Contacts of the helix formed by residues 265 - 280 (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 SER 265 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLU* 2.9 36.2 + - - +
237A ILE* 3.3 35.3 - - - +
263A SER* 2.9 8.3 + - - -
264A ILE* 1.3 81.9 - - - +
266A GLY* 1.3 53.3 + - - +
267A SER* 3.3 6.1 + - - -
268A SER* 3.2 5.4 + - - -
269A THR* 2.7 30.8 + - - -
291A SER* 4.4 0.2 - - - -
292A LYS 4.2 0.7 - - - -
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Residues in contact with GLY 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 3.8 5.8 + - - -
91A MET* 4.8 6.1 - - - -
265A SER* 1.3 68.5 + - - +
267A SER* 1.3 62.4 + - - +
269A THR* 3.2 24.8 - - - -
270A ILE* 3.2 18.2 + - - +
291A SER* 3.7 1.8 - - - -
292A LYS 3.3 23.3 + - - -
293A GLN* 5.3 1.8 - - - -
297A PHE* 4.5 4.6 - - - -
298A LEU* 4.4 9.1 - - - +
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Residues in contact with SER 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 3.0 24.2 + - - +
90A LEU* 3.9 13.9 - - - -
91A MET* 2.5 45.8 + - - +
241A LEU* 3.1 23.3 - - - +
265A SER* 3.2 2.6 + - - -
266A GLY* 1.3 73.4 - - - +
268A SER* 1.3 64.7 + - - +
269A THR 3.1 0.2 - - - -
270A ILE* 3.5 12.1 + - - +
271A ALA 3.7 3.8 + - - -
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Residues in contact with SER 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ILE* 3.8 22.6 - - - +
237A ILE* 3.7 39.5 + - - -
241A LEU* 4.0 10.7 - - - +
244A ILE* 3.9 18.4 - - - +
263A SER* 4.7 0.7 - - - -
265A SER* 3.2 10.0 + - - -
267A SER* 1.3 78.1 - - - +
269A THR* 1.3 63.3 + - - +
271A ALA 3.5 1.4 + - - -
272A LEU* 3.2 22.0 + - - +
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Residues in contact with THR 269 (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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263A SER* 2.7 24.1 + - - -
265A SER 2.7 9.4 + - - -
266A GLY* 3.2 14.3 - - - +
268A SER* 1.3 79.6 - - - +
270A ILE* 1.3 63.1 + - - +
272A LEU* 3.1 34.0 + - + +
273A VAL* 3.4 13.6 + - + +
289A ILE* 4.7 8.7 - - + -
291A SER* 2.8 28.5 + - - +
298A LEU* 4.5 12.3 - - + -
305A ILE* 5.0 5.6 - - + -
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Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET* 3.6 19.1 - - + -
266A GLY 3.2 14.1 + - - +
267A SER* 3.5 6.5 + - - +
268A SER 3.3 0.8 - - - -
269A THR* 1.3 79.1 - - - +
271A ALA* 1.3 62.7 + - - +
273A VAL* 3.6 6.1 + - - +
274A ALA* 3.4 19.4 + - - +
297A PHE* 3.4 31.4 - - + -
298A LEU* 3.7 15.7 - - + -
301A ILE* 4.6 2.9 - - + -
297B PHE* 4.9 0.9 - - + +
300B TRP* 3.4 38.1 - - + +
301B ILE* 4.0 19.5 - - + -
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Residues in contact with ALA 271 (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* 3.3 43.7 - - + +
244A ILE* 3.8 15.7 - - + -
245A ARG* 3.6 10.4 - - - -
267A SER 3.7 2.6 + - - -
268A SER 3.5 1.5 + - - +
269A THR 3.3 0.6 - - - -
270A ILE* 1.3 81.3 - - - +
272A LEU* 1.3 61.8 + - - +
274A ALA* 3.5 12.1 + - - +
275A GLY 3.6 4.5 + - - -
300B TRP* 3.7 20.2 - - + +
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ILE* 3.3 33.7 - - + -
244A ILE* 3.8 15.6 - - + +
248A GLY* 4.5 4.0 - - - -
261A ILE* 4.3 14.8 - - + -
263A SER* 4.4 2.9 - - - -
268A SER 3.2 10.1 + - - +
269A THR* 3.1 35.6 + - + +
271A ALA* 1.3 77.5 - - - +
273A VAL* 1.3 64.9 + - + +
275A GLY* 3.4 3.3 + - - -
276A PHE* 3.3 44.8 + - + -
289A ILE* 3.6 31.0 - - + -
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Residues in contact with VAL 273 (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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269A THR* 3.4 15.3 + - + +
270A ILE* 4.1 7.2 - - - +
271A ALA 3.4 0.4 - - - -
272A LEU* 1.3 75.2 - - + +
274A ALA* 1.3 67.4 + - - +
276A PHE* 3.0 16.5 + - - +
277A GLU* 3.1 26.7 + - - +
283A ILE* 4.1 23.3 - - + -
289A ILE* 3.9 26.5 - - + -
301A ILE* 6.6 0.2 - - + -
302A GLN* 4.9 11.0 - - + -
305A ILE* 4.2 14.6 - - + -
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Residues in contact with ALA 274 (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* 5.0 5.6 - - + -
270A ILE 3.4 11.4 + - - +
271A ALA 3.5 11.9 - - - +
272A LEU 3.2 0.2 - - - -
273A VAL* 1.3 80.9 - - - +
275A GLY* 1.3 56.3 + - - +
277A GLU* 4.1 1.9 - - - +
278A ALA* 3.1 26.5 + - - +
299B ASN 5.5 0.9 - - - +
300B TRP* 3.7 32.9 + - + +
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Residues in contact with GLY 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ARG* 3.4 26.1 + - - +
249A LYS* 3.4 15.8 - - - -
271A ALA 3.6 4.4 + - - -
272A LEU 3.4 5.8 + - - -
273A VAL 3.2 0.2 - - - -
274A ALA* 1.3 77.2 - - - +
276A PHE* 1.3 52.8 + - - +
278A ALA* 3.1 9.7 - - - +
279A ALA* 2.6 34.5 + - - +
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Residues in contact with PHE 276 (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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248A GLY* 3.0 33.4 - - - -
251A LEU* 4.4 4.0 - - + -
252A MET* 4.1 20.9 - - + -
258A PRO* 5.7 0.7 - - + -
261A ILE* 3.3 36.1 - - + -
272A LEU* 3.3 30.3 + - + -
273A VAL* 3.0 12.6 + - + +
275A GLY* 1.3 77.2 - - - +
277A GLU* 1.3 52.9 + - + +
279A ALA* 3.1 9.1 + - - +
280A GLY 2.6 25.8 + - - -
281A VAL* 2.9 34.3 + - + +
283A ILE* 5.3 4.7 - - + -
287A ILE* 4.3 14.1 - - + -
289A ILE* 4.4 10.1 - - + -
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Residues in contact with GLU 277 (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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273A VAL* 3.1 23.0 + - - +
274A ALA* 4.6 2.5 - - - +
276A PHE* 1.3 72.0 - - - +
278A ALA* 1.3 64.5 + - - +
279A ALA 3.2 0.4 - - - -
280A GLY* 3.1 17.9 + - - +
281A VAL 3.5 16.3 - - - +
282A ARG* 5.1 2.6 - - - -
283A ILE* 3.6 15.5 - - + +
302A GLN* 3.4 25.2 + - - +
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Residues in contact with ALA 278 (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 LYS* 4.8 6.7 - - + -
274A ALA 3.1 18.3 + - - +
275A GLY* 3.1 16.8 - - - +
277A GLU* 1.3 79.1 - - - +
279A ALA* 1.3 56.6 + - - -
280A GLY* 3.5 0.5 + - - -
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Residues in contact with ALA 279 (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 LYS* 3.5 10.5 - - - +
252A MET* 4.2 11.0 - - + -
253A GLN* 3.3 35.9 + - - +
275A GLY 2.6 16.2 + - - +
276A PHE* 3.1 14.6 + - - +
278A ALA* 1.3 74.5 - - - +
280A GLY* 1.3 56.9 + - - +
281A VAL* 3.7 3.9 - - + +
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Residues in contact with GLY 280 (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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276A PHE 2.6 9.1 + - - -
277A GLU* 3.1 19.3 + - - -
278A ALA 3.1 0.9 - - - -
279A ALA* 1.3 77.4 - - - +
281A VAL* 1.3 58.5 + - - +
282A ARG 4.1 0.7 + - - -
286A ASP* 4.9 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