2 18.5 - - - +
310A GLN* 3.9 10.3 - - - +
354A THR* 3.1 18.4 + - - +
358A GLU* 2.5 31.2 + - - -
362A MSE 4.6 2.8 - - - +
369A TYR* 3.8 8.4 - - + +
372A TYR* 3.4 30.4 + - + -
373A ALA* 3.9 15.5 - - + -
376A THR* 3.2 29.5 - - - +
380A PHE* 5.6 2.7 - - - -
2B GLC 3.1 22.0 + - - -
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Residues in contact with LEU 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 THR* 3.2 24.6 + - + +
230A LEU* 3.3 21.7 + - + +
232A ARG* 1.3 77.7 - - - +
234A LEU* 1.3 62.6 + - + +
236A PRO* 3.3 12.5 - - - +
237A PHE* 3.4 17.2 - - - -
369A TYR* 3.3 32.8 + - + +
370A VAL* 4.8 11.9 - - + -
373A ALA* 3.7 20.4 - - + -
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Residues in contact with LEU 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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230A LEU* 3.1 45.8 + - + +
231A GLU 3.8 0.4 - - - -
233A LEU* 1.3 77.0 - - + +
235A LEU* 1.3 61.2 + - - +
236A PRO 3.6 0.4 - - - -
237A PHE* 3.4 8.6 + - + -
238A GLY 3.4 2.1 + - - -
239A LEU* 3.0 59.3 + - + +
240A HIS* 3.5 22.0 - - + +
242A MSE 6.0 0.7 - - + -
243A LEU* 4.7 12.6 - - + -
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Residues in contact with LEU 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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231A GLU 3.1 14.2 + - - +
232A ARG* 3.4 51.4 - - - +
233A LEU 3.2 0.2 - - - -
234A LEU* 1.3 77.2 - - - +
236A PRO* 1.3 62.3 - - - +
238A GLY* 2.9 20.3 + - - -
240A HIS* 3.3 19.1 + - + +
354A THR* 3.9 4.5 - - - +
355A GLU* 3.6 28.6 - - + +
358A GLU* 3.2 21.5 - - - +
359A PHE* 4.3 3.0 - - + -
362A MSE 3.8 19.1 - - + -
2B GLC 3.9 7.6 - - - +
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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