Contacts of the helix formed by residues 309 - 318 (chain V) in PDB entry 2GLJ
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 PHE 309 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86V ILE* 3.6 19.0 - - + +
101V ILE* 3.6 21.5 - - + -
288V ILE* 3.7 22.0 - - + -
290V ILE* 3.3 39.0 - - + -
306V GLN* 4.3 10.7 + - - +
307V SER 2.7 4.0 + - - -
308V LYS* 1.3 78.9 - - + +
310V PHE* 1.3 74.6 + - - +
312V ASN* 3.3 3.1 + - - +
313V THR* 3.0 36.4 + - - -
333V LEU* 3.7 26.2 - - + -
423V LEU* 3.9 26.9 - - + -
426V TYR* 4.2 9.0 - + - -
428V MET* 5.6 0.7 - - - -
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Residues in contact with PHE 310 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306V GLN 5.2 0.6 + - - +
307V SER* 2.7 30.1 + - - +
309V PHE* 1.3 82.7 - - - +
311V GLU* 1.3 50.8 + - - +
312V ASN 2.6 14.0 + - - -
313V THR* 3.2 9.0 + - - -
314V VAL* 3.5 19.1 + - + +
328V LYS* 4.6 14.1 - - + -
330V ARG* 6.1 3.8 - - - -
333V LEU* 4.0 15.0 - - + -
426V TYR* 3.0 43.3 - + - +
310W PHE* 6.2 3.6 - + - -
328W LYS* 5.8 1.3 - - - -
330W ARG* 3.0 41.7 - - - -
310X PHE* 6.4 2.0 - + - -
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Residues in contact with GLU 311 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307V SER* 2.7 33.8 + - - +
308V LYS* 3.9 4.1 - - - +
310V PHE* 1.3 69.6 - - - +
312V ASN* 1.3 62.9 + - - +
314V VAL* 4.8 2.2 - - - -
315V ALA* 4.4 10.0 - - - +
330W ARG* 3.0 58.3 - - + +
331W LYS* 5.1 6.9 + - - +
333W LEU* 5.8 0.7 - - - +
334W TYR* 3.4 37.1 + - - +
426W TYR* 4.0 19.7 - - - +
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Residues in contact with ASN 312 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59V ASN* 5.5 3.5 + - - +
78V ALA* 3.4 28.7 - - - +
86V ILE* 4.6 4.7 - - - -
88V PHE* 3.5 24.9 - - - -
308V LYS* 2.7 35.5 + - - +
309V PHE* 3.4 5.2 - - - +
310V PHE 2.6 8.7 + - - -
311V GLU* 1.3 73.8 + - - +
313V THR* 1.3 59.4 + - - +
314V VAL 2.9 2.9 - - - +
315V ALA* 3.5 12.0 - - - +
316V ASP* 2.8 28.8 + - - +
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Residues in contact with THR 313 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88V PHE* 4.1 17.3 - - + -
99V PHE* 3.3 40.6 - - + -
288V ILE* 4.7 0.8 - - + +
309V PHE* 3.0 38.3 + - - -
310V PHE* 4.0 3.6 - - - -
312V ASN* 1.3 77.1 + - - +
314V VAL* 1.3 54.5 + - + +
316V ASP* 3.5 2.6 - - - +
317V ILE* 2.7 41.7 + - + +
332V ALA* 5.6 0.2 - - + -
333V LEU* 4.4 15.9 - - + -
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Residues in contact with VAL 314 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310V PHE* 3.5 20.9 - - + +
311V GLU* 4.8 1.3 - - - -
312V ASN 2.9 1.9 - - - +
313V THR* 1.3 76.9 - - - +
315V ALA* 1.3 56.4 + - - +
316V ASP 2.7 14.2 + - - -
317V ILE* 2.7 24.9 + - + -
318V MET* 2.8 15.0 + - + +
326V GLU 5.0 11.7 - - - +
328V LYS* 5.7 2.7 - - + +
333V LEU* 6.5 0.9 - - + -
328W LYS* 6.1 3.1 - - + -
330W ARG* 3.7 32.1 - - + +
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Residues in contact with ALA 315 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59V ASN* 5.7 2.2 + - - -
63V ILE* 5.6 5.4 - - - +
311V GLU 4.4 3.8 - - - +
312V ASN* 3.3 21.0 + - - +
314V VAL* 1.3 79.1 - - - +
316V ASP* 1.3 57.0 + - - +
318V MET* 3.7 21.2 - - - +
319V SER* 4.4 6.2 + - - -
331W LYS* 3.5 28.3 - - - +
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Residues in contact with ASP 316 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59V ASN* 3.5 13.9 + - - +
70V LEU* 4.3 21.2 - - - +
76V VAL* 3.5 26.8 - - - +
88V PHE* 4.0 26.1 - - + -
90V ILE* 5.0 5.0 - - - +
95V LEU* 5.5 8.3 - - - +
312V ASN* 2.8 19.0 + - - +
313V THR* 3.5 7.6 - - - +
314V VAL 2.7 1.2 + - - -
315V ALA* 1.3 78.8 - - - +
317V ILE* 1.3 64.2 + - - +
318V MET 3.0 2.0 - - - -
319V SER* 3.1 21.2 + - - -
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Residues in contact with ILE 317 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95V LEU* 3.9 34.4 - - + +
96V TYR 5.4 0.4 - - - +
313V THR* 2.7 34.1 + - + +
314V VAL* 2.7 17.8 + - + +
316V ASP* 1.3 72.3 - - - +
318V MET* 1.3 63.3 + - - +
319V SER 3.3 5.4 + - - +
325V ASP* 3.3 32.5 - - + +
326V GLU 4.6 9.6 - - - +
328V LYS 5.7 0.9 - - - +
329V LEU* 4.4 17.5 - - + -
332V ALA* 3.8 28.7 - - + -
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Residues in contact with MET 318 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63V ILE* 4.6 17.0 - - + -
65V ALA* 5.2 11.2 - - + +
314V VAL* 2.8 15.3 + - + +
315V ALA* 3.7 14.4 - - - +
317V ILE* 1.3 78.0 - - - +
319V SER* 1.3 73.4 + - - +
325V ASP* 2.8 28.0 - - - +
326V GLU* 5.7 5.8 - - + +
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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