Contacts of the helix formed by residues 229 - 246 (chain A) in PDB entry 3N51
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 GLU 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A HIS* 3.0 58.9 - - + +
169A LYS* 6.5 0.7 - - - -
171A VAL* 3.7 23.3 - - + +
228A ASP* 1.3 83.6 - - - +
230A LYS* 1.3 83.7 + - + +
232A ASP* 3.0 13.4 + - - +
233A VAL 4.0 0.3 + - - -
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Residues in contact with LYS 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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228A ASP* 3.0 19.3 + - - +
229A GLU* 1.3 92.9 - - + +
231A CYS* 1.3 61.5 + - - +
233A VAL* 3.0 20.0 + - + +
234A TRP 3.2 3.8 + - - -
293A PRO* 2.7 32.8 + - + +
294A SER* 3.8 12.5 + - - +
296A ARG* 2.5 56.8 + - + +
297A ILE 3.7 16.2 - - - +
298A SER* 4.0 19.3 - - - +
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Residues in contact with CYS 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A VAL* 3.8 21.1 - - - -
173A ARG* 3.9 20.6 - - - +
219A ALA* 3.6 15.5 - - + +
221A GLU* 3.4 20.5 + - - +
222A VAL* 3.7 17.9 - - + -
227A TYR* 4.1 6.3 - - + -
228A ASP 3.1 22.1 + - - +
229A GLU 3.1 1.4 + - - -
230A LYS* 1.3 78.1 - - - +
232A ASP* 1.3 59.5 + - - +
234A TRP* 3.3 4.2 + - - +
235A SER* 3.1 29.2 + - - -
296A ARG* 3.8 2.0 - - - +
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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
----------------------------------------------------------
162A ILE* 4.2 12.6 - - + -
166A HIS* 2.8 28.9 + - + +
171A VAL* 3.7 7.1 - - - +
172A HIS* 2.9 30.9 + - - +
173A ARG* 2.8 30.5 + - - -
175A LEU* 3.8 8.0 - - + +
196A PHE* 3.9 3.5 - - - -
229A GLU 3.0 10.3 + - - +
231A CYS* 1.3 75.0 - - - +
233A VAL* 1.3 61.6 + - - +
235A SER* 4.0 5.8 + - - -
236A THR* 2.8 32.1 + - - -
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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
----------------------------------------------------------
159A LEU* 5.6 1.8 - - + -
162A ILE* 5.4 0.7 - - + -
166A HIS* 4.7 4.0 - - + +
229A GLU* 4.5 3.1 - - + +
230A LYS* 3.0 19.6 + - + +
232A ASP* 1.3 74.8 - - - +
234A TRP* 1.3 65.5 + - - +
236A THR* 3.3 1.7 + - - -
237A GLY* 2.9 19.9 + - - -
288A MET* 3.4 42.4 - - + +
296A ARG* 4.1 4.9 - - - -
297A ILE* 3.3 28.7 - - + +
298A SER* 4.4 2.7 - - - -
299A ALA* 3.5 36.6 - - + +
302A ALA* 5.3 0.2 - - + -
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Residues in contact with TRP 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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216A TYR 5.0 0.6 + - - -
217A TYR 3.6 10.5 + - - -
218A ILE 3.6 11.3 + - - -
219A ALA* 3.6 18.6 - - + -
220A PRO* 3.5 31.2 - - + -
230A LYS 3.2 3.6 + - - -
231A CYS 3.5 8.5 - - - +
233A VAL* 1.3 78.3 - - - +
235A SER* 1.3 65.2 + - - +
237A GLY* 3.0 3.5 + - - -
238A VAL* 3.0 31.9 + - + +
250A PHE* 3.2 39.2 - + - -
262A VAL* 4.4 6.2 - - + +
265A GLY* 4.5 10.5 - - - -
288A MET 3.5 12.0 + - - -
289A LEU* 3.2 45.5 - - + +
290A THR 4.0 6.3 - - - -
291A TYR* 4.3 4.7 - + - -
296A ARG* 3.6 32.1 - - - +
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Residues in contact with SER 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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173A ARG 4.4 10.4 + - - -
175A LEU* 3.5 36.4 + - - +
217A TYR* 2.7 28.7 + - - -
218A ILE* 4.6 1.2 - - - -
219A ALA 4.6 0.9 + - - -
231A CYS 3.1 14.7 + - - -
232A ASP* 4.1 3.2 - - - -
233A VAL 3.4 0.2 - - - -
234A TRP* 1.3 79.4 - - - +
236A THR* 1.3 61.5 + - - +
238A VAL* 3.2 4.4 + - - +
239A ILE* 3.1 28.1 + - - +
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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
----------------------------------------------------------
155A ILE* 3.8 28.7 - - + -
158A VAL* 3.9 14.6 - - + -
159A LEU* 4.2 8.5 - - + -
162A ILE* 3.2 20.3 - - - +
175A LEU* 3.2 5.4 - - - +
232A ASP 2.8 24.5 + - - -
233A VAL* 4.4 0.8 - - - -
234A TRP 3.2 0.2 - - - -
235A SER* 1.3 75.2 - - - +
237A GLY* 1.3 56.8 + - - +
239A ILE* 3.2 10.5 + - + +
240A LEU* 2.8 27.2 + - - +
288A MET* 3.6 21.8 - - + -
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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 2.9 14.5 + - - -
234A TRP 3.0 4.2 + - - -
236A THR* 1.3 74.0 - - - +
238A VAL* 1.3 60.1 + - - +
240A LEU* 3.7 3.7 - - - +
241A TYR* 3.0 28.8 + - - +
285A ILE* 4.6 5.2 - - - +
288A MET* 3.6 25.3 - - - +
289A LEU* 3.9 14.5 - - - +
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Residues in contact with VAL 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 TYR* 3.4 25.6 - - + +
217A TYR* 3.4 25.6 - - + -
234A TRP* 3.0 41.4 + - + +
235A SER 3.6 7.0 - - - +
237A GLY* 1.3 74.0 - - - +
239A ILE* 1.3 65.9 + - - +
241A TYR* 3.4 4.2 + - - +
242A ILE* 3.0 24.8 + - + +
249A PRO* 3.9 30.0 - - + +
250A PHE* 4.3 3.8 - - + -
289A LEU* 3.8 9.2 - - + -
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Residues in contact with ILE 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 5.5 0.9 - - + -
137A PHE* 4.4 20.6 - - + -
154A ILE* 5.7 0.4 - - + -
155A ILE* 4.4 13.7 - - + -
158A VAL* 5.7 2.5 - - + -
175A LEU* 4.6 9.0 - - + -
176A LYS* 3.9 33.2 - - - +
177A PRO* 4.0 2.2 - - + -
180A LEU* 4.2 20.6 - - + -
217A TYR* 3.9 18.8 - - + -
235A SER 3.1 18.2 + - - +
236A THR* 3.5 11.2 - - + +
238A VAL* 1.3 76.7 - - - +
240A LEU* 1.3 62.7 + - - +
242A ILE* 3.2 9.8 + - - +
243A LEU* 3.0 28.6 + - + +
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Residues in contact with LEU 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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151A ALA* 4.5 5.4 - - + -
155A ILE* 3.8 26.0 - - + -
236A THR 2.8 17.6 + - - +
237A GLY* 3.7 6.3 - - - +
238A VAL 3.2 0.4 - - - -
239A ILE* 1.3 77.4 - - - +
241A TYR* 1.3 62.7 + - - +
243A LEU* 3.1 12.0 + - + +
244A LEU* 3.2 32.8 + - + +
281A ALA 4.7 2.0 - - - +
284A LEU* 4.1 20.6 - - + -
285A ILE* 3.8 23.6 - - + -
288A MET* 4.5 7.4 - - - -
307A TRP* 3.5 34.8 - - + -
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Residues in contact with TYR 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 3.0 13.5 + - - +
238A VAL 3.4 9.4 - - - +
240A LEU* 1.3 77.2 - - - +
242A ILE* 1.3 55.1 + - - +
244A LEU 3.5 0.7 + - - -
245A SER* 2.9 42.1 + - - -
247A CYS* 3.1 26.5 - - + -
248A PRO 4.0 0.9 - - - -
249A PRO* 3.5 41.8 + - + +
267A TYR* 3.9 7.6 - + - -
268A THR 2.5 29.9 + - - -
269A PHE* 3.8 17.0 - + - -
271A LEU* 4.8 8.1 - - + +
274A TRP* 3.4 31.6 + + - -
285A ILE* 4.0 21.0 - - + +
289A LEU* 4.6 0.7 - - + -
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Residues in contact with ILE 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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137A PHE* 3.9 15.3 - - + -
217A TYR* 3.5 40.8 - - + +
238A VAL* 3.0 18.4 + - + +
239A ILE* 3.2 7.4 + - - +
241A TYR* 1.3 73.0 - - - +
243A LEU* 1.3 62.4 + - - +
246A GLY* 2.6 35.8 + - - -
247A CYS 3.7 19.5 - - - +
248A PRO* 3.7 20.0 - - + -
249A PRO* 4.3 0.2 - - + -
330A ILE* 3.9 25.0 - - + +
333A PHE* 4.3 11.7 - - + -
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Residues in contact with LEU 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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136A LEU* 4.8 1.8 - - + -
137A PHE* 3.8 21.1 - - + -
140A ILE* 3.7 29.6 - - + -
146A PHE* 3.4 30.4 - - + -
151A ALA* 4.0 22.7 - - + +
154A ILE* 3.7 19.5 - - + -
155A ILE* 3.7 34.3 - - + -
239A ILE* 3.0 19.0 + - + +
240A LEU* 3.1 7.2 + - - +
242A ILE* 1.3 75.7 - - - +
244A LEU* 1.3 59.6 + - - +
323A LEU* 4.6 0.7 - - - +
326A ALA* 4.2 8.8 - - - +
330A ILE* 4.4 8.9 - - + +
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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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148A GLU* 3.9 20.6 - - + -
151A ALA* 3.7 21.5 - - + -
240A LEU* 3.2 39.5 + - + +
242A ILE 3.2 0.2 - - - -
243A LEU* 1.3 79.4 - - - +
245A SER* 1.3 57.3 + - - +
273A GLN* 4.6 5.0 - - - +
274A TRP* 3.9 16.1 - - + -
277A VAL* 3.9 23.4 - - + +
281A ALA* 3.9 25.8 - - + -
285A ILE* 4.0 10.8 - - + -
307A TRP* 4.3 2.5 - - + -
323A LEU* 3.8 24.2 - - + +
326A ALA* 3.7 11.1 - - - +
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Residues in contact with SER 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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241A TYR* 2.9 24.4 + - - -
244A LEU* 1.3 79.9 - - - +
246A GLY* 1.3 59.1 + - - +
247A CYS* 3.1 20.8 + - - +
271A LEU* 5.2 0.7 - - - -
273A GLN* 2.7 41.8 + - - -
274A TRP* 3.6 28.0 - - - -
326A ALA* 3.6 9.0 - - - -
329A ASN* 3.5 6.8 + - - -
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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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242A ILE* 2.6 30.4 + - - -
244A LEU 3.9 0.4 - - - -
245A SER* 1.3 71.4 - - - +
247A CYS* 1.3 60.3 + - - +
248A PRO* 4.5 0.3 - - - +
326A ALA* 3.5 22.0 - - - +
329A ASN* 3.3 24.6 - - - +
330A ILE* 3.7 6.5 + - - -
333A PHE* 4.0 11.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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