Contacts of the helix formed by residues 230 - 248 (chain A) in PDB entry 4I93
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 THR 230 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LEU* 3.5 6.1 - - - -
222A GLU* 4.5 8.1 + - + +
226A THR* 6.0 1.1 - - - +
228A ARG* 3.9 10.7 + - + +
229A VAL* 1.3 78.6 - - - +
231A PRO* 1.3 77.1 - - + +
232A GLU* 3.3 15.9 + - - +
233A SER* 3.0 35.9 + - - -
234A VAL* 3.3 9.7 + - - +
297A PRO* 5.6 0.7 - - - +
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Residues in contact with PRO 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A THR* 5.9 2.2 - - + +
177A ALA* 4.0 36.1 - - + +
178A LEU* 3.8 7.6 - - + -
230A THR* 1.3 87.4 - - + +
232A GLU* 1.3 71.3 + - + +
234A VAL* 3.2 14.3 + - + +
235A ILE* 3.4 16.2 + - - +
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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
----------------------------------------------------------
230A THR* 3.3 21.1 + - - +
231A PRO* 1.3 85.5 - - + +
233A SER* 1.3 61.9 + - - +
235A ILE* 3.3 8.9 + - + +
236A TYR 3.2 13.3 + - - -
297A PRO* 3.6 45.8 - - + +
298A ARG* 5.1 3.2 - - - -
300A ARG* 3.0 20.9 + - + +
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Residues in contact with SER 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A PRO* 3.4 22.7 - - - +
222A GLU* 3.6 13.0 - - - -
223A TYR* 5.7 2.9 - - - -
228A ARG 5.1 3.1 - - - -
229A VAL* 3.4 16.8 - - - +
230A THR* 3.0 33.8 + - - -
232A GLU* 1.3 74.7 - - - +
234A VAL* 1.3 65.6 + - - +
236A TYR* 3.2 4.7 + - - +
237A SER* 3.0 24.2 + - - -
300A ARG* 3.7 8.0 - - - +
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Residues in contact with VAL 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 4.0 34.1 - - + -
177A ALA 3.6 15.9 - - - +
179A TYR* 3.4 43.3 - - + +
182A LEU* 4.3 5.9 - - + +
229A VAL* 3.9 5.2 - - + -
230A THR 3.6 13.2 - - - +
231A PRO 3.2 8.2 + - - +
233A SER* 1.3 78.1 + - - +
235A ILE* 1.3 59.4 + - + +
237A SER* 3.1 8.9 + - - -
238A PHE* 2.9 25.8 + - - +
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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
----------------------------------------------------------
168A LEU* 5.4 5.6 - - + -
231A PRO 3.5 13.5 - - - +
232A GLU* 3.3 11.4 + - - +
233A SER 3.2 0.4 - - - -
234A VAL* 1.3 76.1 - - + +
236A TYR* 1.3 65.2 + - - +
238A PHE* 3.1 7.4 + - + +
239A GLY 3.0 16.8 + - - -
292A CYS* 3.4 24.7 - - + +
300A ARG* 3.9 9.2 - - + -
301A PRO* 3.3 37.2 - - + +
302A ASN* 4.9 0.2 - - - -
303A PRO* 4.1 24.7 - - + -
306A LEU* 3.6 25.8 - - + -
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Residues in contact with TYR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ALA 5.2 1.0 + - - -
218A PHE 3.7 19.2 - - - -
219A THR 3.7 5.7 + - - -
220A PRO* 3.6 28.7 - - + -
221A PRO* 3.6 21.1 - - + +
232A GLU 3.2 5.3 + - - -
233A SER 3.2 10.6 + - - +
235A ILE* 1.3 76.2 - - - +
237A SER* 1.3 61.8 + - - +
239A GLY* 2.9 13.0 + - - -
240A THR* 3.1 15.1 + - + -
253A PRO* 3.3 24.1 - - + +
292A CYS 3.3 14.6 + - - +
293A LEU* 3.6 49.1 - - + +
300A ARG* 3.8 27.8 - - - +
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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
----------------------------------------------------------
179A TYR 5.6 2.1 + - - -
181A ASP* 5.8 0.7 + - - -
182A LEU* 3.9 35.9 + - - +
218A PHE 5.1 2.9 + - - -
220A PRO* 4.6 10.7 - - - +
233A SER 3.0 14.1 + - - -
234A VAL* 3.1 10.5 + - - -
236A TYR* 1.3 76.7 - - - +
238A PHE* 1.3 62.7 + - - +
240A THR* 2.6 28.6 + - - -
241A LEU* 3.1 7.8 + - - +
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Residues in contact with PHE 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ALA* 3.5 30.1 - - + -
164A ILE* 4.2 13.0 - - + -
165A ALA* 3.8 21.8 - - + -
168A LEU* 4.0 20.6 - - + -
182A LEU* 3.9 10.0 - - + +
234A VAL 2.9 12.8 + - - +
235A ILE* 3.1 12.8 + - - +
237A SER* 1.3 76.8 - - - +
239A GLY* 1.3 56.1 + - - +
241A LEU* 3.1 15.8 + - + +
242A LEU* 2.9 62.6 + - + +
245A LEU* 6.5 0.2 - - + -
288A LEU* 5.0 3.4 - - + -
292A CYS* 4.2 1.6 - - - -
306A LEU* 3.8 31.0 - - + -
310A MSE 5.1 2.7 - - - -
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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
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235A ILE 3.0 7.3 + - - -
236A TYR 2.9 10.2 + - - -
238A PHE* 1.3 75.6 - - - +
240A THR* 1.3 56.0 + - - +
242A LEU* 3.3 9.2 + - - +
243A LEU* 3.0 30.3 + - - +
289A ALA* 4.3 2.3 - - - +
292A CYS* 3.6 23.6 - - - +
293A LEU* 4.0 12.4 - - - +
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Residues in contact with THR 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LEU 4.3 8.3 + - - -
183A ASN* 5.5 2.4 - - - +
218A PHE* 3.8 37.5 + - + +
236A TYR* 3.1 16.5 + - + +
237A SER* 2.6 22.4 + - - -
239A GLY* 1.3 75.6 - - - +
241A LEU* 1.3 56.6 + - - +
243A LEU* 3.3 11.3 + - - +
244A ASP* 3.0 33.6 + - - +
250A HIS* 5.3 5.1 - - - -
251A ILE 5.9 0.7 - - - -
253A PRO* 3.9 25.4 - - + -
293A LEU* 4.1 1.3 - - + -
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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
----------------------------------------------------------
140A LEU* 3.8 20.9 - - + -
160A VAL* 5.3 1.6 - - + -
161A ALA* 5.8 0.7 - - - -
164A ILE* 4.2 28.5 - - + -
182A LEU* 4.7 10.3 - - + -
183A ASN* 3.9 9.4 - - - +
184A ALA* 3.8 26.2 - - - +
187A VAL* 4.2 11.2 - - + -
237A SER 3.1 10.4 + - - +
238A PHE* 3.1 21.9 + - + +
240A THR* 1.3 75.3 + - - +
242A LEU* 1.3 60.0 + - + +
244A ASP* 3.2 12.6 + - + +
245A LEU* 2.9 44.1 + - + +
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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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161A ALA* 3.8 25.1 - - + -
238A PHE* 2.9 47.5 + - + +
239A GLY* 3.5 7.0 - - - +
241A LEU* 1.3 75.0 - - + +
243A LEU* 1.3 58.1 + - - +
245A LEU* 3.2 9.1 + - + +
246A LEU* 2.9 38.1 + - + +
285A LEU* 4.1 20.9 - - + -
288A LEU* 4.1 17.5 - - + -
289A ALA* 3.9 34.5 - - + +
292A CYS* 4.4 3.1 - - - -
310A MSE 4.4 1.6 - - - -
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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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239A GLY 3.0 17.3 + - - +
240A THR* 3.5 11.9 - - - +
241A LEU 3.2 0.2 - - - -
242A LEU* 1.3 76.4 - - - +
244A ASP* 1.3 56.9 + - - +
246A LEU* 3.9 11.1 - - + +
247A SER* 2.8 36.8 + - - -
249A LYS 4.6 0.2 - - - -
251A ILE* 4.2 21.1 - - + +
253A PRO* 4.2 9.2 - - + -
256A ALA* 3.8 23.6 - - + -
260A ILE* 3.7 26.7 - - + -
268A LEU* 4.7 9.9 - - + +
286A ILE* 6.4 0.2 - - - -
289A ALA* 4.0 15.3 - - + -
293A LEU* 3.5 20.6 - - + -
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Residues in contact with ASP 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 3.5 11.1 - - + +
145A PHE* 3.8 19.2 - - + -
183A ASN* 5.2 1.0 - - - -
184A ALA* 4.4 13.4 + - + +
218A PHE* 5.3 0.5 - - - -
240A THR 3.0 18.5 + - - +
241A LEU* 3.3 18.3 - - + +
243A LEU* 1.3 76.8 - - - +
245A LEU* 1.3 57.9 + - + +
248A GLY* 2.8 31.5 + - - -
249A LYS 3.2 18.6 + - - +
250A HIS* 2.9 36.6 + - - -
251A ILE 4.3 2.8 + - - +
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Residues in contact with LEU 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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140A LEU* 3.9 35.4 - - + -
144A LEU* 4.1 6.7 - - + -
152A MSE 4.5 0.4 - - - -
154A TRP* 6.3 0.2 - - - -
157A ARG* 2.8 82.7 + - + +
160A VAL* 4.3 8.7 - - + -
161A ALA* 4.0 22.9 - - + +
241A LEU* 2.9 32.7 + - + +
242A LEU* 3.6 9.2 - - + +
244A ASP* 1.3 77.6 - - - +
246A LEU* 1.3 55.8 + - + +
273A LEU* 4.4 0.2 - - - +
285A LEU* 5.6 6.1 - - + -
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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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154A TRP* 4.3 6.1 - - + -
242A LEU 2.9 28.8 + - - +
243A LEU* 3.9 12.8 - - + +
245A LEU* 1.3 73.3 - - - +
247A SER* 1.3 58.8 + - - +
268A LEU* 4.2 8.1 - - + -
269A MSE 3.4 43.3 - - + +
270A ASP* 2.9 24.4 + - - +
273A LEU* 3.7 2.3 - - - +
282A GLY 4.3 2.2 - - - +
285A LEU* 3.5 41.1 - - + +
286A ILE* 4.0 31.2 - - + +
289A ALA* 4.5 7.4 - - + -
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Residues in contact with SER 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU 2.8 21.7 + - - -
246A LEU* 1.3 78.1 - - - +
248A GLY* 1.3 58.8 + - - +
249A LYS* 2.9 43.6 + - - +
251A ILE* 3.7 22.4 - - - +
268A LEU* 3.1 25.1 - - - -
270A ASP* 3.4 20.1 - - - +
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Residues in contact with GLY 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 4.2 16.8 - - - +
145A PHE* 3.5 20.4 - - - -
157A ARG* 3.9 5.8 - - - +
244A ASP 2.8 12.9 + - - -
246A LEU 3.7 1.4 - - - -
247A SER* 1.3 75.5 - - - +
249A LYS* 1.3 61.2 + - - +
270A ASP* 3.5 17.5 + - - -
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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