Contacts of the helix formed by residues 266 - 278 (chain A) in PDB entry 4EJJ
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 ASP 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A PHE* 3.3 14.5 - - - -
185A ILE 3.4 12.6 - - - +
186A VAL 3.4 10.0 - - - +
187A PHE* 2.9 23.4 - - - +
188A GLY* 3.3 18.3 - - - +
255A ASN* 2.9 33.2 + - - +
264A PRO 3.5 1.4 - - - -
265A ARG* 1.3 84.5 - - - +
267A PHE* 1.3 65.3 + - - +
268A ILE* 3.3 2.0 + - - +
269A ASP* 3.0 17.8 + - - +
270A SER* 3.3 13.2 + - - -
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Residues in contact with PHE 267 (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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130A PHE* 3.7 22.7 - + - -
131A SER* 3.8 27.8 - - - -
134A THR* 3.3 35.4 - - + -
135A LEU* 4.1 15.0 - - + -
138A PHE* 3.8 8.6 - - - -
185A ILE* 3.0 11.0 + - + +
186A VAL* 3.7 27.6 - - + -
266A ASP* 1.3 73.8 - - - +
268A ILE* 1.3 65.0 + - - +
270A SER* 3.3 4.3 + - - -
271A PHE* 3.2 26.9 + + + +
291A LEU* 5.6 0.4 - - + -
294A THR* 4.0 13.9 - - + -
295A THR* 4.4 14.4 - - - -
298A LEU* 3.7 28.0 - - + -
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Residues in contact with ILE 268 (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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186A VAL 3.2 18.4 + - - +
187A PHE* 4.0 20.9 - - + -
248A ILE* 5.3 0.7 - - + +
251A LYS* 4.3 21.1 - - + +
252A VAL* 4.2 17.9 - - + -
255A ASN* 3.8 26.2 - - + +
266A ASP* 3.3 6.2 - - - +
267A PHE* 1.3 76.4 - - - +
269A ASP* 1.4 52.5 + - - +
271A PHE* 3.3 4.0 + - - +
272A LEU* 2.8 41.5 + - + +
291A LEU* 4.1 19.0 - - + +
295A THR* 4.0 24.9 - - + +
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Residues in contact with ASP 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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255A ASN* 2.9 26.0 + - - +
259A LEU* 3.3 20.1 - - + +
260A ASP 5.5 0.3 + - - -
263A SER 4.6 0.7 - - - +
264A PRO* 3.7 10.1 - - + +
265A ARG* 2.7 61.6 + - - +
266A ASP* 3.0 15.1 + - - +
268A ILE* 1.4 76.3 - - - +
270A SER* 1.3 52.9 + - - +
272A LEU* 3.2 6.4 + - - +
273A ILE* 2.8 39.9 + - + +
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Residues in contact with SER 270 (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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130A PHE* 3.7 10.9 - - - -
134A THR* 3.9 19.3 - - - -
138A PHE* 3.4 19.4 - - - -
264A PRO* 3.7 9.4 - - - +
266A ASP 3.3 11.3 + - - -
267A PHE 3.3 7.9 + - - -
269A ASP* 1.3 75.3 - - - +
271A PHE* 1.3 57.4 + - - +
273A ILE* 3.8 11.4 + - - +
274A ARG* 3.0 27.2 + - - +
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Residues in contact with PHE 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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127A LEU* 3.9 16.4 - - + -
130A PHE* 3.6 28.6 - + + -
267A PHE* 3.2 20.0 + + + +
268A ILE 3.6 7.0 - - - +
270A SER* 1.3 75.2 - - - +
272A LEU* 1.3 58.7 + - - +
274A ARG* 3.4 1.9 + - - -
275A MET* 2.8 41.8 + - + +
286A PHE* 3.6 33.4 - + - -
287A TYR 3.7 9.4 - - - -
290A ASN* 3.9 12.3 - - + -
291A LEU* 3.3 54.7 - - + -
294A THR* 4.6 4.9 - - + -
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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
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252A VAL* 4.4 2.0 - - + +
255A ASN* 3.9 7.6 - - + +
256A GLN* 3.4 60.6 - - + +
259A LEU* 4.0 17.7 - - + -
268A ILE* 2.8 37.1 + - + +
269A ASP* 3.5 13.5 - - - +
271A PHE* 1.3 71.1 - - - +
273A ILE* 1.3 56.5 + - - +
275A MET* 3.1 15.7 + - + +
276A GLN* 2.9 27.7 + - - +
291A LEU* 3.6 20.9 - - + -
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Residues in contact with ILE 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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259A LEU* 4.6 8.1 - - + -
260A ASP 4.5 2.0 - - - +
261A PRO* 3.9 38.1 - - + +
264A PRO* 3.8 33.2 - - + -
269A ASP* 2.8 31.7 + - + +
270A SER* 3.8 6.7 - - - +
272A LEU* 1.3 70.4 - - - +
274A ARG* 1.3 67.1 + - - +
276A GLN* 3.1 13.2 + - - +
277A GLU* 3.0 38.5 + - + +
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Residues in contact with ARG 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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126A GLN* 4.9 6.7 + - - -
129A ARG* 5.4 9.9 - - - +
130A PHE* 4.3 24.5 - - + +
270A SER 3.0 17.8 + - - +
271A PHE 3.4 3.1 + - - +
273A ILE* 1.3 77.9 - - + +
275A MET* 1.3 65.1 + - - +
277A GLU* 3.3 28.4 + - - +
278A GLU* 3.3 50.9 + - + +
286A PHE* 3.9 44.4 - - + -
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Residues in contact with MET 275 (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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256A GLN* 4.6 9.6 - - - +
271A PHE* 2.8 31.0 + - + +
272A LEU* 3.1 22.9 + - + +
274A ARG* 1.3 69.1 - - - +
276A GLN* 1.3 57.7 + - - +
278A GLU* 2.8 22.3 + - - +
279A GLU* 3.5 11.9 + - - +
286A PHE* 3.2 33.9 - - - +
287A TYR* 3.9 5.8 - - - -
288A LEU* 3.5 29.4 - - + +
291A LEU* 3.5 28.0 - - + -
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Residues in contact with GLN 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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259A LEU* 4.3 14.2 - - - +
261A PRO* 4.2 19.5 - - - +
272A LEU 2.9 14.1 + - - +
273A ILE* 3.1 12.0 + - - +
275A MET* 1.3 71.1 - - - +
277A GLU* 1.3 61.3 + - + +
278A GLU 3.0 1.6 + - - -
279A GLU* 3.2 38.1 + - - +
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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 ILE* 3.0 33.0 + - + +
274A ARG* 3.3 34.2 + - - +
275A MET 3.3 0.2 + - - -
276A GLN* 1.3 71.0 - - + +
278A GLU* 1.3 65.2 + - + +
279A GLU 3.6 1.1 + - - -
280A LYS* 4.7 11.3 + - - +
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Residues in contact with GLU 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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274A ARG* 3.3 39.8 + - - +
275A MET 2.8 16.5 + - - +
277A GLU* 1.3 78.7 - - + +
279A GLU* 1.3 63.4 + - - +
280A LYS* 3.1 3.8 + - - +
281A ASN* 3.2 44.5 + - + +
284A THR* 2.8 38.8 + - + +
286A PHE* 4.5 10.7 - - + -
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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