Contacts of the helix formed by residues 308 - 321 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219J VAL* 3.8 17.3 - - - -
307J PRO* 1.4 70.6 - - - +
309J ILE* 1.4 62.8 + - - +
310J ALA 3.4 2.2 + - - -
311J ASP* 3.5 17.8 + - - +
312J ARG* 2.9 26.0 + - - +
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Residues in contact with ILE 309 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153J MET* 5.3 9.2 - - + -
219J VAL* 4.0 15.7 - - + +
261J LEU* 4.4 17.5 - - + -
262J PHE* 4.3 19.5 - - + -
274J ILE* 5.5 1.1 - - + -
299J LEU* 3.8 16.8 - - + -
303J THR 4.1 20.0 - - - +
304J THR* 3.2 30.3 - - - +
306J TYR* 3.1 22.6 + - + +
307J PRO 3.4 1.2 + - - -
308J GLY* 1.4 75.5 - - - +
310J ALA* 1.3 60.4 + - - +
313J MET* 2.8 39.5 + - + +
335J ARG* 4.3 4.7 - - - +
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Residues in contact with ALA 310 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299J LEU* 4.4 2.7 - - - -
308J GLY 3.4 0.6 - - - -
309J ILE* 1.3 83.4 - - + +
311J ASP* 1.3 60.1 + - - +
313J MET* 3.3 1.9 + - - +
314J GLN* 2.9 30.0 + - - +
329J ILE* 3.6 23.4 - - + +
331J ALA* 4.3 19.1 - - + -
335J ARG* 6.0 0.2 - - - +
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Residues in contact with ASP 311 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221J LEU* 4.0 20.2 - - + +
308J GLY* 3.5 17.9 + - - +
310J ALA* 1.3 81.7 - - - +
312J ARG* 1.3 58.4 + - - +
314J GLN* 3.5 8.1 - - - +
315J LYS* 2.9 29.8 + - - +
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Residues in contact with ARG 312 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219J VAL* 3.9 14.2 - - + +
220J ALA 2.6 37.3 + - - +
221J LEU* 3.7 25.8 + - + +
223J PHE* 4.7 5.2 - - - +
259J GLU* 2.8 29.9 + - - -
262J PHE* 3.5 39.6 - - + +
263J GLN* 4.8 5.3 - - - +
275J HIS* 5.6 0.8 - - - -
308J GLY 2.9 17.7 + - - +
309J ILE 4.1 1.8 - - - +
311J ASP* 1.3 74.7 - - - +
313J MET* 1.3 62.6 + - - +
315J LYS* 4.0 7.5 - - - +
316J GLU* 2.7 65.2 + - - +
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Residues in contact with MET 313 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153J MET* 3.8 39.0 - - + -
262J PHE* 4.0 14.4 - - + -
274J ILE* 4.0 17.5 - - + +
275J HIS* 4.1 12.6 - - - -
278J THR* 3.9 13.0 - - + +
297J THR* 5.2 0.9 - - + -
299J LEU* 3.9 16.6 - - + -
309J ILE* 2.8 28.7 + - + +
310J ALA* 3.6 5.2 - - - +
312J ARG* 1.3 74.8 - - - +
314J GLN* 1.3 62.3 + - - +
316J GLU* 3.0 5.2 + - - +
317J ILE* 2.9 43.6 + - + +
329J ILE* 4.3 14.6 - - + -
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Residues in contact with GLN 314 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310J ALA 2.9 18.3 + - - +
311J ASP* 3.5 8.7 - - - +
313J MET* 1.3 73.3 - - - +
315J LYS* 1.3 63.1 + - - +
317J ILE* 3.0 0.9 + - - +
318J THR* 2.7 52.7 + - - +
327J ILE* 3.0 34.1 + - - +
328J LYS* 4.6 0.4 - - - +
329J ILE* 3.9 25.0 - - + +
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Residues in contact with LYS 315 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221J LEU* 2.9 44.2 + - + +
222J ASP* 4.6 14.3 + - - +
311J ASP 2.9 21.0 + - - +
312J ARG* 3.8 6.7 - - - +
314J GLN* 1.3 73.3 - - - +
316J GLU* 1.3 90.4 + - + +
318J THR* 3.7 7.4 - - - +
319J ALA* 3.3 20.3 + - - +
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Residues in contact with GLU 316 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262J PHE* 4.7 1.3 - - + -
275J HIS* 3.7 39.7 + - + -
312J ARG* 2.7 60.5 + - + +
313J MET 3.0 4.1 + - - +
314J GLN 2.9 0.2 + - - -
315J LYS* 1.3 98.1 + - - +
317J ILE* 1.3 63.3 + - - +
319J ALA* 3.4 15.9 + - - +
320J LEU* 3.2 22.0 + - - +
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Residues in contact with ILE 317 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275J HIS* 4.1 15.7 - - - +
278J THR* 3.6 30.5 - - + -
279J PHE* 5.4 6.0 - - + +
282J ILE* 5.8 0.4 - - + -
294J TYR* 4.1 18.8 - - + -
297J THR* 4.2 7.0 - - + +
313J MET* 2.9 36.6 + - - +
314J GLN 3.9 1.6 - - - +
316J GLU* 1.3 77.0 - - - +
318J THR* 1.3 58.2 + - - +
319J ALA 3.2 0.3 + - - -
320J LEU* 3.3 6.2 + - + +
321J ALA* 2.9 28.1 + - - +
327J ILE* 3.6 28.7 - - + -
329J ILE* 4.1 15.3 - - + -
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Residues in contact with THR 318 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314J GLN* 2.7 41.7 + - - +
315J LYS* 3.7 7.9 - - - -
317J ILE* 1.3 78.0 - - - +
319J ALA* 1.3 60.9 + - - +
321J ALA* 3.9 10.6 - - - +
327J ILE* 3.6 18.0 - - + +
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Residues in contact with ALA 319 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315J LYS 3.3 14.3 + - - +
316J GLU* 3.7 15.5 - - - +
317J ILE 3.2 1.2 - - - -
318J THR* 1.3 78.3 - - - +
320J LEU* 1.3 64.2 + - + +
321J ALA 3.6 2.9 + - - +
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Residues in contact with LEU 320 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246H GLN* 6.0 0.5 - - - +
275J HIS* 3.9 38.4 - - + +
276J GLU* 3.5 22.2 - - - +
279J PHE* 3.4 47.8 - - + -
316J GLU 3.2 20.4 + - - +
317J ILE* 3.3 5.8 + - - +
319J ALA* 1.3 77.2 - - + +
321J ALA* 1.3 62.9 + - - +
322J PRO* 3.8 1.6 - - - +
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Residues in contact with ALA 321 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244H ASP 3.8 5.4 - - - +
279J PHE* 4.4 0.6 - - - -
294J TYR* 3.7 19.5 - - + -
317J ILE 2.9 18.9 + - - +
318J THR 3.9 10.2 - - - +
319J ALA 3.4 3.6 - - - +
320J LEU* 1.3 78.5 - - - +
322J PRO* 1.4 77.8 - - + +
323J SER* 3.5 3.1 + - - -
325J MET* 4.2 0.7 - - + -
327J ILE* 3.4 23.8 - - + -
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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