Contacts of the helix formed by residues 241 - 254 (chain A) in PDB entry 2Q41
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 HIS 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A MSE 3.0 41.4 - - + +
55A TRP* 4.8 5.6 - + - -
236A GLU* 3.1 49.8 + - + -
237A SER* 2.8 29.4 + - - +
240A LEU* 1.3 102.5 + - + +
242A MSE 1.3 57.4 + - - +
243A ASP* 3.2 10.3 - - - -
244A ILE* 3.1 25.2 + - + +
245A ILE* 2.7 39.3 + - + +
271A PRO* 5.5 2.0 - - - +
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Residues in contact with MSE 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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238A LEU* 3.0 53.2 - - + +
239A TRP 5.8 0.7 - - - -
240A LEU 3.9 1.5 - - - -
241A HIS* 1.3 73.7 - - - +
243A ASP* 1.3 56.2 + - - +
245A ILE* 3.4 20.7 - - + +
246A GLU* 2.7 43.8 + - - +
324A PHE* 3.6 24.7 - - + +
325A ALA* 3.6 16.2 - - - -
328A VAL* 5.3 12.4 - - + +
329A ILE* 5.3 3.4 - - + -
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Residues in contact with ASP 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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240A LEU 4.6 2.4 - - - +
241A HIS* 3.6 13.5 - - - -
242A MSE 1.3 75.2 + - - +
244A ILE* 1.3 85.4 + - - +
246A GLU* 3.0 21.0 + - - +
247A ASP* 3.0 22.2 + - - +
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Residues in contact with ILE 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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54A MSE 4.3 22.9 - - + -
205A PRO* 4.9 18.4 - - + -
213A PHE* 5.9 0.9 - - + -
236A GLU* 4.4 15.7 - - + -
241A HIS* 3.1 30.0 + - + +
243A ASP* 1.3 94.0 + - - +
245A ILE* 1.3 65.9 + - - +
247A ASP* 3.1 18.9 + - - +
248A ILE* 3.1 34.2 + - + +
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Residues in contact with ILE 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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235A ALA* 3.2 19.1 - - + +
236A GLU* 4.2 1.1 - - + -
237A SER 3.5 18.8 - - - +
238A LEU 3.8 0.4 - - - +
241A HIS* 2.7 25.2 + - + +
242A MSE 3.4 29.6 - - + +
244A ILE* 1.3 72.3 - - - +
246A GLU* 1.3 57.4 + - - +
248A ILE* 3.0 14.1 + - - +
249A VAL* 2.9 33.1 + - + +
262A TYR* 3.2 50.7 - - + +
278A MSE 5.2 0.2 - - - -
329A ILE* 4.4 12.8 - - + -
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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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242A MSE 2.7 25.4 + - - +
243A ASP* 3.0 9.8 + - - +
245A ILE* 1.3 71.3 - - - +
247A ASP* 1.3 66.0 + - - +
249A VAL* 3.1 10.9 + - + +
250A SER* 3.1 28.7 + - - +
328A VAL* 3.0 37.4 - - + +
329A ILE* 5.9 2.7 - - - -
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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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243A ASP* 3.0 23.2 + - - +
244A ILE* 3.1 10.9 + - - +
246A GLU* 1.3 75.2 - - - +
248A ILE* 1.3 57.2 + - + +
250A SER* 3.2 7.4 + - - -
251A ASN* 2.8 43.2 + - - +
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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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213A PHE* 4.3 29.4 - - + +
218A PHE* 4.0 22.0 - - + -
233A THR* 5.3 2.0 - - - +
235A ALA* 4.0 22.7 - - + -
236A GLU* 5.5 0.4 - - + -
244A ILE* 3.1 30.7 + - + +
245A ILE* 3.1 19.3 - - - +
247A ASP* 1.3 74.8 - - + +
249A VAL* 1.3 58.3 + - - +
251A ASN* 3.7 6.3 - - - +
252A CYS* 2.9 24.6 + - - +
278A MSE 3.3 32.6 - - + +
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Residues in contact with VAL 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 ILE* 2.9 25.2 + - + +
246A GLU* 3.1 10.3 + - + +
248A ILE* 1.3 76.5 - - - +
250A SER* 1.3 54.3 + - - +
252A CYS* 3.4 1.0 + - - +
253A ARG* 2.8 75.9 + - + +
260A VAL* 4.4 9.4 - - + -
262A TYR* 5.1 0.9 - - + -
278A MSE 3.4 23.5 - - + +
329A ILE* 4.3 28.3 - - + +
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Residues in contact with SER 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* 3.1 16.9 + - - +
247A ASP* 3.2 11.7 + - - -
249A VAL* 1.3 77.1 - - - +
251A ASN* 1.3 65.4 + - - +
253A ARG* 3.2 12.3 + - - +
254A GLU* 2.9 36.5 + - - +
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Residues in contact with ASN 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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213A PHE 3.9 3.9 + - - -
214A GLU* 3.5 16.6 + - - +
215A LYS* 2.9 50.7 - - - +
218A PHE* 3.7 16.2 - - + -
247A ASP* 2.8 32.4 + - - +
248A ILE 3.7 4.9 - - - +
250A SER* 1.3 78.2 - - - +
252A CYS* 1.3 64.1 + - - +
254A GLU* 3.1 12.7 + - - +
255A ILE* 3.1 20.3 - - - +
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Residues in contact with CYS 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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218A PHE* 4.0 27.6 - - - -
231A VAL* 5.8 1.1 - - - -
233A THR* 6.3 0.7 - - - -
248A ILE* 2.9 15.6 + - - +
249A VAL 3.9 0.2 - - - +
251A ASN* 1.3 76.6 - - - +
253A ARG* 1.3 58.0 + - - +
255A ILE* 3.2 0.4 + - - -
256A PHE* 2.9 51.6 + - - +
260A VAL* 3.6 4.0 - - + +
278A MSE 3.4 31.2 - - + -
280A CYS* 3.4 28.3 - - - -
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Residues in contact with ARG 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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249A VAL* 2.8 41.1 + - - +
250A SER* 3.5 10.9 + - - +
252A CYS* 1.3 77.9 - - - +
254A GLU* 1.3 58.4 + - + +
255A ILE 3.1 4.4 + - - -
256A PHE 3.8 12.0 - - - +
260A VAL* 3.7 24.2 - - + +
329A ILE 2.8 27.1 + - - -
330A GLU* 2.6 43.6 + - - +
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Residues in contact with GLU 254 (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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215A LYS* 3.0 36.6 + - - +
250A SER* 2.9 26.2 + - - +
251A ASN* 3.1 5.6 + - - +
253A ARG* 1.3 76.0 - - + +
255A ILE* 1.3 70.3 + - - +
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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