Contacts of the helix formed by residues 228 - 246 (chain A) in PDB entry 5UU1
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 SER 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A VAL* 3.5 13.5 - - - +
193A TYR* 4.4 3.8 - - - -
199A HIS* 3.7 20.4 - - - -
220A ASP* 4.4 1.3 + - - -
226A ALA 3.6 1.0 + - - -
227A LEU* 1.3 74.1 - - - +
229A ARG* 1.3 65.5 + - - +
230A ARG* 3.6 16.5 - - - +
231A SER* 2.6 28.8 + - - -
232A ASP 3.8 0.5 + - - -
300A TYR* 2.8 41.9 + - - -
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Residues in contact with ARG 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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158A HIS* 3.5 32.4 + - + +
163A VAL* 3.7 2.4 - - - +
193A TYR* 3.2 39.0 + - + +
199A HIS* 4.3 11.3 + - - -
228A SER* 1.3 75.1 - - - +
230A ARG* 1.3 63.4 + - - +
232A ASP* 3.1 20.4 + - - +
233A VAL* 3.4 6.4 + - - +
300A TYR 5.0 0.4 + - - -
301A ASP 3.0 27.1 + - - -
302A GLU 4.2 4.0 + - - +
303A LYS* 3.4 40.5 - - - +
304A PRO* 3.6 25.1 - - + -
306A TYR* 3.8 9.6 + - - -
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Residues in contact with ARG 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TYR* 4.2 11.5 - - - -
220A ASP* 2.9 35.1 + - - +
228A SER* 3.6 12.3 + - - +
229A ARG* 1.3 76.9 - - - +
231A SER* 1.3 66.0 + - - +
233A VAL* 3.3 3.8 + - - +
234A GLU* 3.0 30.0 + - - +
295A ALA 4.6 6.4 - - - +
296A HIS 5.8 0.2 + - - -
298A LEU* 3.1 55.4 + - + -
299A ALA* 3.5 15.5 - - - +
300A TYR* 3.4 32.7 + - - +
302A GLU 5.2 2.3 + - - +
304A PRO* 4.7 1.0 - - - +
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Residues in contact with SER 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A VAL* 5.0 0.5 - - - +
165A GLY* 5.7 0.5 - - - -
218A SER* 3.3 29.3 - - - -
220A ASP* 4.4 9.6 - - - -
227A LEU* 3.6 20.7 - - - +
228A SER 2.6 31.2 + - - -
230A ARG* 1.3 82.5 - - - +
232A ASP* 1.3 64.8 + - - +
234A GLU* 3.3 5.6 + - - +
235A ILE* 3.0 33.0 + - - +
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Residues in contact with ASP 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 3.5 23.5 - - + +
158A HIS* 2.7 30.3 + - + +
163A VAL* 3.3 9.3 - - - -
164A HIS* 2.9 24.1 + - - +
165A GLY* 3.0 28.1 + - - -
167A ILE* 4.2 5.9 - - - +
229A ARG 3.1 11.3 + - - +
231A SER* 1.3 80.2 + - - +
233A VAL* 1.3 64.1 + - - +
235A ILE* 3.4 8.6 + - - +
236A LEU* 3.1 21.7 + - - +
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 4.9 4.5 - - + -
154A LEU* 4.5 10.8 - - + -
158A HIS* 4.9 2.7 - - + -
229A ARG 3.7 12.8 - - - +
230A ARG* 3.3 8.9 + - - +
232A ASP* 1.3 75.0 - - - +
234A GLU* 1.3 63.5 + - - +
236A LEU* 3.2 6.8 + - - +
237A GLY 3.0 18.0 + - - -
291A PHE* 3.4 27.9 - - + -
295A ALA* 3.5 22.0 - - + -
298A LEU* 4.7 2.9 - - + -
304A PRO* 4.0 26.7 - - + -
306A TYR* 5.2 1.3 - - + -
309A LEU* 4.0 17.9 - - + -
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Residues in contact with GLU 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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218A SER* 3.5 5.8 - - - -
219A LEU* 2.9 35.8 + - - +
220A ASP* 5.1 5.0 + - - +
230A ARG* 3.0 22.2 + - - +
231A SER* 3.5 7.2 - - - +
233A VAL* 1.3 76.2 - - - +
235A ILE* 1.3 62.4 + - - +
237A GLY* 3.0 11.7 + - - -
238A TYR* 2.7 51.0 + - + +
268A LEU* 4.2 15.1 - - + +
292A LEU* 4.4 5.5 - - + +
295A ALA* 4.4 15.3 - - + +
296A HIS* 4.6 9.5 + - - +
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Residues in contact with ILE 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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165A GLY* 3.7 38.1 - - - +
166A ASP* 4.1 1.6 - - - +
167A ILE* 3.3 35.2 - - + +
216A PHE* 3.3 31.9 - - + +
217A THR* 4.6 3.6 - - - +
218A SER* 3.9 18.2 - - - +
227A LEU* 6.0 0.7 - - + -
231A SER* 3.0 20.6 + - - +
232A ASP* 3.7 9.6 - - - +
234A GLU* 1.3 73.9 - - - +
236A LEU* 1.3 57.9 + - - +
238A TYR* 3.1 4.2 + - - +
239A CYS* 2.9 27.9 + - - +
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Residues in contact with LEU 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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147A GLY* 3.6 33.4 - - - +
150A MET* 3.8 31.0 - - + -
151A LEU* 3.9 23.6 - - + +
154A LEU* 4.4 5.6 - - + -
167A ILE* 4.3 16.4 - - + +
232A ASP 3.1 11.2 + - - +
233A VAL* 3.2 9.8 + - - +
235A ILE* 1.3 78.8 - - - +
237A GLY* 1.3 58.0 + - - +
239A CYS* 3.3 6.6 + - - +
240A MET* 3.0 33.5 + - + +
243A TRP* 4.6 11.4 - - + -
291A PHE* 4.1 11.4 - - + -
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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 VAL 3.0 11.1 + - - -
234A GLU 3.0 5.3 + - - -
236A LEU* 1.3 75.9 - - - +
238A TYR* 1.4 58.5 + - - +
240A MET* 3.3 7.0 + - - +
241A LEU* 3.1 23.6 + - - +
288A ILE* 4.2 5.2 - - - +
291A PHE* 3.6 22.3 - - - -
292A LEU* 3.7 18.6 - - - -
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Residues in contact with TYR 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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216A PHE* 3.4 37.9 - - + -
217A THR 3.6 15.9 - - - -
218A SER* 4.5 0.2 - - - -
219A LEU* 3.8 1.4 - - - +
234A GLU* 2.7 55.7 + - + -
235A ILE* 3.7 3.1 - - - +
237A GLY* 1.4 73.8 - - - +
239A CYS* 1.4 62.5 + - - +
241A LEU* 3.4 8.7 + - + +
242A ARG* 3.0 24.9 + - - +
248A LEU* 3.8 4.7 - - + +
250A TRP* 3.9 32.1 - + + -
264A LYS* 3.7 27.3 - - + +
267A LEU* 4.6 7.0 - - + -
268A LEU* 3.4 31.2 - - + +
292A LEU* 4.8 5.8 - - + -
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Residues in contact with CYS 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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167A ILE* 3.0 37.5 - - - -
168A LYS* 3.9 10.8 - - - -
216A PHE* 4.0 21.5 - - - -
235A ILE* 2.9 15.0 + - - +
236A LEU* 3.3 12.6 - - + +
238A TYR* 1.4 75.4 - - - +
240A MET* 1.4 56.5 + - - +
242A ARG* 3.2 3.6 + - - +
243A TRP* 2.9 58.1 + - + -
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Residues in contact with MET 240 (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 VAL* 3.7 32.7 - - + +
144A LEU* 4.9 0.4 - - - -
147A GLY* 3.8 23.6 - - - -
236A LEU* 3.0 22.9 + - + +
237A GLY* 3.3 4.7 + - - +
239A CYS* 1.4 69.9 - - - +
241A LEU* 1.3 65.8 + - - +
243A TRP* 3.2 16.0 + - + +
244A LEU* 3.0 26.0 + - - +
288A ILE* 3.8 17.3 - - + -
291A PHE* 3.7 50.7 - - + -
313A LEU* 3.9 19.5 - - + -
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Residues in contact with LEU 241 (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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237A GLY 3.1 13.4 + - - +
238A TYR* 3.7 9.9 - - + +
240A MET* 1.3 76.4 - - - +
242A ARG* 1.3 56.8 + - - +
244A LEU 3.6 0.2 + - - -
245A CYS* 2.9 47.0 + - - +
247A LYS 4.3 0.2 - - - +
248A LEU* 3.8 20.0 - - + -
249A PRO* 5.1 0.4 - - + -
250A TRP* 5.1 0.4 - - + -
267A LEU* 4.1 31.6 - - + -
275A VAL* 3.8 25.8 - - + +
278A TRP* 4.1 15.9 - - + -
285A CYS* 3.7 28.3 - - - -
288A ILE* 4.1 11.3 - - + +
292A LEU* 4.7 4.0 - - + -
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Residues in contact with ARG 242 (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 ASN* 2.9 35.1 + - - +
136A GLY* 3.3 15.7 + - - +
215A GLU* 3.1 25.3 + - - -
216A PHE* 3.6 27.8 - - + -
238A TYR 3.0 13.9 + - - +
239A CYS 3.4 9.0 - - - +
241A LEU* 1.3 75.2 - - - +
243A TRP* 1.3 63.2 + - + +
246A GLY* 2.8 38.9 + - - -
247A LYS* 3.7 24.0 - - - +
248A LEU* 3.8 9.8 - - + +
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Residues in contact with TRP 243 (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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128A LEU* 5.8 0.4 - - + -
136A GLY 4.1 10.3 - - - -
137A THR* 3.2 8.5 - - - -
138A PHE* 2.8 49.5 + + + +
143A VAL* 3.7 19.5 - - + -
146A LEU* 3.9 32.8 - - + -
147A GLY 4.9 0.2 - - - -
150A MET* 5.2 0.4 - - + -
167A ILE* 4.9 2.9 - - + -
168A LYS* 4.4 0.9 - - - -
169A ALA* 3.8 36.7 - - + +
172A LEU* 3.8 25.4 - - + -
216A PHE* 5.4 4.0 - + - -
236A LEU* 4.6 13.5 - - + -
239A CYS* 2.9 40.9 + - + +
240A MET* 3.2 30.7 + - + +
242A ARG* 1.3 85.1 - - + +
244A LEU* 1.3 60.1 + - - +
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Residues in contact with LEU 244 (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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137A THR* 4.3 6.0 - - - +
138A PHE 4.2 7.0 - - - +
140A LYS* 3.6 49.4 - - + +
143A VAL* 4.3 7.0 - - + -
144A LEU* 6.0 1.1 - - + -
240A MET 3.0 15.3 + - - +
241A LEU 4.2 1.6 - - - +
243A TRP* 1.3 79.6 - - - +
245A CYS* 1.3 63.6 + - - +
280A PRO* 4.1 12.9 - - + +
283A SER* 3.5 26.3 + - - +
284A SER 4.2 4.0 - - - +
285A CYS* 3.5 27.8 - - - -
288A ILE* 4.3 15.3 - - + -
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Residues in contact with CYS 245 (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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137A THR* 4.0 3.4 - - - +
241A LEU* 2.9 22.6 + - - +
244A LEU* 1.3 79.8 - - - +
246A GLY* 1.3 60.1 + - - +
247A LYS* 3.3 4.5 + - - +
278A TRP* 3.6 36.6 - - + +
279A ALA* 3.8 2.0 - - - -
280A PRO* 3.8 27.5 - - + +
285A CYS* 3.7 28.5 - - - -
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Residues in contact with GLY 246 (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 ASN* 3.5 23.9 - - - +
137A THR* 3.3 22.8 - - - +
242A ARG* 2.8 34.0 + - - -
245A CYS* 1.3 73.1 - - - +
247A LYS* 1.3 62.7 + - - +
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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