Contacts of the helix formed by residues 220 - 239 (chain A) in PDB entry 5UNH
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 PHE 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A ASN* 2.9 12.6 + - + +
219A GLY* 1.4 77.4 - - - +
221A ILE* 1.3 72.0 + - + +
223A PRO* 3.5 5.4 - - - +
224A LEU* 2.8 50.2 + - + +
265A PHE* 3.7 25.5 - + - -
266A ILE* 3.9 19.5 - - + -
269A TRP* 3.7 18.6 - - + -
270A LEU* 3.6 55.4 - - + -
273A HIS* 3.6 29.2 - + + +
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Residues in contact with ILE 221 (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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216A ASN* 2.8 28.2 + - + +
217A ILE* 3.8 31.2 - - + +
220A PHE* 1.3 88.9 - - + +
222A ILE* 1.4 66.2 + - + +
224A LEU* 3.7 3.3 - - - +
225A ILE* 3.0 42.6 + - + +
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Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ILE* 3.0 41.4 + - + +
218A LEU* 4.9 14.8 - - + +
221A ILE* 1.4 72.2 - - + +
223A PRO* 1.4 71.8 - - + +
225A ILE* 3.2 24.2 + - + +
226A PHE* 3.1 40.0 - - + -
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Residues in contact with PRO 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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132A ILE* 3.6 30.7 - - + -
133A PHE* 5.1 5.2 - - + -
136A THR* 4.1 14.4 - - + +
217A ILE 3.7 0.4 - - - +
218A LEU 3.4 24.5 - - - +
219A GLY 3.8 5.6 - - - -
220A PHE 3.5 15.5 - - - +
222A ILE* 1.4 93.4 - - + +
224A LEU* 1.4 61.1 + - - +
226A PHE* 3.0 19.7 + - + +
227A ILE* 3.1 18.7 + - + +
265A PHE* 4.0 10.3 - - + -
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Residues in contact with LEU 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 PHE* 2.8 35.8 + - + +
221A ILE* 3.7 4.3 - - - +
223A PRO* 1.4 68.9 - - - +
225A ILE* 1.4 64.4 - - + +
227A ILE* 4.0 5.6 - - + -
228A ALA* 3.0 37.6 + - + +
262A VAL* 4.3 20.2 - - + -
265A PHE* 3.8 20.1 - - + -
266A ILE* 3.7 31.4 - - + -
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Residues in contact with ILE 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* 3.0 38.0 + - + +
222A ILE* 3.2 16.8 + - + +
224A LEU* 1.4 75.2 - - + +
226A PHE* 1.4 61.1 + - + +
228A ALA* 3.8 3.3 - - - +
229A THR* 2.8 47.0 + - - +
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Residues in contact with PHE 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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136A THR* 3.5 31.0 - - + +
139A SER* 5.2 0.4 - - - -
140A VAL* 4.3 18.8 - - + -
222A ILE* 3.1 43.7 + - + -
223A PRO* 3.0 6.8 + - + +
225A ILE* 1.4 82.7 - - + +
227A ILE* 1.4 65.1 + - - +
229A THR* 3.3 4.8 + - - -
230A CYS* 3.0 33.3 + - - -
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Residues in contact with ILE 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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135A ILE* 3.8 25.6 - - + -
136A THR* 3.7 29.8 - - - +
139A SER* 3.7 21.7 + - - +
223A PRO* 3.1 24.2 + - + +
224A LEU* 4.0 11.2 - - + +
226A PHE* 1.4 74.0 - - - +
228A ALA* 1.3 56.2 + - - +
230A CYS* 3.7 2.1 + - - +
231A TYR* 3.1 27.9 + - - +
261A VAL* 4.3 8.1 - - + +
262A VAL* 3.7 36.1 - - + +
265A PHE* 4.8 11.9 - - + -
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Residues in contact with ALA 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 LEU* 3.0 29.5 + - + +
225A ILE* 3.8 3.6 - - - +
227A ILE* 1.3 74.6 - - - +
229A THR* 1.4 64.1 + - - +
231A TYR* 3.4 2.5 + - - +
232A PHE* 3.1 43.7 + - + -
262A VAL* 4.1 12.7 - - + +
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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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143A TYR* 5.2 1.1 - - + -
225A ILE* 2.8 35.7 + - - +
226A PHE* 3.3 5.4 + - - -
228A ALA* 1.4 72.1 - - - +
230A CYS* 1.4 58.8 - - - +
232A PHE* 3.8 3.4 - - - +
233A GLY* 2.9 26.3 + - - -
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Residues in contact with CYS 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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139A SER* 3.4 42.0 - - - +
140A VAL* 3.7 20.2 - - - -
143A TYR* 3.9 19.5 - - + -
226A PHE* 3.0 22.3 + - - +
227A ILE 3.9 3.4 - - - +
229A THR* 1.4 76.2 - - - +
231A TYR* 1.4 60.5 + - - +
233A GLY* 3.3 0.9 + - - -
234A ILE* 2.9 37.4 + - + +
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Residues in contact with TYR 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 ILE 3.1 18.6 + - - +
228A ALA* 3.4 4.2 + - - +
230A CYS* 1.4 75.1 - - - +
232A PHE* 1.3 89.8 + + - +
234A ILE* 3.3 8.8 + - - +
235A ARG* 2.8 59.5 + - + +
255A LEU* 3.9 15.5 + - + +
258A ALA* 3.6 28.3 - - + +
259A ALA* 3.7 28.8 - - + +
262A VAL* 4.2 21.3 - - + -
263A LEU* 6.5 0.4 - - + -
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Residues in contact with PHE 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 ALA* 3.1 35.9 + - + +
229A THR* 3.8 3.6 - - - +
231A TYR* 1.3 97.0 - + - +
233A GLY* 1.3 57.1 + - - +
235A ARG* 3.4 40.7 - - + +
236A LYS* 3.0 29.6 + - - +
262A VAL* 6.5 0.2 - - + -
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Residues in contact with GLY 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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143A TYR* 3.5 28.2 - - - -
147A ILE* 4.0 1.9 - - - +
229A THR 2.9 18.7 + - - -
230A CYS 3.6 0.4 - - - -
231A TYR 3.2 0.4 - - - -
232A PHE* 1.3 76.7 - - - +
234A ILE* 1.4 61.3 + - - +
236A LYS* 3.8 5.5 + - - +
237A HIS* 3.5 19.4 + - - +
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Residues in contact with ILE 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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139A SER* 4.7 2.2 - - - +
142A ARG* 3.8 17.0 - - + +
143A TYR* 3.8 36.3 - - + +
146A VAL* 3.8 22.9 - - + -
230A CYS* 2.9 23.2 + - + +
231A TYR* 3.6 5.2 - - - +
233A GLY* 1.4 72.7 - - - +
235A ARG* 1.4 64.2 + - - +
237A HIS* 3.0 12.3 + - - +
238A LEU* 3.1 35.6 + - + +
254A VAL* 5.4 4.7 - - + -
255A LEU* 4.4 5.4 - - + -
258A ALA* 4.2 26.7 - - + -
325A PHE* 5.0 4.3 - - + -
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Residues in contact with ARG 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 TYR* 2.8 48.3 + - + +
232A PHE* 3.4 35.7 - - + +
234A ILE* 1.4 72.7 - - - +
236A LYS* 1.4 58.8 - - - +
238A LEU 3.6 0.3 + - - -
239A LEU* 3.3 53.7 + - + +
255A LEU* 3.6 24.2 - - + -
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Residues in contact with LYS 236 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A PHE 3.0 19.7 + - - +
233A GLY* 4.0 6.7 - - - +
234A ILE 3.3 0.2 - - - -
235A ARG* 1.4 75.9 - - - +
237A HIS* 1.4 58.8 + - - +
239A LEU* 4.1 6.8 + - - +
240A LYS* 3.7 20.4 + - - +
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Residues in contact with HIS 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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146A VAL* 3.8 14.8 - - + +
147A ILE* 3.7 29.6 - - + -
233A GLY 3.5 4.1 + - - +
234A ILE 3.0 9.7 + - - +
236A LYS* 1.4 78.6 - - - +
238A LEU* 1.3 58.9 + - + +
239A LEU 3.5 0.2 - - - -
240A LYS* 3.0 21.1 - - - +
241A THR* 4.1 8.3 - - - -
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Residues in contact with LEU 238 (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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146A VAL* 4.2 18.2 - - + -
234A ILE* 3.1 43.8 + - + +
235A ARG 4.3 0.2 - - - +
237A HIS* 1.3 73.9 - - - +
239A LEU* 1.4 59.9 + - - +
240A LYS 3.2 15.4 - - - +
241A THR 4.9 1.2 - - - +
251A ARG* 3.5 48.4 - - + +
254A VAL* 4.0 17.9 - - + -
255A LEU* 3.9 21.5 - - + -
332A VAL* 5.6 12.3 - - + -
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Residues in contact with LEU 239 (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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235A ARG* 3.3 51.1 + - + +
236A LYS* 4.4 6.5 - - - +
237A HIS 3.5 0.2 - - - -
238A LEU* 1.4 76.3 - - - +
240A LYS* 1.3 56.6 + - - +
255A LEU* 4.0 24.9 - - + -
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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