Contacts of the helix formed by residues 238 - 252 (chain B) in PDB entry 4OE5
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 ALA 238 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLN* 3.7 2.7 - - - +
151B GLN* 3.5 28.7 - - + +
212B PHE 4.5 3.1 - - - +
214B ALA 4.0 20.2 - - - +
215B ILE* 4.4 1.8 - - + -
235B SER* 3.0 13.2 + - - +
237B THR* 1.3 79.7 + - - +
239B MET* 1.3 65.1 + - - +
240B LEU 3.2 3.0 + - - -
241B ALA* 3.4 3.6 + - - -
242B SER* 2.8 36.4 + - - +
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Residues in contact with MET 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 4.0 16.4 - - + -
81B GLN* 3.3 11.4 + - + +
92B ALA* 4.8 0.7 - - + -
94B PHE* 3.7 48.7 - - + -
234B PRO* 4.1 10.5 - - + +
235B SER 3.2 20.9 + - - +
236B ASP* 3.4 15.5 + - - +
238B ALA* 1.3 76.2 - - - +
240B LEU* 1.3 57.8 + - - +
242B SER* 3.6 2.2 - - - -
243B TYR* 2.9 31.7 + - - +
261B PHE* 3.6 30.1 - - - -
263B PRO* 3.7 24.0 - - + -
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Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LEU* 4.4 17.0 - - + -
62B GLU* 3.6 31.5 - - + +
64B ILE* 3.9 9.1 - - + +
81B GLN* 2.7 25.1 + - - +
91B VAL* 3.9 39.3 - - + +
92B ALA* 4.6 1.1 - - + -
146B LYS* 3.9 44.5 + - + +
149B VAL* 5.2 0.9 - - + -
150B GLY* 4.7 4.3 - - - +
238B ALA 3.2 0.2 + - - -
239B MET* 1.3 72.8 - - - +
241B ALA* 1.3 62.5 + - - +
243B TYR* 3.6 3.1 + - - +
244B ALA* 3.1 20.6 + - - +
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Residues in contact with ALA 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ILE* 3.8 6.5 - - + +
146B LYS* 4.1 13.2 + - + +
147B THR* 3.6 22.4 - - + +
151B GLN* 3.4 24.0 + - - +
215B ILE* 3.7 9.9 - - + -
238B ALA 3.4 1.8 + - - -
240B LEU* 1.3 77.0 - - - +
242B SER* 1.3 66.0 + - - +
244B ALA* 3.1 10.0 + - - +
245B VAL* 3.0 25.6 + - - +
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Residues in contact with SER 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ILE* 3.5 29.8 + - - +
232B TRP* 3.8 10.7 - - - -
234B PRO* 3.9 29.1 - - - +
235B SER 4.7 0.5 + - - -
238B ALA* 2.8 33.0 + - - +
239B MET 3.6 4.3 - - - -
241B ALA* 1.3 76.4 - - - +
243B TYR* 1.3 63.1 - - - +
245B VAL* 3.1 6.8 + - - +
246B TYR* 3.0 18.0 + - - +
261B PHE* 4.1 3.8 - - - -
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Residues in contact with TYR 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLU* 3.4 28.0 - - - -
63B ALA 5.3 0.4 - - - -
64B ILE* 3.4 30.5 - - + -
65B PRO* 3.9 24.1 - - + +
67B VAL* 3.9 25.9 - - + +
72B GLU* 4.3 9.5 + - - -
239B MET 2.9 16.7 + - - +
240B LEU 3.9 1.3 - - - +
242B SER* 1.3 76.0 - - - +
244B ALA* 1.3 59.3 + - - +
246B TYR* 3.2 15.3 + + - +
247B ARG* 2.9 40.0 + - + +
261B PHE* 3.6 28.8 - + + -
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Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLU* 6.2 0.2 - - - -
142B GLU* 3.5 25.8 - - - +
143B ILE* 4.2 9.2 - - + -
146B LYS* 3.7 17.3 - - + +
240B LEU 3.1 13.9 + - - +
241B ALA* 3.1 12.2 + - - +
243B TYR* 1.3 77.7 - - - +
245B VAL* 1.3 60.7 + - - +
247B ARG* 3.6 6.3 + - - +
248B ILE* 3.2 32.1 + - + +
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 4.8 5.2 - - + -
143B ILE* 3.9 18.4 - - + -
166B LEU* 3.9 36.8 - - + -
170B PHE* 4.2 18.4 - - + -
215B ILE* 4.1 14.8 - - + -
217B GLY* 5.2 5.2 - - - -
232B TRP* 4.9 7.4 - - + -
241B ALA 3.0 13.4 + - - +
242B SER 3.6 6.3 - - - +
244B ALA* 1.3 74.3 - - - +
246B TYR* 1.3 65.8 + - - +
248B ILE* 3.2 8.6 + - + +
249B LEU* 2.9 30.1 + - + +
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Residues in contact with TYR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B VAL* 3.5 31.8 + - + +
69B GLY 3.9 1.7 + - - -
232B TRP* 4.3 7.6 - + + -
242B SER 3.0 9.3 + - - +
243B TYR* 3.2 24.2 + + - +
245B VAL* 1.3 77.0 - - - +
247B ARG* 1.3 65.5 + - - +
249B LEU* 3.2 11.1 + - + +
250B ARG* 3.0 68.9 + - + +
254B LEU* 5.7 0.2 - - + -
259B ILE* 2.9 53.0 + - + -
261B PHE* 3.8 36.9 + + + -
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Residues in contact with ARG 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ARG* 5.1 4.5 - - - +
243B TYR* 2.9 29.3 + - + +
244B ALA* 3.9 6.5 - - - +
246B TYR* 1.3 81.0 - - - +
248B ILE* 1.3 57.1 + - - +
250B ARG* 3.4 6.9 + - - +
251B GLU* 2.9 44.1 + - + +
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Residues in contact with ILE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ALA* 4.1 31.4 - - + +
134B MET* 4.2 12.0 - - + +
135B LEU* 3.6 31.4 - - + -
139B ARG* 3.6 49.1 - - + +
142B GLU* 4.6 6.1 - - - +
143B ILE* 5.7 0.9 - - + -
244B ALA* 3.2 22.0 + - + +
245B VAL* 3.6 6.1 - - - +
247B ARG* 1.3 74.0 - - - +
249B LEU* 1.3 60.7 + - + +
251B GLU* 3.2 6.8 + - - +
252B ALA* 2.8 28.2 + - - +
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 4.2 5.6 - - + +
128B PHE* 3.8 33.0 - - + -
131B ALA* 3.8 22.4 - - + -
170B PHE* 4.0 15.5 - - + -
217B GLY 6.0 1.6 - - - +
221B GLY* 5.6 2.7 - - - +
232B TRP* 5.7 3.8 - - + -
245B VAL* 2.9 32.9 + - + +
246B TYR* 3.6 11.7 - - + +
248B ILE* 1.3 73.5 - - + +
250B ARG* 1.3 62.5 + - - +
252B ALA* 3.2 14.3 + - - +
253B GLY 3.3 0.7 + - - -
254B LEU* 3.1 34.7 + - + +
259B ILE* 4.3 23.3 - - + -
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Residues in contact with ARG 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 4.6 1.8 - - - +
69B GLY 3.0 24.7 + - - -
70B ASP* 2.6 24.6 + - - +
246B TYR* 3.0 53.0 + - + +
247B ARG* 3.6 8.1 - - - +
249B LEU* 1.3 75.3 - - - +
251B GLU* 1.3 58.0 + - + +
253B GLY* 2.8 22.7 + - - -
254B LEU* 2.9 40.2 + - - +
255B PRO 3.8 2.1 + - - -
256B PRO* 3.2 30.9 - - - +
257B ASN 5.0 0.4 - - - +
259B ILE 5.2 0.7 - - - -
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Residues in contact with GLU 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B MET* 3.7 13.2 - - + +
139B ARG* 2.9 43.6 + - - -
247B ARG* 2.9 31.2 + - + +
248B ILE 3.7 4.3 - - - +
250B ARG* 1.3 73.2 - - + +
252B ALA* 1.3 57.2 + - - +
253B GLY* 3.1 4.6 + - - -
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Residues in contact with ALA 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 3.6 35.7 - - + +
130B LYS* 4.0 12.0 - - + +
131B ALA* 3.8 20.9 - - + +
134B MET* 4.1 8.5 - - - -
248B ILE 2.8 16.9 + - - +
249B LEU 3.4 6.3 - - - +
250B ARG 3.1 0.4 - - - -
251B GLU* 1.3 76.4 - - - +
253B GLY* 1.3 58.6 + - - +
254B LEU 3.7 0.2 - - - -
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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
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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