Contacts of the helix formed by residues 329 - 350 (chain A) in PDB entry 4LOU
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 SER 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A ASN 4.2 0.4 + - - -
328A PHE* 1.3 78.7 - - - +
330A MET* 1.3 58.3 + - - +
331A GLY* 3.1 6.1 + - - -
332A MET* 2.7 27.7 + - - +
333A LEU* 3.1 23.2 + - - +
373A MET* 4.5 0.9 - - - -
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Residues in contact with MET 330 (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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329A SER* 1.3 71.9 - - - +
331A GLY* 1.3 60.2 + - - +
333A LEU* 3.8 3.8 - - - -
334A VAL* 3.0 39.2 + - + +
370A ALA* 3.4 50.3 - - + +
373A MET* 4.2 22.2 - - - +
374A VAL* 3.6 19.7 - - + -
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Residues in contact with GLY 331 (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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329A SER* 3.1 6.9 + - - -
330A MET* 1.3 78.4 - - - +
332A MET* 1.3 59.1 + - - +
334A VAL* 3.3 4.9 + - - +
335A PHE* 2.8 32.6 + - - +
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Residues in contact with MET 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ALA* 5.4 5.6 - - + -
328A PHE* 3.5 35.9 - - + -
329A SER* 2.7 26.1 + - - +
331A GLY* 1.3 72.8 - - - +
333A LEU* 1.3 54.1 + - - +
335A PHE* 3.2 31.3 + - + -
336A ILE* 2.7 50.0 + - + +
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Residues in contact with LEU 333 (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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323A ALA* 4.4 7.4 - - + -
328A PHE* 3.6 30.5 - - + -
329A SER 3.1 13.6 + - - +
330A MET* 3.9 5.4 - - - +
332A MET* 1.3 76.7 - - - +
334A VAL* 1.3 62.3 + - - +
336A ILE* 4.7 1.3 - - + -
337A PHE* 3.2 19.8 + - - +
366A VAL* 3.2 29.7 - - + +
369A THR* 3.5 33.0 - - + -
370A ALA* 3.6 31.6 - - + +
373A MET* 3.8 22.2 - - + -
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Residues in contact with VAL 334 (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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330A MET* 3.0 38.6 + - + +
331A GLY* 3.8 4.9 - - - +
333A LEU* 1.3 73.5 - - + +
335A PHE* 1.3 70.3 + - - +
337A PHE* 3.3 5.7 + - - +
338A VAL* 3.2 31.3 + - + +
370A ALA* 5.6 2.7 - - + -
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Residues in contact with PHE 335 (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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309A ALA* 4.7 13.2 - - + -
311A ALA* 6.0 0.9 - - + -
312A THR* 3.8 28.7 - - + -
331A GLY 2.8 22.1 + - - +
332A MET* 3.5 31.0 - - + +
334A VAL* 1.3 76.9 - - - +
336A ILE* 1.3 70.3 + - + +
338A VAL* 3.9 3.5 - - + +
339A ALA* 3.0 34.6 + - + +
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Residues in contact with ILE 336 (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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311A ALA* 3.6 31.6 - - + +
312A THR* 5.1 0.9 - - - -
319A LEU* 4.5 4.7 - - + -
328A PHE* 3.9 33.0 - - + -
332A MET* 2.7 35.4 + - + +
333A LEU* 4.1 4.9 - - - +
335A PHE* 1.3 86.3 - - + +
337A PHE* 1.3 57.8 + - - +
339A ALA* 3.9 3.3 - - - -
340A ARG* 2.8 59.4 + - + +
366A VAL* 4.0 20.6 - - + -
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Residues in contact with PHE 337 (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* 6.0 0.4 - + - -
265A PHE* 3.9 34.1 - + - -
333A LEU 3.2 18.6 + - - +
334A VAL* 3.6 6.3 - - - +
335A PHE 3.2 0.4 + - - -
336A ILE* 1.3 77.0 - - - +
338A VAL* 1.3 59.9 + - + +
340A ARG* 3.6 0.5 - - - -
341A VAL* 2.8 49.1 + - + +
363A LEU* 3.2 51.6 - - + +
366A VAL* 4.0 13.0 - - + -
367A LEU* 3.8 30.7 - - + -
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Residues in contact with VAL 338 (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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334A VAL* 3.2 22.3 + - + +
335A PHE* 3.9 3.4 - - + +
337A PHE* 1.3 85.5 - - + +
339A ALA* 1.3 66.0 + - + +
341A VAL* 3.2 9.7 + - - +
342A ILE* 3.1 36.3 + - + +
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Residues in contact with ALA 339 (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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312A THR* 3.5 31.9 - - + -
335A PHE* 3.0 28.8 + - + +
336A ILE 3.9 1.1 - - - +
338A VAL* 1.3 80.3 - - - +
340A ARG* 1.3 58.6 + - - +
342A ILE* 3.5 8.9 + - - +
343A THR* 3.1 32.4 + - + +
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Residues in contact with ARG 340 (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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144A VAL* 3.6 15.5 - - - +
311A ALA 3.0 33.0 + - - +
312A THR* 3.8 11.0 - - - +
313A SER 3.7 15.4 + - - +
314A GLY 3.0 28.0 + - - -
315A GLY 3.7 4.0 + - - -
316A GLY* 3.4 27.1 - - - +
319A LEU* 4.0 9.8 - - - +
336A ILE* 2.8 36.1 + - - +
337A PHE 4.0 1.3 - - - +
339A ALA* 1.3 70.7 - - - +
341A VAL* 1.3 63.4 + - - +
342A ILE 3.3 0.2 - - - -
343A THR* 3.6 6.7 + - - +
344A THR* 2.4 35.4 + - - +
359A PRO* 4.3 11.7 + - - +
362A ALA* 4.3 11.3 - - - +
363A LEU* 4.2 14.2 - - + +
366A VAL* 5.8 1.1 - - - -
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Residues in contact with VAL 341 (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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265A PHE* 4.4 11.9 - - + -
269A PHE* 4.5 7.4 - - + -
272A TRP* 3.8 32.5 - - + -
337A PHE* 2.8 40.2 + - + +
338A VAL* 3.2 8.5 + - - +
340A ARG* 1.3 77.6 - - - +
342A ILE* 1.3 66.8 + - + +
344A THR* 3.8 3.4 - - - -
345A LEU* 3.1 30.8 + - + +
363A LEU* 3.9 20.4 - - + +
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Residues in contact with ILE 342 (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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301A LEU* 6.5 1.1 - - + -
338A VAL* 3.1 25.9 + - + +
339A ALA* 3.5 12.1 - - - +
341A VAL* 1.3 85.0 - - + +
343A THR* 1.3 69.6 + - + +
345A LEU* 3.5 7.8 + - + +
346A LEU* 3.1 33.2 + - + +
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Residues in contact with THR 343 (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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144A VAL* 3.3 20.5 - - + +
301A LEU* 5.5 7.6 - - + -
302A CYS* 5.3 5.4 - - - -
305A LEU* 3.9 23.6 - - + -
312A THR* 3.0 25.9 + - - +
339A ALA* 3.1 17.5 + - + +
340A ARG* 3.6 6.8 + - - -
342A ILE* 1.3 81.1 - - + +
344A THR* 1.3 58.9 + - - +
346A LEU* 3.8 8.0 - - + +
347A CYS* 3.1 32.2 + - - +
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Residues in contact with THR 344 (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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144A VAL* 3.7 19.1 - - - +
269A PHE* 4.3 14.1 - - + -
340A ARG* 2.4 29.0 + - - +
341A VAL* 3.8 4.9 - - - -
342A ILE 3.2 0.2 - - - -
343A THR* 1.3 76.6 + - - +
345A LEU* 1.3 60.4 + - + +
347A CYS* 3.5 1.0 + - - +
348A PHE* 2.9 35.1 + - + +
356A ILE* 4.1 21.8 - - + -
359A PRO* 4.0 26.8 - - + +
360A MET* 5.8 0.4 - - + -
363A LEU* 4.2 11.4 - - + +
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Residues in contact with LEU 345 (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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269A PHE* 3.6 27.8 - - + -
272A TRP* 3.7 36.6 - - + -
273A VAL* 3.8 29.8 - - + +
276A MET* 4.1 23.1 - - + +
341A VAL* 3.1 22.0 + - + +
342A ILE* 3.7 6.5 - - - +
344A THR* 1.3 72.6 - - - +
346A LEU* 1.3 60.9 + - + +
348A PHE* 4.9 1.6 - - + -
349A SER* 2.8 38.5 + - - +
356A ILE* 6.2 0.4 - - + -
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Residues in contact with LEU 346 (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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276A MET* 4.6 19.1 - - + -
280A LEU* 4.1 10.7 - - + +
298A ILE* 4.0 32.5 - - + +
301A LEU* 4.0 26.9 - - + -
342A ILE* 3.1 26.4 + - + +
343A THR* 3.8 8.7 - - + +
344A THR 3.3 0.2 - - - -
345A LEU* 1.3 82.5 - - + +
347A CYS* 1.3 63.5 + - - +
350A SER* 3.1 24.8 + - - -
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Residues in contact with CYS 347 (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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143A MET* 3.4 24.2 - - + -
144A VAL 3.4 22.9 - - - +
145A LEU* 3.3 26.3 - - + +
298A ILE* 4.1 3.4 - - - -
302A CYS* 3.4 33.4 - - - -
343A THR 3.1 17.0 + - - +
346A LEU* 1.3 80.3 - - - +
348A PHE* 1.3 60.3 + - - +
350A SER* 3.8 3.9 + - - -
352A ALA* 3.7 20.1 + - - +
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Residues in contact with PHE 348 (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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106A GLY* 4.7 5.4 - - - -
107A SER* 3.8 30.1 - - - -
145A LEU* 3.8 8.5 - - + -
273A VAL* 3.8 29.2 - - + -
277A GLN* 4.9 5.6 + - - -
344A THR* 2.9 20.5 + - + +
345A LEU* 4.9 1.1 - - + -
347A CYS* 1.3 76.1 - - - +
349A SER* 1.3 63.9 + - - +
350A SER 3.1 2.3 + - - -
351A GLY* 3.4 12.5 + - - -
352A ALA 5.1 2.5 - - - +
354A GLY 3.6 25.1 - - - -
355A GLY 4.3 2.9 - - - -
356A ILE* 3.7 49.1 - - + -
444A LEU* 4.6 3.1 - - + -
445A TYR* 4.9 3.4 - + - -
448A ILE* 4.4 17.9 - - + -
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Residues in contact with SER 349 (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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273A VAL* 2.9 45.4 + - - +
276A MET* 3.6 20.7 - - - +
277A GLN* 3.5 33.5 - - - +
280A LEU* 4.3 4.0 - - - +
345A LEU* 2.8 24.6 + - - -
348A PHE* 1.3 72.9 - - - +
350A SER* 1.3 63.3 + - - +
351A GLY* 3.5 0.5 + - - -
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Residues in contact with SER 350 (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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94A TYR* 2.4 34.7 + - - -
280A LEU* 3.5 16.3 - - - +
284A HIS* 4.8 1.6 + - - -
291A TRP* 3.3 29.5 + - - -
294A MET* 4.5 4.2 - - - +
298A ILE* 3.7 13.2 - - - -
346A LEU 3.1 21.5 + - - -
347A CYS 4.1 1.6 - - - -
348A PHE 3.1 0.4 - - - -
349A SER* 1.3 79.6 - - - +
351A GLY* 1.3 58.6 + - - +
352A ALA* 3.1 8.1 + - - +
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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