Contacts of the helix formed by residues 293 - 304 (chain G) in PDB entry 6CAJ
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 PRO 293 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202G GLU 4.4 0.3 - - - +
203G ASN 3.0 22.0 - - - +
204G GLY* 3.3 27.4 + - - +
278G PRO* 4.2 11.0 - - + +
281G ILE* 3.6 26.7 - - + +
282G THR 3.4 17.9 - - - +
284G LEU* 3.7 23.6 - - + -
291G LEU 4.3 0.2 - - - +
292G THR* 1.3 90.2 - - - +
294G SER* 1.3 58.4 + - - +
295G ALA 3.2 0.8 + - - -
296G VAL* 3.9 8.3 + - + +
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Residues in contact with SER 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C SER* 3.0 37.4 + - - -
337C TYR* 2.7 28.0 + - - -
510E SER* 3.3 28.2 + - - +
511E SER* 5.1 0.9 + - - -
514E VAL* 5.6 0.3 - - - +
203G ASN 4.5 3.1 - - - -
292G THR* 3.1 11.5 + - - +
293G PRO* 1.3 76.5 - - - +
295G ALA* 1.3 56.5 + - - +
296G VAL 3.5 0.7 - - - -
297G SER* 3.9 7.8 + - - +
298G ASP 3.7 8.7 + - - -
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Residues in contact with ALA 295 (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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337C TYR* 3.6 28.5 - - + -
291G LEU* 3.8 33.0 - - + -
292G THR* 3.0 17.3 + - + +
294G SER* 1.3 78.9 + - - +
296G VAL* 1.3 60.3 + - - +
297G SER 3.3 0.4 - - - -
298G ASP* 3.2 3.2 + - - +
299G GLU* 2.9 32.9 + - + +
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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* 3.9 2.7 - - + -
201G VAL 3.7 21.5 - - - +
202G GLU 3.8 6.3 - - - +
204G GLY* 4.8 2.0 - - - +
235G PHE* 3.6 38.1 - - + -
284G LEU* 3.7 31.0 - - + -
286G THR* 5.6 0.2 - - + -
291G LEU* 5.2 5.6 - - + -
292G THR 4.7 5.4 - - - +
293G PRO 4.2 9.4 - - - +
294G SER 3.5 0.6 - - - -
295G ALA* 1.3 76.7 - - - +
297G SER* 1.3 57.5 + - - +
299G GLU* 3.3 7.4 + - - +
300G LEU* 2.9 38.6 + - + +
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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
----------------------------------------------------------
508E PRO* 3.4 20.0 - - - +
510E SER* 5.3 0.2 - - - -
511E SER* 2.4 30.9 + - - -
202G GLU* 3.1 38.3 + - - +
203G ASN* 4.7 0.9 - - - -
294G SER* 3.9 9.9 + - - -
295G ALA 3.3 0.4 - - - -
296G VAL* 1.3 74.1 - - - +
298G ASP* 1.3 59.3 + - - +
300G LEU* 3.4 0.9 + - - +
301G ILE* 2.9 33.9 + - - +
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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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337C TYR* 3.2 40.6 + - + +
338C ARG* 3.8 11.4 - - - +
511E SER* 4.9 0.6 + - - -
514E VAL* 3.3 18.2 - - + +
517E ARG* 2.6 34.8 + - - -
294G SER 3.7 1.8 + - - -
295G ALA 3.2 9.8 + - - +
297G SER* 1.3 78.6 - - - +
299G GLU* 1.3 58.0 + - + +
301G ILE* 3.3 1.2 + - - +
302G LYS* 2.9 44.2 + - - +
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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* 4.6 15.3 - - + -
288G LEU* 3.4 33.7 - - + +
291G LEU* 4.7 12.7 - - + +
295G ALA* 2.9 22.3 + - + +
296G VAL* 3.3 8.0 + - - +
298G ASP* 1.3 76.6 - - + +
300G LEU* 1.3 57.3 + - - +
302G LYS* 3.4 28.4 + - - +
303G LEU* 2.9 31.3 + - - +
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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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71G LEU* 5.4 1.1 - - + -
202G GLU* 3.8 30.5 - - + +
235G PHE* 3.8 34.1 - - + +
236G VAL 3.9 9.9 - - - +
237G ARG* 3.4 47.1 + - + -
296G VAL* 2.9 30.0 + - + +
297G SER 4.0 2.7 - - - +
298G ASP 3.3 0.2 - - - -
299G GLU* 1.3 75.1 - - - +
301G ILE* 1.3 62.2 + - - +
303G LEU* 3.7 20.0 - - + -
304G TYR* 2.9 20.3 + - - -
305G LEU* 3.6 4.9 + - - +
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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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504E LEU* 5.2 7.2 - - + -
507E ILE* 3.7 25.8 - - + -
511E SER* 3.8 16.6 - - - +
514E VAL* 3.8 29.8 - - + -
515E VAL* 4.1 11.2 - - + -
518E VAL* 4.3 24.7 - - + -
202G GLU* 4.0 11.4 - - - +
237G ARG* 5.3 2.5 - - - +
297G SER* 2.9 22.6 + - - +
298G ASP 3.8 2.7 - - - +
300G LEU* 1.3 74.8 - - - +
302G LYS* 1.3 63.8 + - - +
303G LEU 3.2 0.2 - - - -
304G TYR* 3.2 36.1 - - + +
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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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338C ARG* 3.3 32.6 - - - +
341C SER* 6.0 0.2 - - - -
517E ARG* 4.4 7.0 - - - +
518E VAL* 4.9 11.9 - - + -
298G ASP* 2.9 41.7 + - - +
299G GLU* 3.4 32.7 + - - +
301G ILE* 1.3 76.4 - - + +
303G LEU* 1.3 58.4 + - - +
304G TYR* 3.8 13.5 - - - -
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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
----------------------------------------------------------
71G LEU* 3.7 31.2 - - + -
74G ARG* 2.8 44.4 + - - +
235G PHE* 6.0 3.6 - - + -
299G GLU* 2.9 18.8 + - + +
300G LEU* 4.2 17.0 - - + +
302G LYS* 1.3 78.6 - - - +
304G TYR* 1.3 57.2 + - - +
305G LEU 4.1 10.3 - - - +
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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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504E LEU* 4.4 31.3 - - + +
518E VAL* 4.0 28.3 + - + +
519E LYS* 6.0 0.5 - - - +
74G ARG* 3.1 30.2 + - - +
237G ARG* 4.0 3.4 - - - +
300G LEU 2.9 12.0 + - - -
301G ILE* 3.2 31.0 - - + +
302G LYS* 3.8 14.8 - - - -
303G LEU* 1.3 77.4 - - - +
305G LEU* 1.3 66.9 + - - +
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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