Contacts of the helix formed by residues 308 - 321 (chain G) in PDB entry 3LUE
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 GLY 308 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219G VAL* 3.8 17.4 - - - +
221G LEU* 5.7 0.2 - - - +
306G TYR 3.5 0.2 + - - -
307G PRO* 1.4 71.0 - - - +
309G ILE* 1.4 62.6 + - - +
310G ALA 3.4 2.2 + - - -
311G ASP* 3.5 18.3 + - - +
312G ARG* 2.9 26.2 + - - +
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Residues in contact with ILE 309 (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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153G MET* 5.3 9.4 - - + -
219G VAL* 4.1 15.9 - - + -
261G LEU* 4.4 16.8 - - + -
262G PHE* 4.3 18.6 - - + -
274G ILE* 5.5 1.6 - - + -
299G LEU* 3.8 17.0 - - + -
303G THR 4.1 19.5 - - - +
304G THR* 3.2 30.5 - - - +
306G TYR* 3.1 23.2 + - + +
307G PRO 3.5 1.2 + - - -
308G GLY* 1.4 75.9 - - - +
310G ALA* 1.3 59.4 + - - +
312G ARG* 4.5 0.4 - - - +
313G MET* 2.8 38.9 + - + +
335G ARG* 4.3 5.4 - - - +
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Residues in contact with ALA 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299G LEU* 4.4 3.1 - - - -
308G GLY 3.4 0.4 - - - -
309G ILE* 1.3 83.6 - - + +
311G ASP* 1.3 60.2 + - - +
313G MET* 3.6 2.1 - - - +
314G GLN* 2.9 29.6 + - - +
329G ILE* 3.6 22.7 - - + +
331G ALA* 4.3 20.4 - - + -
335G ARG* 6.0 0.2 - - - +
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Residues in contact with ASP 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221G LEU* 4.0 19.3 - - + +
308G GLY* 3.5 18.4 + - - +
310G ALA* 1.3 81.7 - - - +
312G ARG* 1.3 57.4 + - - +
314G GLN* 3.5 8.1 + - - +
315G LYS* 2.9 29.8 + - - +
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Residues in contact with ARG 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G VAL* 3.9 13.7 - - + +
220G ALA 2.6 37.3 + - - +
221G LEU* 3.7 26.5 + - + +
223G PHE* 4.7 5.2 - - - +
259G GLU* 2.8 28.5 + - - -
262G PHE* 3.5 40.1 - - + +
263G GLN* 4.8 5.3 - - - +
275G HIS* 5.6 0.8 - - - -
308G GLY 2.9 18.1 + - - +
309G ILE* 4.1 1.8 - - - +
311G ASP* 1.3 74.1 - - - +
313G MET* 1.3 63.5 + - - +
315G LYS* 4.0 6.4 - - - +
316G GLU* 2.7 64.1 + - - +
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Residues in contact with MET 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153G MET* 3.8 38.6 - - + -
262G PHE* 4.0 15.3 - - + -
274G ILE* 4.0 17.3 - - + +
275G HIS* 4.1 12.1 - - - -
278G THR* 3.9 13.2 - - + +
297G THR* 5.2 0.9 - - + -
299G LEU* 3.9 16.4 - - + -
309G ILE* 2.8 28.2 + - + +
310G ALA* 3.6 5.4 - - - +
312G ARG* 1.3 74.4 - - - +
314G GLN* 1.3 62.6 + - - +
316G GLU* 3.0 5.4 + - - +
317G ILE* 2.9 43.2 + - + +
329G ILE* 4.3 13.9 - - + -
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Residues in contact with GLN 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310G ALA 2.9 17.1 + - - +
311G ASP* 3.5 9.2 - - - +
313G MET* 1.3 73.6 - - - +
315G LYS* 1.3 62.1 + - - +
317G ILE* 3.0 1.0 + - - +
318G THR* 2.7 53.9 + - - +
327G ILE* 3.0 34.3 + - - +
328G LYS* 4.6 0.2 - - - +
329G ILE* 3.9 24.4 - - + +
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Residues in contact with LYS 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221G LEU* 2.9 44.7 + - + +
222G ASP* 4.6 14.9 + - - +
311G ASP 2.9 21.3 + - - +
312G ARG* 3.8 7.5 - - - +
314G GLN* 1.3 72.5 - - + +
316G GLU* 1.3 91.1 + - + +
318G THR* 3.7 7.3 - - - -
319G ALA* 3.3 20.3 + - - +
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Residues in contact with GLU 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262G PHE* 4.7 1.6 - - + -
275G HIS* 3.7 39.8 + - + -
312G ARG* 2.7 61.1 + - + +
313G MET 3.0 4.2 + - - +
314G GLN 2.9 0.2 + - - -
315G LYS* 1.3 97.4 + - - +
317G ILE* 1.3 64.8 + - - +
319G ALA* 3.4 15.5 + - - +
320G LEU* 3.2 22.0 + - - +
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Residues in contact with ILE 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G HIS* 4.1 17.5 - - - +
278G THR* 3.6 31.2 - - + -
279G PHE* 5.4 6.5 - - + +
282G ILE* 5.8 0.7 - - + -
294G TYR* 4.0 18.6 - - + -
297G THR* 4.2 6.7 - - + +
313G MET* 2.9 37.4 + - - +
314G GLN 3.9 1.8 - - - +
316G GLU* 1.3 76.5 - - - +
318G THR* 1.3 59.7 + - - +
319G ALA 3.2 0.5 + - - -
320G LEU* 3.3 6.0 + - + +
321G ALA* 2.9 28.4 + - - +
327G ILE* 3.6 29.4 - - + -
329G ILE* 4.1 15.3 - - + -
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Residues in contact with THR 318 (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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314G GLN* 2.7 41.0 + - - +
315G LYS* 3.7 8.7 - - - -
317G ILE* 1.3 77.4 - - - +
319G ALA* 1.3 60.4 + - - +
321G ALA* 3.9 10.6 - - - +
327G ILE* 3.6 19.2 - - + +
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Residues in contact with ALA 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315G LYS 3.3 14.0 + - - +
316G GLU* 3.7 15.7 - - - +
317G ILE 3.2 1.2 - - - -
318G THR* 1.3 77.7 - - - +
320G LEU* 1.3 62.7 + - + +
321G ALA 4.2 2.6 - - - +
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Residues in contact with LEU 320 (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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246E GLN* 6.0 0.5 - - - +
275G HIS* 3.9 38.6 - - + +
276G GLU* 3.5 22.4 - - - +
279G PHE* 3.4 46.6 - - + -
316G GLU 3.2 21.0 + - - +
317G ILE* 3.3 5.6 + - - +
319G ALA* 1.3 76.1 - - + +
321G ALA* 1.3 64.3 + - - +
322G PRO* 3.8 1.4 - - - +
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Residues in contact with ALA 321 (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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244E ASP 3.8 5.4 - - - +
279G PHE* 4.4 0.6 - - - -
294G TYR* 3.7 20.0 - - + -
317G ILE 2.9 18.3 + - - +
318G THR 3.9 10.7 - - - +
319G ALA 3.4 3.2 - - - +
320G LEU* 1.3 79.2 - - - +
322G PRO* 1.4 76.2 - - + +
323G SER* 3.5 3.1 + - - -
325G MET* 4.2 0.4 - - + -
327G ILE* 3.4 24.2 - - + -
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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