Contacts of the helix formed by residues 286 - 297 (chain E) in PDB entry 3EXG
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 286 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43E ARG* 2.7 34.6 + - - -
260E TYR* 3.3 17.9 + - - +
281E VAL 3.8 0.6 + - - -
282E ARG* 2.9 25.8 + - + +
285E SER* 1.3 75.9 - - - +
287E PRO* 1.3 73.0 - - - +
288E ILE* 2.7 34.8 + - - +
289E MET* 3.1 21.7 + - + +
290E LEU* 3.0 21.1 + - - +
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Residues in contact with PRO 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E MET* 4.2 8.3 - - - +
43E ARG* 4.0 3.1 - - - +
67E GLY 4.2 5.2 - - - +
69E GLU* 3.4 29.2 - - + +
70E ALA* 3.6 22.9 - - + +
228E MET* 3.2 36.6 - - + +
230E ILE* 4.7 2.8 - - - +
260E TYR* 4.0 6.7 - - - +
285E SER 3.3 3.7 - - - +
286E ASP* 1.3 94.6 - - - +
288E ILE* 1.3 64.5 + - + +
290E LEU* 3.3 4.4 + - + +
291E LEU* 3.2 21.3 + - - +
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Residues in contact with ILE 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E TYR* 3.5 28.9 - - + +
39E MET* 3.6 37.9 - - + +
40E GLN* 3.3 31.0 - - + +
43E ARG* 3.6 34.1 - - + +
69E GLU* 4.8 1.8 - - - +
286E ASP* 2.7 13.8 + - - +
287E PRO* 1.3 77.6 - - + +
289E MET* 1.3 65.5 + - - +
291E LEU* 3.6 2.4 + - - +
292E LYS* 3.1 21.2 + - + +
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Residues in contact with MET 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E ARG 4.6 3.6 - - - +
283E SER* 3.5 28.3 - - - +
284E LYS 4.5 4.9 - - - +
286E ASP* 3.1 19.9 + - + +
288E ILE* 1.3 79.4 - - - +
290E LEU* 1.3 102.9 + - + +
291E LEU 3.1 0.2 - - - -
292E LYS* 3.1 12.0 + - + +
293E ASP* 2.9 49.7 + - - +
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Residues in contact with LEU 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E ASP* 5.5 1.8 - - - +
228E MET* 3.4 30.7 - - + +
229E ASP* 4.6 12.3 - - + +
230E ILE* 5.9 1.8 - - + -
284E LYS 4.1 3.8 - - - +
285E SER* 3.8 28.5 - - - +
286E ASP 3.0 16.4 + - - +
287E PRO 3.3 5.6 + - - +
289E MET* 1.3 102.8 - - + +
291E LEU* 1.3 60.4 + - - +
293E ASP* 3.7 4.0 + - - +
294E ARG* 3.2 28.0 + - - +
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Residues in contact with LEU 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E LEU* 4.9 12.6 - - + -
32E GLY* 3.8 8.5 - - - +
35E TYR* 4.2 5.6 - - + -
36E TYR* 3.5 36.1 - - + +
39E MET* 3.4 33.9 - - + -
230E ILE* 3.9 24.2 - - + +
231E LEU* 5.0 9.9 - - + -
287E PRO 3.2 7.0 + - - +
288E ILE 3.9 3.1 - - - +
289E MET 3.1 0.8 - - - -
290E LEU* 1.3 76.5 - - - +
292E LYS* 1.3 67.9 + - - +
294E ARG* 3.0 13.0 + - + +
295E MET* 2.8 40.8 + - + +
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Residues in contact with LYS 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E TYR* 4.5 13.6 - - + +
288E ILE* 3.1 12.8 + - + +
289E MET* 3.1 16.8 + - + +
291E LEU* 1.3 77.9 - - - +
293E ASP* 1.3 65.4 + - - +
295E MET* 3.0 4.3 + - - +
296E VAL* 2.9 42.1 + - + +
303E VAL* 3.2 38.4 + - - +
306E LEU* 3.6 30.0 - - + +
307E LYS* 5.7 4.0 - - - +
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Residues in contact with ASP 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289E MET* 2.9 43.1 + - - +
290E LEU* 4.1 3.8 - - - +
292E LYS* 1.3 84.0 - - - +
294E ARG* 1.3 62.7 + - - +
296E VAL* 4.6 3.0 - - - +
297E ASN* 3.0 44.6 + - - +
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Residues in contact with ARG 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E PHE* 3.1 46.3 - - + +
8E GLU 3.1 26.7 + - - -
9E ILE* 3.5 8.9 - - - +
27E LEU* 6.3 1.3 - - + -
229E ASP* 2.8 42.2 + - - -
230E ILE* 5.1 1.6 - - - +
231E LEU* 3.2 35.1 - - + +
290E LEU* 3.2 14.9 + - - +
291E LEU* 3.0 17.5 + - + +
293E ASP* 1.3 78.6 - - + +
295E MET* 1.3 59.4 + - + +
297E ASN* 4.2 0.8 - - - -
298E SER* 3.0 22.5 + - - -
300E LEU* 4.8 0.2 - - - -
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Residues in contact with MET 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E LEU* 4.2 11.9 - - + -
29E ARG 5.3 1.3 - - - +
32E GLY* 3.1 42.6 - - - +
33E LEU* 3.6 23.6 - - + +
36E TYR* 3.9 15.9 - - + -
291E LEU* 2.8 35.4 + - + +
292E LYS* 3.4 6.1 - - - +
294E ARG* 1.3 72.7 - - + +
296E VAL* 1.3 65.2 + - - +
298E SER* 3.3 5.4 + - - -
300E LEU* 2.9 41.8 + - + -
301E ALA* 4.0 17.5 - - + -
306E LEU* 4.0 13.7 - - + -
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Residues in contact with VAL 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E LYS* 2.9 34.0 + - - +
293E ASP* 4.6 1.6 - - - +
295E MET* 1.3 73.2 - - - +
297E ASN* 1.3 68.8 + - - +
298E SER 2.7 13.3 + - - -
299E ASN* 3.0 12.3 + - - -
301E ALA 3.6 12.7 - - - +
302E SER* 4.4 1.3 - - - -
303E VAL* 3.9 32.8 - - + +
306E LEU* 4.6 6.1 - - + -
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Residues in contact with ASN 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PHE* 5.4 1.4 - - - -
293E ASP* 3.0 33.5 + - - +
294E ARG* 4.2 2.4 - - - +
296E VAL* 1.3 89.6 - - - +
298E SER* 1.3 59.4 + - - +
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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