Contacts of the helix formed by residues 295 - 305 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291G LEU* 4.0 21.1 - - + -
292G THR* 2.9 20.8 + - - +
294G SER* 1.3 78.4 + - - +
296G VAL* 1.3 67.0 + - - +
297G SER 3.4 1.1 - - - -
298G ASP* 3.4 9.9 + - - +
299G GLU* 3.2 23.3 + - + +
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Residues in contact with VAL 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200G VAL* 3.8 12.6 - - + -
201G VAL 3.7 22.9 - - - +
204G GLY* 3.6 24.5 - - - +
235G PHE* 4.0 15.9 - - + -
284G LEU* 3.9 30.3 - - + -
291G LEU* 4.6 11.9 - - + +
292G THR 4.4 1.8 - - - +
293G PRO* 3.4 5.1 + - + +
295G ALA* 1.3 77.3 - - - +
297G SER* 1.3 56.3 + - - +
299G GLU* 2.9 7.5 + - - +
300G LEU* 2.6 39.3 + - + +
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Residues in contact with SER 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202G GLU* 3.1 25.1 + - - +
203G ASN* 5.1 0.4 - - - -
204G GLY 4.9 0.2 - - - +
293G PRO 4.7 1.4 + - - -
294G SER 4.0 4.1 + - - -
296G VAL* 1.3 78.6 - - - +
298G ASP* 1.3 61.2 + - - +
300G LEU* 3.3 6.8 + - - +
301G ILE* 2.9 27.3 + - - +
202H GLU* 2.8 27.4 + - - -
239H PHE* 3.0 31.5 - - - +
297H SER* 5.3 7.9 - - - -
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Residues in contact with ASP 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294G SER 5.8 0.4 - - - +
295G ALA* 3.4 9.5 + - - +
296G VAL 3.3 0.6 - - - -
297G SER* 1.3 78.4 + - - +
299G GLU* 1.3 68.4 + - + +
301G ILE* 3.0 7.5 - - - +
302G LYS* 2.9 31.5 + - - +
202H GLU* 3.2 16.6 + - - +
237H ARG* 2.7 46.5 + - - +
239H PHE* 5.9 1.8 - - + -
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Residues in contact with GLU 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235G PHE* 4.3 11.4 - - + -
288G LEU* 3.7 29.6 - - + +
291G LEU* 3.6 34.0 - - + +
295G ALA* 3.2 12.5 + - + +
296G VAL* 2.9 10.2 + - - +
298G ASP* 1.3 76.4 - - + +
300G LEU* 1.3 56.5 + - - +
302G LYS* 2.9 35.3 + - - +
303G LEU* 2.7 38.2 + - - +
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Residues in contact with LEU 300 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200G VAL 4.5 0.9 - - - +
201G VAL 4.4 3.6 - - - +
202G GLU* 3.6 41.7 - - + +
235G PHE* 3.8 33.3 - - + -
236G VAL 3.6 14.1 - - - +
237G ARG* 4.5 1.8 - - + -
296G VAL* 2.6 20.9 + - + +
297G SER* 3.5 6.1 - - - +
299G GLU* 1.3 73.5 - - - +
301G ILE* 1.3 56.5 + - - +
303G LEU* 3.1 5.2 + - - +
304G TYR* 2.8 50.3 + - + -
301H ILE* 3.6 24.0 - - + -
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Residues in contact with ILE 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297G SER 2.9 20.8 + - - +
298G ASP* 3.0 26.2 - - - +
300G LEU* 1.3 70.5 - - - +
302G LYS* 1.3 57.7 + - - +
303G LEU 2.8 10.8 + - - -
304G TYR* 4.3 1.1 - - - +
305G LEU* 2.9 40.9 + - + +
202H GLU* 4.6 5.4 - - - +
237H ARG* 3.5 33.7 - - - +
300H LEU* 4.3 11.7 - - + +
301H ILE* 3.9 23.3 - - + -
304H TYR* 3.6 24.5 - - + -
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Residues in contact with LYS 302 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298G ASP* 2.9 24.6 + - - +
299G GLU* 2.9 33.6 + - - +
301G ILE* 1.3 77.4 - - - +
303G LEU* 1.3 56.6 + - - +
305G LEU* 3.8 14.2 - - - +
306G ALA* 4.8 3.8 - - - +
74H ARG* 6.3 2.2 - - - +
237H ARG* 4.0 17.3 - - - +
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Residues in contact with LEU 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G LEU* 3.4 39.7 - - + -
75G PHE* 3.1 20.2 - - + -
232G SER* 4.6 19.5 - - - +
235G PHE* 4.9 4.9 - - + -
288G LEU* 4.6 24.9 - - + -
299G GLU 2.7 10.8 + - - +
300G LEU* 3.2 10.3 - - - +
301G ILE 2.8 1.6 + - - -
302G LYS* 1.3 78.1 - - - +
304G TYR* 1.3 73.6 + - + +
305G LEU 3.1 2.0 + - - -
306G ALA* 3.5 9.9 - - + +
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Residues in contact with TYR 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G SER* 3.7 21.1 + - - -
70G GLU* 2.8 37.8 + - + -
71G LEU* 3.7 26.9 - - + +
74G ARG* 3.9 19.1 + - - +
75G PHE* 3.0 21.2 - - - -
235G PHE* 2.9 28.3 + - + -
236G VAL* 3.9 4.2 - - - +
237G ARG* 3.6 22.2 + - + +
300G LEU* 2.8 48.6 + - + +
301G ILE* 4.1 3.6 - - - +
303G LEU* 1.3 79.5 - - + +
305G LEU* 1.3 67.6 + - + +
306G ALA 3.4 0.3 + - - -
301H ILE* 4.5 7.4 - - + -
305H LEU* 4.8 3.3 - - + +
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Residues in contact with LEU 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301G ILE* 2.9 31.0 + - + +
302G LYS* 3.8 12.0 - - - +
303G LEU 3.8 1.3 - - - -
304G TYR* 1.3 80.6 - - + +
306G ALA* 1.3 57.9 + - - +
307G ALA 3.9 2.9 + - - -
74H ARG* 6.3 0.9 - - - +
301H ILE* 3.6 34.1 - - + +
304H TYR* 3.6 21.5 - - + +
305H LEU* 3.6 40.2 - - + +
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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