Contacts of the helix formed by residues 264 - 276 (chain A) in PDB entry 3E4E
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 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A TYR* 2.7 28.3 + - - -
182A ASP 4.3 1.8 - - - +
183A ILE 3.5 10.8 - - - +
184A LEU 3.3 7.9 - - - +
185A PHE 3.1 14.4 - - - +
186A ARG* 3.6 16.4 - - + +
253A HIS* 2.5 32.2 + - - -
262A PRO* 3.3 1.6 - - - +
263A ARG* 1.3 85.3 - - - +
265A LEU* 1.3 61.5 + - - +
266A THR 3.1 2.9 + - - -
267A ASP* 2.7 35.1 + - - +
268A CYS* 3.3 16.1 + - - -
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Residues in contact with LEU 265 (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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128A PHE* 6.4 0.2 - - + -
129A SER* 4.7 5.2 - - - +
132A THR* 3.9 29.6 - - + -
133A LEU* 3.9 20.9 - - + +
136A TYR* 4.0 2.9 - - + -
183A ILE* 2.9 40.8 + - + +
184A LEU* 3.8 20.0 - - + -
264A ASP* 1.3 74.3 - - - +
266A THR* 1.3 66.2 + - - +
267A ASP 3.1 2.0 - - - -
268A CYS* 3.1 17.0 + - - +
269A LEU* 3.2 35.2 + - + +
293A VAL* 4.4 2.7 - - + -
296A LEU* 3.9 15.5 - - + -
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Residues in contact with THR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LEU* 2.4 35.7 - - - +
185A PHE* 3.5 20.6 - - + -
250A VAL* 4.1 13.5 - - - +
253A HIS* 3.6 17.7 - - + +
264A ASP* 3.3 8.1 - - - +
265A LEU* 1.3 76.4 - - - +
267A ASP* 1.3 62.4 + - - +
269A LEU* 4.0 11.1 - - - +
270A LEU* 3.1 38.7 + - - +
289A ILE* 4.9 2.3 - - - +
293A VAL* 4.1 17.0 - - + -
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Residues in contact with ASP 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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253A HIS* 3.6 10.1 - - - +
257A LEU* 3.8 14.6 - - + +
261A CYS 3.3 6.2 - - - +
262A PRO* 3.6 15.5 - - + -
263A ARG* 2.6 62.8 + - - +
264A ASP* 2.7 27.4 + - - +
266A THR* 1.3 71.9 + - - +
268A CYS* 1.3 58.9 + - - +
270A LEU* 2.9 7.8 + - - +
271A VAL* 2.9 31.5 + - - +
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Residues in contact with CYS 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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128A PHE* 3.4 30.8 - - + -
132A THR* 3.7 22.4 - - + -
136A TYR* 3.4 15.9 - - - -
262A PRO* 4.0 16.4 - - - -
264A ASP 3.3 15.3 - - - -
265A LEU 3.1 7.7 + - - +
267A ASP* 1.3 78.6 - - - +
269A LEU* 1.3 56.2 + - - +
271A VAL* 3.7 8.9 + - - +
272A GLU* 3.2 19.4 + - - +
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Residues in contact with LEU 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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125A ILE* 5.3 2.0 - - + -
128A PHE* 3.8 26.7 - - + -
129A SER* 4.3 14.8 - - - +
265A LEU* 3.2 36.7 + - + +
266A THR* 4.0 2.5 - - - +
267A ASP 3.1 0.6 - - - -
268A CYS* 1.3 74.1 - - - +
270A LEU* 1.3 68.1 + - - +
272A GLU* 3.1 15.0 + - - +
273A MET* 3.1 12.8 + - - +
284A TYR* 3.9 23.0 - - + -
289A ILE* 3.7 32.5 - - + -
292A THR* 3.9 16.6 - - + -
293A VAL* 3.8 14.4 - - + -
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Residues in contact with LEU 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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250A VAL* 3.9 8.7 - - + +
253A HIS* 3.6 31.9 - - + +
254A HIS* 3.9 25.5 - - + +
257A LEU* 4.1 16.6 - - + -
266A THR* 3.1 23.9 + - - +
267A ASP* 2.9 11.6 + - - +
269A LEU* 1.3 78.1 - - - +
271A VAL* 1.3 54.8 + - - +
273A MET* 2.8 28.1 + - - +
274A GLU* 3.0 15.2 + - - +
286A MET* 4.4 16.4 - - - -
289A ILE* 3.8 29.6 - - + -
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Residues in contact with VAL 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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257A LEU* 4.0 21.5 - - + -
259A PRO* 4.1 32.1 - - + +
262A PRO* 4.7 11.4 - - + -
267A ASP 2.9 21.0 + - - +
268A CYS* 3.9 8.5 - - - +
270A LEU* 1.3 69.8 - - - +
272A GLU* 1.3 60.9 + - - +
273A MET 2.9 10.6 + - - -
274A GLU* 3.0 17.4 + - + +
275A LYS* 3.1 33.2 + - - +
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Residues in contact with GLU 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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128A PHE* 3.9 30.6 - - + +
268A CYS 3.2 14.5 + - - +
269A LEU* 3.1 14.3 + - - +
271A VAL* 1.3 76.2 - - - +
273A MET* 1.3 56.7 + - - +
275A LYS* 3.9 30.3 + - - +
276A GLU* 3.4 19.9 - - - +
284A TYR* 3.5 35.9 + - + +
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Residues in contact with MET 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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254A HIS* 6.0 3.8 - - - -
269A LEU 3.1 8.6 + - - +
270A LEU* 2.8 17.8 + - - +
272A GLU* 1.3 76.0 - - - +
274A GLU* 1.3 64.0 + - - +
275A LYS 3.3 1.6 - - - -
276A GLU* 3.7 5.8 + - - +
277A LYS* 3.5 10.4 + - - +
282A ARG* 3.3 45.7 + - - +
284A TYR* 3.9 19.7 - - + +
285A THR* 3.7 10.3 - - + -
286A MET* 3.5 41.7 - - + +
289A ILE* 3.6 21.1 - - + -
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Residues in contact with GLU 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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254A HIS* 3.6 24.0 + - + -
257A LEU* 4.2 19.5 - - + +
259A PRO* 5.7 7.6 - - + -
270A LEU 3.0 12.9 + - - +
271A VAL* 3.0 9.8 + - + +
273A MET* 1.3 76.7 - - + +
275A LYS* 1.3 64.0 + - - +
277A LYS* 3.2 60.4 + - - +
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Residues in contact with LYS 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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271A VAL* 3.1 35.6 + - - +
272A GLU* 3.9 26.5 + - - +
273A MET 3.3 0.2 - - - -
274A GLU* 1.3 79.2 - - - +
276A GLU* 1.3 59.6 - - + +
277A LYS* 3.3 5.2 + - - +
278A HIS* 4.6 4.3 + - - +
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Residues in contact with GLU 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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272A GLU 3.4 15.9 - - - +
273A MET* 4.1 6.5 - - - +
274A GLU 3.4 0.4 - - - -
275A LYS* 1.3 75.9 - - + +
277A LYS* 1.3 64.4 + - - +
278A HIS 3.1 4.5 + - - -
279A SER* 3.2 30.5 + - - +
281A GLU 4.2 4.5 - - - +
282A ARG* 3.3 22.9 + - + +
283A LEU* 2.7 45.2 + - - +
284A TYR* 3.5 19.7 + - - +
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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