Contacts of the helix formed by residues 295 - 305 (chain E) in PDB entry 3ECS
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 ALA 295 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239C PHE* 5.3 1.1 - - - -
291E LEU* 4.7 12.3 - - + -
292E THR* 2.7 32.9 + - - +
294E SER* 1.3 74.6 + - - +
296E VAL* 1.3 62.1 + - - +
297E SER 3.4 1.0 + - - -
298E ASP* 3.5 10.5 + - + +
299E GLU* 3.3 23.1 + - + +
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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
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200E VAL* 3.9 7.9 - - + +
201E VAL 3.7 21.1 - - - +
202E GLU* 4.6 1.8 - - - +
204E GLY* 3.7 16.2 - - - +
235E PHE* 3.9 20.4 - - + -
284E LEU* 4.2 19.1 - - + -
291E LEU* 4.2 17.0 - - + -
292E THR 4.2 1.1 - - - +
293E PRO* 3.2 24.2 + - + +
295E ALA* 1.3 77.6 - - - +
297E SER* 1.3 65.1 + - - +
299E GLU* 3.0 17.6 + - - +
300E LEU* 3.0 13.9 + - + +
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Residues in contact with SER 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C GLU* 2.8 34.4 + - - +
239C PHE* 3.0 22.1 - - - -
297C SER* 4.6 11.2 - - - -
301C ILE* 5.1 2.8 - - - +
202E GLU* 3.4 25.8 + - - +
293E PRO 4.9 0.2 + - - -
294E SER 4.0 1.6 + - - -
296E VAL* 1.3 79.2 - - - +
298E ASP* 1.3 62.9 + - - +
300E LEU* 3.2 13.1 + - - +
301E ILE* 3.2 22.3 + - - +
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Residues in contact with ASP 298 (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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202C GLU* 3.3 20.9 - - - +
237C ARG* 2.9 46.5 + - - +
239C PHE* 6.3 0.4 - - + -
295E ALA* 3.5 11.7 + - + +
296E VAL 3.3 0.6 - - - -
297E SER* 1.3 82.1 + - - +
299E GLU* 1.3 59.1 + - + +
301E ILE* 3.4 4.6 - - - +
302E LYS* 2.9 44.7 + - - +
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Residues in contact with GLU 299 (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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235E PHE* 3.9 16.2 - - + -
288E LEU* 3.6 33.1 - - + +
291E LEU* 3.5 30.6 - - + +
295E ALA* 3.3 14.3 + - + +
296E VAL 3.0 12.1 + - - +
298E ASP* 1.3 78.5 - - + +
300E LEU* 1.3 57.9 + - - +
302E LYS* 3.5 30.7 + - - +
303E LEU* 2.8 31.4 + - - +
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Residues in contact with LEU 300 (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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301C ILE* 3.5 20.4 - - + -
71E LEU* 6.2 0.7 - - + -
200E VAL 5.8 0.4 - - - +
202E GLU* 4.5 13.5 - - + -
235E PHE* 4.3 30.9 - - + +
236E VAL 3.9 23.1 - - - +
237E ARG* 4.1 11.2 - - - -
296E VAL* 3.0 13.3 + - + +
297E SER* 3.2 11.4 + - - +
299E GLU* 1.3 76.5 - - - +
301E ILE* 1.3 65.2 + - + +
303E LEU* 3.0 18.8 + - + +
304E TYR* 3.0 52.9 + - + +
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Residues in contact with ILE 301 (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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202C GLU* 4.9 4.7 - - - +
237C ARG* 3.1 48.2 - - - +
300C LEU* 5.1 2.9 - - + -
301C ILE* 3.4 41.1 - - + +
304C TYR* 4.4 13.5 - - + +
305C LEU* 5.8 1.8 - - + -
297E SER 3.2 17.2 + - - +
298E ASP* 3.4 6.5 - - - +
299E GLU 3.3 0.2 - - - -
300E LEU* 1.3 79.2 - - + +
302E LYS* 1.3 63.9 + - - +
304E TYR* 3.5 7.4 + - - +
305E LEU* 3.1 40.4 + - + +
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Residues in contact with LYS 302 (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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237C ARG* 3.4 18.2 - - - +
298E ASP* 2.9 33.7 + - - +
299E GLU* 3.5 28.7 + - - +
300E LEU 3.2 0.2 - - - -
301E ILE* 1.3 80.2 - - - +
303E LEU* 1.3 64.0 + - - +
305E LEU* 3.4 21.5 + - + +
306E ALA* 4.0 1.2 + - - +
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Residues in contact with LEU 303 (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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71E LEU* 4.0 28.7 - - + -
232E SER* 4.1 26.5 - - - +
235E PHE* 4.5 13.5 - - + -
288E LEU* 4.0 29.2 - - + -
299E GLU 2.8 12.1 + - - +
300E LEU* 3.0 13.2 + - + +
302E LYS* 1.3 75.9 - - - +
304E TYR* 1.3 66.3 + - + +
306E ALA* 2.9 29.4 - - + +
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Residues in contact with TYR 304 (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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301C ILE* 3.5 19.3 - - + -
305C LEU* 4.3 26.0 - - + -
70E GLU* 3.3 21.1 + - - +
71E LEU* 3.1 35.4 - - + +
74E ARG* 3.6 24.6 + - + -
235E PHE 5.3 1.9 + - - -
237E ARG* 3.5 17.6 - - - +
300E LEU* 3.0 42.0 + - + +
301E ILE* 4.0 8.3 - - - +
302E LYS 3.4 0.2 - - - -
303E LEU* 1.3 76.4 - - + +
305E LEU* 1.3 54.2 + - - +
306E ALA* 2.4 27.3 + - - +
307E ALA 4.2 5.2 - - - +
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Residues in contact with LEU 305 (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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74C ARG* 3.2 42.4 - - - +
237C ARG* 4.8 4.5 - - - +
304C TYR* 3.6 23.1 - - + +
305C LEU* 3.9 12.6 - - + -
306C ALA 6.0 0.4 - - - +
301E ILE* 3.1 37.3 + - + +
302E LYS* 3.7 13.0 - - + +
303E LEU 3.3 0.4 - - - -
304E TYR* 1.3 72.6 - - - +
306E ALA* 1.3 57.7 + - - +
307E ALA 3.2 8.7 + - - +
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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