Contacts of the helix formed by residues 240 - 251 (chain A) in PDB entry 7CE1
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 PRO 240 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A GLU 3.4 6.0 - - - +
239A THR* 1.3 91.2 - - + +
241A LEU* 1.3 60.5 + - + +
242A ASP* 3.4 19.7 - - - +
243A LYS* 3.2 12.7 + - + +
244A ILE* 2.9 25.1 + - - +
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Residues in contact with LEU 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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90A LEU* 3.9 34.8 - - + -
237A ILE 5.5 1.3 - - - +
239A THR 5.1 4.5 - - - +
240A PRO* 1.3 71.9 - - + +
242A ASP* 1.3 66.1 + - - +
244A ILE* 4.2 2.9 - - + -
245A ARG* 3.0 20.3 + - - +
267A SER* 3.1 34.3 - - - +
268A SER* 4.0 7.9 - - - -
271A ALA* 3.3 23.8 - - + +
300B TRP* 3.6 26.5 + - + -
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Residues in contact with ASP 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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240A PRO* 4.0 12.4 - - - +
241A LEU* 1.3 77.1 - - - +
243A LYS* 1.3 90.7 + - - +
245A ARG* 3.1 21.6 - - - +
246A ASP* 3.3 14.8 + - - +
300B TRP* 4.0 15.2 - - + -
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Residues in contact with LYS 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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235A ILE* 5.6 2.3 - - + +
239A THR* 5.5 2.7 - - - -
240A PRO* 3.2 23.5 + - + +
242A ASP* 1.3 91.2 + - - +
244A ILE* 1.3 64.8 + - - +
246A ASP* 3.5 8.4 + - - +
247A PHE* 3.2 23.0 + - - +
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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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202A ILE* 6.0 0.7 - - + -
235A ILE* 3.5 35.0 - - + -
236A THR 4.0 4.9 - - - +
237A ILE 5.1 0.2 - - - +
239A THR* 3.0 32.3 - - - +
240A PRO 2.9 19.6 + - - +
241A LEU* 3.6 10.3 - - + +
242A ASP 3.3 0.2 - - - -
243A LYS* 1.3 76.5 - - - +
245A ARG* 1.3 53.6 + - - +
247A PHE* 3.7 3.7 - - + +
248A GLY* 2.8 32.7 + - - -
268A SER* 3.9 20.2 - - - +
271A ALA* 3.8 18.4 - - + +
272A LEU* 3.8 19.5 - - + +
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Residues in contact with ARG 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 LEU 3.0 13.2 + - - +
242A ASP* 3.1 14.8 - - - +
244A ILE* 1.3 78.0 - - - +
246A ASP* 1.3 65.0 + - - +
248A GLY 3.4 0.2 + - - -
249A LYS* 3.1 18.7 + - - +
271A ALA 3.6 16.2 - - - +
274A ALA* 5.0 4.5 - - + -
275A GLY* 3.4 17.5 - - - +
300B TRP* 4.5 9.0 - - - +
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Residues in contact with ASP 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 ASP* 3.3 15.4 + - - +
243A LYS* 4.0 8.5 - - - +
245A ARG* 1.3 75.3 - - - +
247A PHE* 1.3 67.0 + - - +
249A LYS* 3.2 15.2 + - - +
250A ARG* 3.5 32.9 + - - +
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Residues in contact with PHE 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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230A PHE* 6.5 0.2 - + - -
232A LEU* 3.3 48.9 - - + -
234A ALA* 4.2 11.7 - - + -
235A ILE* 3.9 29.2 - - + -
243A LYS 3.2 15.6 + - - +
244A ILE* 3.7 6.3 - - + +
246A ASP* 1.3 77.7 - - - +
248A GLY* 1.3 70.7 + - - +
249A LYS 3.3 0.3 + - - -
250A ARG* 3.5 18.1 + - + +
251A LEU* 3.3 51.9 + - + -
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Residues in contact with GLY 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 ILE* 2.8 17.7 + - - -
245A ARG 3.8 1.6 - - - -
247A PHE* 1.3 83.9 - - - +
249A LYS* 1.3 57.2 + - - +
251A LEU* 2.8 21.9 + - - +
272A LEU* 4.5 9.4 - - - -
275A GLY 4.3 0.9 - - - -
276A PHE* 3.0 34.4 - - - -
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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 ARG 3.1 13.1 + - - +
246A ASP* 3.5 11.9 - - - +
247A PHE 3.1 0.8 - - - -
248A GLY* 1.3 75.9 - - - +
250A ARG* 1.3 50.2 + - - +
251A LEU 2.6 10.0 - - - +
253A GLN* 2.5 38.6 + - - +
275A GLY* 3.4 24.4 - - - +
278A ALA* 4.8 7.2 - - + -
279A ALA* 3.5 3.3 - - - +
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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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246A ASP* 3.5 27.9 + - - +
247A PHE* 3.7 20.1 - - + +
249A LYS* 1.3 72.5 - - - +
251A LEU* 1.3 69.8 + - + +
253A GLN* 2.9 35.4 + - + +
254A SER* 3.1 12.6 + - - -
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Residues in contact with LEU 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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230A PHE* 3.8 26.7 - - + -
232A LEU* 6.0 0.4 - - + -
247A PHE* 3.3 54.3 + - + +
248A GLY* 2.8 14.3 - - - +
249A LYS 2.6 16.8 - - - +
250A ARG* 1.3 77.3 - - + +
252A MET* 1.3 71.6 + - + +
254A SER* 4.2 7.2 - - - +
256A ASP 3.6 23.1 - - - +
258A PRO* 3.9 14.1 - - + -
276A PHE* 5.1 3.4 - - + -
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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