Contacts of the helix formed by residues 238 - 252 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLN* 3.8 4.5 - - - +
151A GLN* 3.5 27.1 - - + +
212A PHE 4.5 4.0 - - - +
214A ALA 3.4 25.4 - - - +
215A ILE* 4.6 0.9 - - - -
235A SER* 3.0 14.6 + - - +
237A THR* 1.3 79.3 + - - +
239A MET* 1.3 62.7 + - - +
240A LEU 3.3 2.9 - - - -
241A ALA* 3.3 6.2 + - - -
242A SER* 3.0 25.7 + - - +
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Residues in contact with MET 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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64A ILE* 4.0 15.0 - - + -
81A GLN* 3.3 9.8 + - + +
92A ALA* 4.9 0.2 - - + -
94A PHE* 3.8 37.9 - - + -
234A PRO* 4.0 14.1 - - + +
235A SER 3.2 22.1 + - - +
236A ASP* 3.3 17.9 + - - +
238A ALA* 1.3 78.2 - - - +
240A LEU* 1.3 63.3 + - - +
242A SER* 3.3 2.3 + - - -
243A TYR* 2.9 24.9 + - - +
261A PHE* 3.7 22.2 - - - -
263A PRO* 3.6 38.6 - - + -
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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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57A LEU* 4.3 18.2 - - + -
62A GLU* 3.4 34.8 - - + +
64A ILE* 3.9 7.4 - - + +
81A GLN* 2.7 24.6 + - - +
91A VAL* 3.9 36.6 - - + +
92A ALA* 4.5 3.8 - - + -
146A LYS* 3.7 44.0 - - + +
149A VAL* 5.3 0.9 - - + -
150A GLY* 5.0 3.1 - - - +
238A ALA 3.3 0.4 - - - -
239A MET* 1.3 72.9 - - - +
241A ALA* 1.3 61.7 + - - +
243A TYR* 3.6 3.1 + - - +
244A ALA* 3.2 21.0 + - - +
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Residues in contact with ALA 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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143A ILE* 3.6 10.7 - - + +
146A LYS* 4.1 14.3 + - + +
147A THR* 3.5 23.1 - - + +
151A GLN* 3.3 25.5 + - - +
215A ILE* 4.4 7.6 - - + -
238A ALA 3.3 3.0 + - - +
240A LEU* 1.3 77.0 - - - +
242A SER* 1.3 65.9 + - - +
244A ALA* 3.2 4.5 + - - +
245A VAL* 3.1 26.5 + - - +
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Residues in contact with SER 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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214A ALA 4.4 0.5 + - - -
215A ILE* 2.5 36.7 + - - -
232A TRP* 3.5 16.6 - - - -
234A PRO* 3.9 26.9 - - - +
235A SER 4.9 0.3 + - - -
238A ALA* 3.0 22.6 + - - +
239A MET* 3.7 4.5 - - - -
241A ALA* 1.3 78.0 - - - +
243A TYR* 1.3 61.9 + - - +
245A VAL* 3.3 2.4 + - - +
246A TYR* 3.0 18.0 + - - +
261A PHE* 4.0 4.7 - - - -
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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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62A GLU* 3.4 28.0 - - - -
63A ALA 5.2 0.7 - - - -
64A ILE* 3.4 28.7 - - + -
65A PRO* 3.7 24.9 - - + +
67A VAL* 3.9 25.9 - - + +
72A GLU* 4.2 9.2 + - - -
239A MET 2.9 16.7 + - - +
240A LEU 4.1 0.7 - - - +
242A SER* 1.3 77.4 - - - +
244A ALA* 1.3 59.4 + - - +
246A TYR* 3.1 13.1 + + - +
247A ARG* 2.9 58.7 + - + +
261A PHE* 3.5 31.3 - + + -
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Residues in contact with ALA 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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62A GLU* 6.1 0.2 - - - -
139A ARG* 5.0 0.5 + - - -
142A GLU* 3.4 26.9 - - - +
143A ILE* 4.3 9.6 - - + -
146A LYS* 3.8 16.4 - - + +
240A LEU 3.2 14.2 + - - +
241A ALA* 3.2 11.4 + - - +
242A SER 3.2 1.0 - - - -
243A TYR* 1.3 79.0 - - - +
245A VAL* 1.3 56.5 + - - +
247A ARG* 3.5 5.9 + - - +
248A ILE* 3.1 35.5 + - + +
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Residues in contact with VAL 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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135A LEU* 4.6 7.6 - - + -
143A ILE* 3.8 18.2 - - + -
166A LEU* 3.9 27.6 - - + -
170A PHE* 4.4 8.7 - - + -
215A ILE* 3.8 17.0 - - + -
217A GLY* 4.2 12.1 - - - -
232A TRP* 4.8 3.8 - - + -
241A ALA 3.1 14.1 + - - +
242A SER* 3.6 7.9 - - - +
243A TYR 3.2 0.2 - - - -
244A ALA* 1.3 73.9 - - - +
246A TYR* 1.3 58.8 + - - +
248A ILE* 3.3 9.0 + - + +
249A LEU* 2.9 43.5 + - + +
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Residues in contact with TYR 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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67A VAL* 3.5 33.5 + - + +
69A GLY 4.0 1.7 + - - -
232A TRP* 4.1 9.4 - + + -
242A SER 3.0 13.8 + - - +
243A TYR* 3.1 24.4 + + - +
245A VAL* 1.3 77.2 - - - +
247A ARG* 1.3 70.5 + - + +
249A LEU* 3.1 13.7 + - + +
250A ARG* 3.0 63.3 + - + +
254A LEU* 5.3 0.7 - - + -
257A ASN 5.6 0.2 + - - -
259A ILE* 2.8 50.8 + - + -
260A GLN* 5.0 0.2 + - - -
261A PHE* 3.7 31.9 + + + -
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Residues in contact with ARG 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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70A ASP* 5.7 1.0 + - - -
72A GLU* 5.6 5.5 + - - -
139A ARG* 4.8 4.0 - - - +
243A TYR* 2.9 50.6 + - + +
244A ALA* 3.8 7.2 - - - +
246A TYR* 1.3 80.6 - - - +
248A ILE* 1.3 58.8 + - - +
250A ARG* 3.3 33.7 + - - +
251A GLU* 2.8 62.4 + - - +
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Residues in contact with ILE 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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131A ALA* 3.9 28.0 - - + +
134A MET* 4.0 16.9 - - + +
135A LEU* 3.5 25.4 - - + -
139A ARG* 3.5 53.6 - - + +
142A GLU* 4.8 5.4 - - - +
143A ILE* 5.7 1.6 - - + -
244A ALA* 3.1 22.3 + - + +
245A VAL* 3.6 5.6 - - - +
246A TYR 3.2 0.2 - - - -
247A ARG* 1.3 76.8 - - - +
249A LEU* 1.3 56.0 + - + +
251A GLU* 3.2 7.6 + - - +
252A ALA* 2.8 28.8 + - - +
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Residues in contact with LEU 249 (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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127A ILE* 4.0 5.7 - - + +
128A PHE* 3.9 28.3 - - + -
131A ALA* 3.7 23.1 - - + -
170A PHE* 3.9 13.9 - - + -
217A GLY 5.3 4.5 - - - +
220A ALA* 6.0 0.7 - - + -
221A GLY* 5.5 0.4 - - - -
232A TRP* 5.3 6.3 - - + -
245A VAL* 2.9 34.1 + - + +
246A TYR* 3.4 12.6 - - + +
248A ILE* 1.3 76.7 - - + +
250A ARG* 1.3 61.6 + - - +
252A ALA* 3.2 12.4 + - - +
253A GLY 3.3 0.9 + - - -
254A LEU* 3.1 33.9 + - + +
259A ILE* 4.1 24.5 - - + -
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Residues in contact with ARG 250 (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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67A VAL* 4.4 3.8 - - - +
69A GLY 2.9 24.9 + - - -
70A ASP* 2.7 25.2 + - - -
246A TYR* 3.0 57.9 + - + +
247A ARG* 3.8 26.9 - - - +
249A LEU* 1.3 74.6 - - - +
251A GLU* 1.3 58.6 + - - +
253A GLY* 2.8 21.8 + - - -
254A LEU* 2.8 39.3 + - - +
255A PRO 3.8 1.9 + - - -
256A PRO* 3.3 29.8 - - - +
257A ASN 5.0 0.4 - - - +
259A ILE 5.1 0.4 - - - -
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Residues in contact with GLU 251 (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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134A MET* 3.6 14.3 - - + +
139A ARG* 2.7 46.9 + - - -
247A ARG* 2.8 47.2 + - - +
248A ILE 3.6 4.7 - - - +
250A ARG* 1.3 71.6 - - - +
252A ALA* 1.3 58.3 + - - +
253A GLY* 3.1 1.8 + - - -
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Residues in contact with ALA 252 (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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127A ILE* 3.5 37.1 - - + +
130A LYS* 4.0 11.9 - - + +
131A ALA* 3.8 20.9 - - + +
134A MET* 4.1 8.5 - - - -
248A ILE 2.8 15.8 + - - +
249A LEU 3.4 7.0 - - - +
250A ARG 3.1 0.4 - - - -
251A GLU* 1.3 75.9 - - - +
253A GLY* 1.3 56.8 + - - +
254A 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
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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