Contacts of the helix formed by residues 236 - 250 (chain A) in PDB entry 3EBV
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 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A TYR* 3.7 11.0 - - - -
235A VAL* 1.3 78.6 - - - +
237A PRO* 1.3 75.1 - - - +
238A SER* 2.8 26.6 + - - -
239A VAL* 2.9 26.1 + - - +
240A VAL 3.3 7.6 + - - -
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Residues in contact with PRO 237 (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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234A TYR* 3.7 13.9 - - + +
235A VAL 3.5 1.5 - - - +
236A SER* 1.3 84.3 - - - +
238A SER* 1.3 62.9 + - - +
240A VAL* 3.1 7.5 + - + +
241A ASN* 2.9 28.8 + - - -
282A ALA* 4.2 9.0 - - + +
283A TRP* 4.0 28.7 - - + +
286A SER* 3.4 26.5 - - - +
287A VAL* 3.8 17.0 - - + -
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Residues in contact with SER 238 (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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236A SER* 2.8 24.1 + - - -
237A PRO* 1.3 79.0 - - - +
239A VAL* 1.3 58.1 + - - +
241A ASN* 3.5 10.5 + - - +
242A ALA* 2.9 28.8 + - - +
286A SER* 4.7 0.8 + - - -
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Residues in contact with VAL 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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197A GLY 5.8 1.6 - - - +
198A THR* 4.2 1.1 - - - -
199A VAL* 3.8 34.4 - - + +
202A LEU* 4.4 3.4 - - + -
235A VAL* 3.7 29.2 - - + -
236A SER* 2.9 25.5 + - - +
238A SER* 1.3 78.1 + - - +
240A VAL* 1.3 66.2 + - - +
242A ALA* 3.3 6.4 + - - +
243A ALA* 3.0 22.3 + - - +
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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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202A LEU* 4.3 7.2 - - - -
221A LEU* 4.8 4.9 - - + -
223A LEU* 3.8 24.7 - - + -
235A VAL* 3.6 22.4 - - + -
236A SER 3.3 5.4 + - - +
237A PRO* 3.1 6.9 + - + +
239A VAL* 1.3 77.0 - - - +
241A ASN* 1.3 59.3 + - - +
243A ALA* 3.2 4.0 + - - +
244A LEU* 2.9 37.5 + - + +
268A ALA* 4.3 11.4 - - + -
283A TRP* 4.0 18.4 - - + +
287A VAL* 4.0 26.9 - - + -
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Residues in contact with ASN 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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237A PRO 2.9 18.1 + - - +
238A SER* 3.8 8.2 - - - +
240A VAL* 1.3 76.4 - - - +
242A ALA* 1.3 58.1 + - - +
244A LEU* 3.3 8.3 + - - +
245A ASP* 2.9 34.8 + - - +
286A SER* 3.0 34.1 + - - -
287A VAL* 3.6 15.6 - - - +
290A HIS* 3.2 44.0 + - + +
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Residues in contact with ALA 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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199A VAL* 4.2 7.6 - - + -
238A SER 2.9 18.6 + - - +
239A VAL* 3.6 7.4 - - - +
241A ASN* 1.3 77.0 - - - +
243A ALA* 1.3 56.8 + - - +
245A ASP* 3.2 4.2 + - - +
246A CYS* 2.8 30.7 + - - +
252A ASN* 3.7 34.9 - - + +
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Residues in contact with ALA 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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199A VAL* 3.8 11.3 - - + +
202A LEU* 3.7 35.4 - - + -
203A THR* 3.8 12.3 - - + -
221A LEU* 3.9 7.0 - - + -
239A VAL 3.0 14.2 + - - +
240A VAL 3.5 7.9 - - - +
242A ALA* 1.3 76.7 - - - +
244A LEU* 1.3 63.4 + - - +
246A CYS* 3.2 1.0 + - - +
247A LEU* 3.0 31.5 + - - +
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Residues in contact with LEU 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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221A LEU* 3.9 12.6 - - + -
240A VAL* 2.9 28.3 + - + +
241A ASN* 3.5 22.4 - - - +
243A ALA* 1.3 77.1 - - - +
245A ASP* 1.3 53.1 + - - +
247A LEU* 3.5 0.5 + - - +
248A THR* 2.8 42.3 + - - +
265A LEU* 3.7 26.2 - - + -
267A GLY* 3.8 25.8 - - - +
268A ALA* 4.9 0.9 - - + -
287A VAL* 4.6 0.2 - - + -
290A HIS* 4.2 12.1 - - + -
291A VAL* 3.6 26.7 - - + -
294A LEU* 4.6 13.0 - - + -
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Residues in contact with ASP 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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241A ASN* 2.9 18.5 + - - +
242A ALA 3.2 5.6 + - - +
244A LEU* 1.3 73.5 - - - +
246A CYS* 1.3 62.1 + - - +
248A THR* 3.8 5.2 - - - -
249A LYS* 2.9 52.4 + - - +
250A ALA 3.1 6.2 + - - -
251A THR* 3.1 20.7 + - - +
252A ASN* 2.9 24.0 + - - +
290A HIS* 2.6 33.1 + - - -
294A LEU* 4.7 3.3 - - - +
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Residues in contact with CYS 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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199A VAL* 5.4 0.2 - - + -
203A THR* 3.8 19.7 - - + -
242A ALA 2.8 20.5 + - - +
243A ALA* 3.2 5.1 + - - +
245A ASP* 1.3 73.2 - - - +
247A LEU* 1.3 61.8 + - - +
250A ALA* 3.2 19.2 + - - +
251A THR 2.9 12.2 + - - +
252A ASN 4.3 0.2 - - - +
253A CYS* 2.1 53.9 - - - -
256A PHE 4.0 2.2 - - - -
257A LYS* 5.1 0.5 + - - -
258A PRO* 3.4 25.0 - - - +
260A LYS 5.0 2.6 - - - +
261A THR* 5.1 0.2 - - - +
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Residues in contact with LEU 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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203A THR* 4.0 26.5 - - + +
206A ALA* 3.9 20.9 - - + -
207A CYS* 4.9 1.3 - - - +
210A LEU* 3.8 20.4 - - + -
221A LEU* 4.3 13.0 - - + -
243A ALA 3.0 20.1 + - - +
244A LEU 4.0 2.2 - - - +
246A CYS* 1.3 76.8 - - - +
248A THR* 1.3 60.0 + - - +
258A PRO* 3.9 26.0 - - + -
260A LYS 4.2 0.2 - - - +
261A THR* 3.4 7.1 - - - -
262A TYR* 2.8 32.0 + - + -
265A LEU* 3.9 30.1 - - + -
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Residues in contact with THR 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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244A LEU 2.8 29.3 + - - +
245A ASP* 3.7 5.2 + - - -
247A LEU* 1.3 76.9 - - - +
249A LYS* 1.3 69.7 + - - +
250A ALA 3.9 0.2 - - - -
261A THR* 3.6 14.1 - - - -
262A TYR 3.5 20.2 - - - +
263A PRO* 3.8 28.6 - - - +
265A LEU* 3.6 23.8 - - + -
294A LEU* 4.0 27.0 - - + +
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Residues in contact with LYS 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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245A ASP* 2.9 45.9 + - - +
248A THR* 1.3 86.0 - - - +
250A ALA* 1.3 74.3 + - - +
251A THR* 3.3 24.1 + - + +
261A THR* 3.9 7.8 - - - +
290A HIS* 5.2 5.1 + - - -
294A LEU* 5.8 3.8 - - + +
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Residues in contact with ALA 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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245A ASP 3.1 3.0 + - - -
246A CYS* 3.2 15.2 + - - +
249A LYS* 1.3 81.1 - - - +
251A THR* 1.3 63.3 + - - +
253A CYS* 4.5 5.7 - - - -
257A LYS* 3.8 29.1 - - - +
261A THR* 3.8 17.9 - - + +
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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