Contacts of the helix formed by residues 308 - 321 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A VAL* 3.8 17.5 - - - -
220A ALA 5.9 0.2 - - - -
221A LEU* 5.7 0.2 - - - +
307A PRO* 1.4 70.4 - - - +
309A ILE* 1.4 62.6 + - - +
310A ALA 3.4 2.7 - - - -
311A ASP* 3.5 17.8 + - - +
312A ARG* 2.9 25.3 + - - +
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Residues in contact with ILE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A MET* 5.3 9.2 - - + -
219A VAL* 4.1 15.3 - - + -
261A LEU* 4.4 17.7 - - + -
262A PHE* 4.3 19.3 - - + -
274A ILE* 5.5 1.1 - - + -
299A LEU* 3.8 16.2 - - + -
303A THR 4.1 20.0 - - - +
304A THR* 3.2 29.8 - - + +
306A TYR* 3.1 22.9 + - + +
307A PRO 3.4 1.0 + - - -
308A GLY* 1.4 75.9 - - - +
310A ALA* 1.3 60.6 + - - +
312A ARG* 4.6 0.2 - - - -
313A MET* 2.8 39.1 + - + +
335A ARG* 4.3 5.4 - - - +
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 4.4 2.7 - - - -
308A GLY 3.4 0.4 - - - -
309A ILE* 1.3 83.3 - - + +
311A ASP* 1.3 60.8 + - - +
313A MET* 3.3 1.7 + - - +
314A GLN* 2.9 29.8 + - - +
329A ILE* 3.6 23.2 - - + +
331A ALA* 4.3 19.1 - - + -
335A ARG* 6.0 0.2 - - - +
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Residues in contact with ASP 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A LEU* 4.0 19.6 - - + +
308A GLY* 3.5 17.4 + - - +
310A ALA* 1.3 80.7 - - - +
312A ARG* 1.3 56.7 - - - +
314A GLN* 3.5 8.0 + - - +
315A LYS* 2.9 30.0 + - - +
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Residues in contact with ARG 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A VAL* 3.9 15.1 - - + +
220A ALA 2.6 36.9 + - - +
221A LEU* 3.7 25.3 + - + +
223A PHE* 4.7 5.2 - - - +
259A GLU* 2.8 28.5 + - - -
262A PHE* 3.5 39.7 - - + +
263A GLN* 4.8 5.7 - - - +
275A HIS* 5.6 0.6 - - - -
308A GLY 2.9 17.7 + - - +
309A ILE 4.1 1.8 - - - +
311A ASP* 1.3 74.2 - - - +
313A MET* 1.3 62.4 + - - +
315A LYS* 4.0 6.4 - - - +
316A GLU* 2.7 65.7 + - - +
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Residues in contact with MET 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A MET* 3.8 40.6 - - + -
262A PHE* 4.0 15.7 - - + -
274A ILE* 4.0 16.6 - - + +
275A HIS* 4.1 12.1 - - - -
278A THR* 3.9 11.9 - - + +
297A THR* 5.2 0.9 - - + -
299A LEU* 3.9 16.2 - - + -
309A ILE* 2.8 27.6 + - + +
310A ALA* 3.6 5.4 - - - +
312A ARG* 1.3 73.6 - - - +
314A GLN* 1.3 63.2 + - - +
316A GLU* 3.0 5.2 + - - +
317A ILE* 2.9 43.4 + - + +
329A ILE* 4.3 15.0 - - + -
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Residues in contact with GLN 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ALA 2.9 17.1 + - - +
311A ASP* 3.5 8.3 - - - +
313A MET* 1.3 73.9 - - - +
315A LYS* 1.3 63.1 + - - +
317A ILE 3.0 0.3 + - - -
318A THR* 2.7 53.5 + - - +
327A ILE* 3.0 33.9 + - - +
328A LYS* 4.6 0.2 - - - +
329A ILE* 3.9 25.5 - - + +
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Residues in contact with LYS 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A LEU* 2.9 44.5 + - + +
222A ASP* 4.6 14.3 + - - +
311A ASP 2.9 21.0 + - - +
312A ARG* 3.8 7.1 - - - +
314A GLN* 1.3 72.3 - - - +
316A GLU* 1.3 89.4 + - + +
318A THR* 3.7 7.0 - - - -
319A ALA* 3.3 20.6 + - - +
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Residues in contact with GLU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A PHE* 4.7 1.3 - - + -
275A HIS* 3.7 39.4 + - + -
312A ARG* 2.7 59.5 + - + +
313A MET 3.0 4.7 + - - +
314A GLN 2.9 0.2 + - - -
315A LYS* 1.3 98.6 + - - +
317A ILE* 1.3 64.8 + - - +
319A ALA* 3.4 16.4 + - - +
320A LEU* 3.2 21.7 + - - +
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Residues in contact with ILE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A HIS* 4.1 16.4 - - - +
278A THR* 3.6 30.7 - - + -
279A PHE* 5.4 6.3 - - + +
282A ILE* 5.8 0.9 - - + -
294A TYR* 4.0 18.4 - - + -
297A THR* 4.2 6.7 - - + +
313A MET* 2.9 36.3 + - - +
314A GLN 3.9 1.8 - - - +
316A GLU* 1.3 76.6 - - - +
318A THR* 1.3 59.7 + - - +
319A ALA 3.2 0.3 + - - -
320A LEU* 3.3 6.8 + - + +
321A ALA* 2.9 27.9 + - - +
327A ILE* 3.6 28.5 - - + -
329A ILE* 4.1 15.3 - - + -
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Residues in contact with THR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A GLN* 2.7 39.8 + - - +
315A LYS* 3.7 8.5 - - - -
317A ILE* 1.3 77.4 - - - +
319A ALA* 1.3 58.2 + - - +
321A ALA* 3.9 10.4 - - - +
327A ILE* 3.6 19.3 - - + +
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A LYS* 3.3 14.0 + - + +
316A GLU* 3.7 15.0 - - - +
317A ILE 3.2 1.0 - - - -
318A THR* 1.3 79.0 - - - +
320A LEU* 1.3 62.8 + - + +
321A ALA 3.6 2.8 + - - +
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A HIS* 3.9 38.6 - - + +
276A GLU* 3.5 22.7 - - - +
279A PHE* 3.4 46.3 - - + -
316A GLU 3.2 20.4 + - - +
317A ILE* 3.3 5.6 + - - +
319A ALA* 1.3 76.5 - - + +
321A ALA* 1.3 62.5 + - - +
322A PRO* 3.8 1.6 - - - +
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Residues in contact with ALA 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PHE* 4.4 0.6 - - - -
294A TYR* 3.7 19.3 - - + -
317A ILE 2.9 17.7 + - - +
318A THR 3.9 10.3 - - - +
319A ALA 3.4 2.7 - - - +
320A LEU* 1.3 78.8 - - - +
322A PRO* 1.4 80.5 - - + +
323A SER* 3.5 3.6 + - - -
325A MET* 4.2 3.1 - - + -
327A ILE* 3.4 24.5 - - + -
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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