Contacts of the helix formed by residues 245 - 259 (chain A) in PDB entry 5EWL
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 SER 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A SER* 4.5 2.2 + - - -
170A ASP* 5.4 4.4 + - - -
244A ALA* 1.3 76.6 - - - +
246A GLU* 1.3 55.3 + - - +
247A ASP* 3.9 6.1 + - - +
248A ASP* 3.1 28.7 + - - +
249A ALA* 2.7 31.9 + - - +
273A ARG* 3.4 29.4 - - - +
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Residues in contact with GLU 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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244A ALA 3.9 0.4 + - - -
245A SER* 1.3 71.2 - - - +
247A ASP* 1.3 68.0 + - - +
249A ALA* 3.4 0.6 + - - -
250A THR* 2.9 27.0 + - - -
273A ARG* 3.7 30.1 + - + +
276A SER* 3.4 28.8 - - - +
277A GLY* 3.9 5.3 + - - -
278A SER* 3.4 28.5 + - - +
279A ALA* 3.5 8.9 - - - +
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Residues in contact with ASP 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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223A LYS* 3.9 16.6 + - - +
245A SER* 3.3 6.2 + - - +
246A GLU* 1.3 83.1 - - - +
248A ASP* 1.4 61.7 + - - +
250A THR* 3.6 9.1 - - - -
251A ALA 3.5 14.0 + - - -
278A SER* 3.3 17.5 + - - -
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Residues in contact with ASP 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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168A SER* 4.6 4.2 - - - -
170A ASP* 5.0 1.4 - - - +
218A PHE* 3.9 23.5 - - + -
220A PRO* 3.4 22.2 - - - +
221A GLY* 2.9 29.2 + - - -
222A THR 4.3 1.6 + - - +
223A LYS* 3.6 8.5 + - - -
225A LEU* 4.6 0.3 - - - +
244A ALA* 3.9 10.5 - - + -
245A SER* 3.1 22.3 + - - +
247A ASP* 1.4 75.2 - - - +
249A ALA* 1.3 65.6 + - - +
250A THR 3.3 0.4 - - - -
251A ALA* 3.2 8.3 + - - +
252A VAL* 3.2 25.1 + - - +
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Residues in contact with ALA 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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242A LEU* 4.2 11.9 - - + -
244A ALA* 4.0 3.1 - - - +
245A SER 2.7 19.8 + - - +
246A GLU 3.4 5.8 + - - +
248A ASP* 1.3 72.0 - - - +
250A THR* 1.4 57.0 + - - +
252A VAL* 3.2 4.2 + - - +
253A TYR* 2.9 40.6 + - + -
274A GLU* 3.9 28.7 - - + -
279A ALA* 3.9 15.9 - - + -
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Residues in contact with THR 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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246A GLU 2.9 16.6 + - - -
247A ASP* 3.6 9.2 - - - -
249A ALA* 1.4 75.0 - - - +
251A ALA* 1.3 61.7 + - - +
253A TYR* 3.2 12.2 + - - +
254A LYS* 3.0 48.5 + - - +
278A SER* 3.2 28.2 + - - +
279A ALA* 4.5 0.4 - - - +
282A TYR* 3.4 35.0 - - + -
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Residues in contact with ALA 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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218A PHE* 6.4 0.2 - - + -
222A THR 3.6 24.0 - - - +
223A LYS* 3.6 30.3 - - + +
225A LEU* 3.6 10.5 - - + -
247A ASP 3.5 2.9 + - - +
248A ASP* 3.2 11.8 + - - +
250A THR* 1.3 79.4 - - - +
252A VAL* 1.4 55.8 + - - +
254A LYS* 3.6 8.9 + - - +
255A SER* 2.8 31.9 + - - -
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Residues in contact with VAL 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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166A ILE* 4.9 6.3 - - + -
218A PHE* 4.1 15.7 - - + -
225A LEU* 3.8 18.4 - - + -
228A LEU* 5.3 1.8 - - + -
229A LEU* 3.6 18.3 - - + +
242A LEU* 3.9 30.1 - - + -
248A ASP 3.2 14.7 + - - +
249A ALA* 3.2 6.3 + - - +
251A ALA* 1.4 71.3 - - - +
253A TYR* 1.3 56.6 + - + +
255A SER 3.3 1.9 + - - -
256A ALA* 2.8 32.9 + - - +
268A TRP* 3.9 30.7 - - + -
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Residues in contact with TYR 253 (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 LEU* 4.0 19.3 - - + -
249A ALA* 2.9 27.4 + - + +
250A THR* 3.2 6.9 + - - +
252A VAL* 1.3 77.3 - - - +
254A LYS* 1.4 59.9 + - - +
256A ALA* 3.5 4.7 + - + +
257A ALA* 3.2 23.2 + - - +
262A THR* 4.2 4.2 - - + +
268A TRP* 4.2 15.7 - + - -
270A VAL* 3.5 5.5 - - - +
274A GLU* 2.9 41.9 + - - +
279A ALA 3.3 23.1 - - - -
282A TYR* 3.4 21.2 - - + +
283A ALA* 3.5 12.8 - - + -
284A PRO* 3.6 12.1 - - + +
287A ILE* 3.3 33.6 - - + +
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Residues in contact with LYS 254 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A THR* 3.0 39.1 + - + +
251A ALA* 3.9 7.6 - - - +
253A TYR* 1.4 68.7 - - - +
255A SER* 1.3 61.4 + - - +
257A ALA* 3.2 9.7 + - - +
258A MET* 3.0 32.7 + - + +
282A TYR* 3.7 49.0 + - + -
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Residues in contact with SER 255 (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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223A LYS 4.0 5.7 + - - -
224A ASN* 4.6 1.4 + - - -
225A LEU* 3.7 18.3 + - - +
226A THR* 3.8 22.1 - - - +
229A LEU* 3.5 20.2 - - - -
251A ALA 2.8 21.6 + - - -
254A LYS* 1.3 74.5 - - - +
256A ALA* 1.3 64.9 + - - +
258A MET* 3.2 8.6 + - - +
259A LEU* 3.0 27.7 + - - +
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Residues in contact with ALA 256 (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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229A LEU* 3.4 13.4 - - + +
252A VAL 2.8 20.7 + - - +
253A TYR* 3.8 3.1 - - - +
255A SER* 1.3 73.4 - - - +
257A ALA* 1.3 57.1 + - - +
259A LEU* 3.4 3.5 + - - +
260A ASP 3.2 3.6 + - - -
261A MET* 2.8 38.1 + - + +
262A THR* 3.7 10.5 - - + -
268A TRP* 3.5 36.3 - - + -
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Residues in contact with ALA 257 (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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253A TYR 3.2 14.3 + - - +
254A LYS* 3.4 11.9 - - - +
256A ALA* 1.3 75.3 - - - +
258A MET* 1.4 61.8 + - + +
260A ASP* 3.0 24.9 + - - +
262A THR* 3.6 21.9 + - + +
282A TYR 5.9 1.3 - - - +
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Residues in contact with MET 258 (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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226A THR* 5.7 4.5 - - + -
254A LYS* 3.0 19.1 + - + +
255A SER* 3.2 11.9 + - - +
257A ALA* 1.4 80.2 - - - +
259A LEU* 1.3 58.0 + - + +
260A ASP* 3.3 10.5 - - - +
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Residues in contact with LEU 259 (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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226A THR* 3.9 27.4 - - + +
229A LEU* 3.4 39.7 - - + -
230A LEU* 3.8 30.1 - - + -
233A LYS* 2.8 36.4 + - + +
255A SER 3.0 17.6 + - - +
256A ALA 3.4 1.3 + - - +
257A ALA 3.2 0.2 - - - -
258A MET* 1.3 76.5 - - + +
260A ASP* 1.4 64.5 + - - +
261A MET* 3.2 16.2 + - - +
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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