Contacts of the helix formed by residues 231 - 248 (chain A) in PDB entry 3DAE
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 PRO 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A HIS* 3.3 46.9 - - + +
174A VAL* 3.7 17.9 - - + -
228A TYR* 5.3 2.9 - - + +
230A GLY* 1.3 79.0 - - - +
232A GLU* 1.3 64.7 + - - +
233A VAL* 2.7 15.7 + - - -
234A ASP 3.4 6.6 + - - -
235A VAL* 3.6 8.8 + - - +
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Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLU* 4.1 4.3 - - - +
228A TYR* 5.3 1.2 - - - +
230A GLY* 3.0 24.5 + - - +
231A PRO* 1.3 88.6 - - + +
233A VAL* 1.3 57.3 + - - +
235A VAL* 3.6 10.3 - - - +
236A TRP 3.4 4.9 + - - -
291A PRO* 3.9 34.9 - - + +
294A ARG* 2.4 47.9 + - + +
295A ILE 5.6 1.1 - - - +
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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
----------------------------------------------------------
174A VAL* 3.8 8.5 - - + -
176A ARG* 4.3 12.3 - - - -
219A ALA* 3.4 28.0 + - + +
221A GLU* 3.5 21.5 - - + +
222A VAL* 3.6 18.2 - - + -
229A ALA* 4.3 11.4 - - + -
230A GLY 2.9 26.2 - - - +
231A PRO 2.7 4.0 - - - -
232A GLU* 1.3 78.3 - - - +
234A ASP* 1.3 70.8 + - - +
235A VAL 3.2 0.9 - - - -
236A TRP* 3.1 6.2 + - - +
237A SER* 3.1 27.8 + - - -
294A ARG* 4.0 2.2 - - - +
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Residues in contact with ASP 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A VAL* 3.8 10.2 - - + +
168A CYS* 5.7 0.3 - - - +
169A HIS* 2.9 30.7 + - - +
174A VAL* 3.4 7.9 - - - +
175A HIS* 2.8 27.0 + - - +
176A ARG* 2.9 26.9 + - - -
178A LEU* 3.7 19.3 - - + +
231A PRO 3.9 1.3 - - - +
233A VAL* 1.3 73.8 - - - +
235A VAL* 1.3 60.0 + - - +
237A SER* 3.3 7.5 + - - -
238A CYS* 2.8 37.5 + - - +
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PRO 3.6 11.1 + - - +
232A GLU* 3.6 12.8 - - - +
233A VAL 3.2 0.4 - - - -
234A ASP* 1.3 77.9 - - - +
236A TRP* 1.3 62.9 + - - +
238A CYS* 3.2 7.9 + - - +
239A GLY* 3.0 19.8 + - - -
286A MET* 4.0 23.4 - - + +
294A ARG* 3.9 15.3 - - + -
295A ILE* 3.5 27.8 - - + +
296A SER* 4.5 1.1 - - - -
297A ILE* 3.7 37.2 - - + +
300A ILE* 4.6 4.7 - - + -
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Residues in contact with TRP 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ASN 5.0 1.0 + - - -
217A TYR 3.5 8.2 - - - -
218A ALA 3.4 12.9 + - - -
219A ALA* 3.3 28.9 - - + -
220A PRO* 3.7 18.8 - - + -
232A GLU 3.4 2.2 + - - -
233A VAL 3.1 10.7 + - - +
235A VAL* 1.3 77.6 - - - +
237A SER* 1.3 67.3 + - - +
239A GLY* 2.9 12.8 + - - -
240A VAL* 3.1 20.9 + - + +
252A PHE* 3.3 38.7 - + - -
264A ILE* 4.0 20.8 - - + +
267A GLY* 4.4 4.9 - - - -
286A MET 3.7 12.3 - - - -
287A LEU* 3.3 46.3 - - + +
288A ILE 3.6 10.5 - - - -
289A VAL* 4.1 3.1 - - - -
294A ARG* 3.7 24.0 - - - +
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Residues in contact with SER 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ARG 5.2 4.3 + - - -
178A LEU* 3.5 39.1 + - - +
217A TYR* 3.2 26.0 + - - -
218A ALA* 5.1 1.7 - - - -
219A ALA 5.2 0.7 + - - -
233A VAL 3.1 14.2 + - - -
234A ASP* 3.3 11.4 + - - -
236A TRP* 1.3 74.9 - - - +
238A CYS* 1.3 58.2 + - - +
240A VAL* 2.9 22.9 + - - +
241A ILE* 3.0 16.4 + - - +
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Residues in contact with CYS 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE* 3.3 18.4 - - + -
161A ILE* 3.7 29.6 - - - -
162A ILE* 4.1 24.5 - - + -
165A VAL* 4.1 17.9 - - - -
178A LEU* 4.2 7.9 - - - -
234A ASP 2.8 26.6 + - - +
235A VAL* 3.5 7.2 - - - +
237A SER* 1.3 74.5 - - - +
239A GLY* 1.3 55.1 + - - +
241A ILE* 3.5 10.6 + - - +
242A LEU 3.0 21.8 + - - -
286A MET* 4.5 1.3 - - - -
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Residues in contact with GLY 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A VAL 3.0 6.5 + - - -
236A TRP 2.9 8.6 + - - -
238A CYS* 1.3 73.5 - - - +
240A VAL* 1.3 63.5 + - - +
242A LEU* 3.4 3.0 + - - +
243A TYR* 3.0 24.5 + - - +
283A ILE* 4.3 4.8 - - - +
286A MET* 3.8 33.7 - - - -
287A LEU* 4.1 9.4 - - - -
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Residues in contact with VAL 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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216A ASN 3.5 18.6 - - - +
217A TYR* 3.1 31.4 - - + -
236A TRP* 3.1 35.3 + - + +
237A SER 2.9 6.9 + - - +
239A GLY* 1.3 74.3 - - - +
241A ILE* 1.3 60.5 + - - +
243A TYR* 3.2 2.6 + - - +
244A VAL* 2.9 30.2 + - - +
250A LEU* 4.1 1.6 - - + -
251A PRO* 3.3 36.1 - - + -
252A PHE* 4.7 3.4 - - + -
287A LEU* 3.9 9.1 - - + +
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Residues in contact with ILE 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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139A LEU* 4.7 4.0 - - + -
143A ILE* 5.5 0.6 - - + +
158A PHE* 5.4 1.1 - - + -
161A ILE* 4.0 26.2 - - + -
178A LEU* 4.2 11.2 - - + +
179A LYS* 4.1 14.8 - - - +
180A PRO* 4.2 15.0 - - + -
183A LEU* 3.7 23.1 - - + -
217A TYR* 4.0 17.5 - - + -
237A SER 3.0 20.1 + - - +
238A CYS* 3.7 20.0 - - - +
239A GLY 3.3 0.2 - - - -
240A VAL* 1.3 71.8 - - - +
242A LEU* 1.3 68.8 + - - +
244A VAL* 3.3 3.0 + - - +
245A MET* 3.1 34.0 + - + +
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Residues in contact with LEU 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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154A ALA* 4.4 7.0 - - + -
158A PHE* 3.6 30.3 - - + -
238A CYS 3.0 15.5 + - - +
239A GLY* 3.5 9.6 - - - +
241A ILE* 1.3 78.5 - - - +
243A TYR* 1.3 59.0 + - - +
244A VAL 3.0 0.7 + - - -
245A MET* 3.1 16.6 + - + +
246A LEU* 2.9 48.2 + - + +
279A ALA* 5.1 1.1 - - - +
282A LEU* 4.2 8.1 - - + -
283A ILE* 3.8 16.6 - - + +
286A MET* 3.4 27.4 - - + -
305A TRP* 4.1 18.4 - - + -
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Residues in contact with TYR 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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239A GLY 3.0 13.9 + - - +
240A VAL 3.5 4.9 - - - +
242A LEU* 1.3 80.1 - - - +
244A VAL* 1.3 57.1 + - - +
246A LEU* 4.4 1.6 - - - -
247A CYS* 2.7 45.2 + - + +
249A ARG* 3.0 27.2 - - + +
250A LEU 3.8 2.9 + - - -
251A PRO* 3.5 45.5 + - + +
269A TYR* 4.1 7.6 - + - -
270A THR* 2.8 34.6 + - - +
271A LEU* 4.5 3.6 - - + -
272A PRO* 3.8 16.1 - - + +
283A ILE* 3.8 34.1 - - + +
287A LEU* 5.0 0.2 - - + -
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Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE* 4.5 26.6 - - + +
180A PRO* 5.8 0.7 - - + -
217A TYR* 3.9 11.4 - - + +
240A VAL 2.9 20.3 + - - +
241A ILE* 3.8 5.4 - - - +
242A LEU 3.0 0.2 - - - -
243A TYR* 1.3 76.7 - - - +
245A MET* 1.3 61.6 + - - +
248A ARG* 2.6 36.0 + - - +
249A ARG 3.7 21.8 - - - +
250A LEU* 3.2 38.6 - - + -
251A PRO* 4.0 2.5 - - + -
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Residues in contact with MET 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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139A LEU* 4.1 15.7 - - - -
143A ILE* 4.0 24.9 - - + -
148A LYS* 4.4 1.0 - - - +
149A MET* 3.4 37.4 + - - +
154A ALA* 3.7 35.4 - - + +
157A PHE* 3.9 28.9 - - + -
158A PHE* 4.3 13.5 - - + +
161A ILE* 4.7 0.7 - - + -
241A ILE* 3.1 27.3 + - + +
242A LEU* 3.6 17.5 - - + +
244A VAL* 1.3 78.7 - - - +
246A LEU* 1.3 63.3 + - - +
248A ARG* 4.2 4.2 + - - +
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Residues in contact with LEU 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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148A LYS* 3.4 20.8 - - - +
149A MET 4.3 9.5 - - - +
151A GLU* 4.0 23.6 - - + +
154A ALA* 3.6 23.8 - - + -
242A LEU* 2.9 38.1 + - + +
243A TYR* 4.0 4.7 - - - +
245A MET* 1.3 80.0 - - - +
247A CYS* 1.3 64.1 + - - +
274A PHE* 3.8 9.5 - - - -
275A LEU* 4.5 10.8 - - + -
279A ALA* 3.7 31.2 - - + -
283A ILE* 4.3 7.2 - - + -
305A TRP* 4.6 4.3 - - + -
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Residues in contact with CYS 247 (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 LYS* 4.2 7.7 - - - +
243A TYR* 2.7 47.1 + - + +
246A LEU* 1.3 76.2 - - - +
248A ARG* 1.3 72.1 + - - +
249A ARG* 3.1 12.0 + - + +
272A PRO* 3.6 36.1 - - + -
274A PHE* 4.0 11.3 - - + -
275A LEU* 3.8 19.3 - - - -
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Residues in contact with ARG 248 (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 ILE* 3.7 21.9 + - + +
144A VAL* 3.7 19.3 + - - +
146A ARG 2.9 9.9 + - - -
147A ASP* 2.8 52.7 - - - +
148A LYS* 3.5 20.2 - - + +
149A MET* 5.1 1.1 - - + +
244A VAL* 2.6 29.1 + - - +
245A MET* 4.6 3.6 - - - +
246A LEU 3.6 0.4 - - - -
247A CYS* 1.3 73.7 - - - +
249A ARG* 1.3 66.1 + - - +
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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