Contacts of the helix formed by residues 322 - 338 (chain A) in PDB entry 1L2L
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 ASP 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A ARG* 3.6 31.5 + - - +
315A ILE* 4.3 4.1 + - - -
318A LYS* 4.3 21.4 + - + +
320A PRO 3.1 6.0 + - - -
321A ALA* 1.3 66.2 - - - +
323A PRO* 1.3 68.6 - - - +
324A ILE* 3.1 26.2 + - - +
325A ALA* 3.2 17.0 + - + +
326A VAL* 2.9 29.8 + - - +
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Residues in contact with PRO 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PRO* 5.0 3.4 - - + +
321A ALA 2.8 7.1 - - - +
322A ASP* 1.3 83.4 - - - +
324A ILE* 1.3 79.6 + - + +
326A VAL* 3.6 2.2 - - + +
327A ILE* 3.0 32.0 + - - +
349A TYR* 3.6 14.4 - - + +
351A LEU* 5.2 1.3 - - + -
402A VAL* 3.8 26.2 - - + -
405A ILE* 3.6 28.9 - - + -
406A LEU* 4.0 17.3 - - + -
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Residues in contact with ILE 324 (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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322A ASP* 3.1 13.9 + - - +
323A PRO* 1.3 77.4 - - + +
325A ALA* 1.3 60.9 + - - +
327A ILE* 3.4 7.8 + - - +
328A GLU* 2.9 51.7 + - + +
405A ILE* 3.4 34.8 - - + -
406A LEU* 5.8 2.7 - - + -
409A GLU* 4.7 24.5 - - + +
410A PHE* 6.4 0.9 - - + -
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Residues in contact with ALA 325 (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 LEU* 4.3 1.8 - - + -
314A ARG* 3.7 18.2 - - + +
315A ILE* 3.2 30.6 - - + +
322A ASP* 3.2 32.1 + - + +
324A ILE* 1.3 79.6 - - - +
326A VAL* 1.3 55.7 + - - +
328A GLU* 3.2 14.8 + - - +
329A GLY 2.9 24.1 + - - -
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Residues in contact with VAL 326 (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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299A LEU* 3.8 10.8 - - + +
315A ILE* 3.9 18.2 - - + +
321A ALA* 3.9 10.5 - - + -
322A ASP 2.9 20.7 + - - +
323A PRO* 3.6 5.6 - - + +
325A ALA* 1.3 74.1 - - - +
327A ILE* 1.3 58.8 + - - +
329A GLY* 3.1 2.6 + - - -
330A LEU* 2.8 41.9 + - + +
344A PHE* 3.6 51.8 - - + -
349A TYR* 3.7 11.0 - - - +
351A LEU* 4.4 7.4 - - + -
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Residues in contact with ILE 327 (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 PRO 3.0 19.5 + - - +
324A ILE* 3.8 5.6 - - - +
326A VAL* 1.3 75.6 - - - +
328A GLU* 1.3 59.7 + - + +
330A LEU* 3.0 11.7 + - + +
331A LEU* 2.8 46.8 + - + +
351A LEU* 3.9 21.1 - - + -
353A LEU* 5.1 7.9 - - + -
406A LEU* 3.6 31.4 - - + -
410A PHE* 3.8 30.1 - - + -
419A ILE* 5.6 4.5 - - + -
424A LEU* 4.4 13.5 - - + -
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Residues in contact with GLU 328 (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 LEU* 3.5 28.4 - - + +
314A ARG* 4.8 8.5 + - - -
324A ILE* 2.9 39.0 + - + +
325A ALA* 3.6 8.6 - - - +
327A ILE* 1.3 76.0 - - + +
329A GLY* 1.3 63.5 + - - +
331A LEU* 3.2 13.2 + - + +
332A LYS* 3.0 23.0 + - - +
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Residues in contact with GLY 329 (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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299A LEU* 4.3 20.0 - - - +
303A VAL* 4.8 8.1 - - - +
306A MET* 5.8 0.7 - - - +
311A LEU* 4.1 14.5 - - - +
315A ILE* 5.1 2.7 - - - -
325A ALA 2.9 14.1 + - - -
326A VAL 3.1 3.8 + - - -
328A GLU* 1.3 78.3 - - - +
330A LEU* 1.3 59.6 + - - +
332A LYS* 3.3 6.2 + - - +
333A LEU* 3.1 19.9 + - - +
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Residues in contact with LEU 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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294A LEU* 4.4 9.0 - - + -
299A LEU* 3.9 24.2 - - + -
326A VAL* 2.8 36.3 + - + +
327A ILE* 3.0 14.8 + - + +
329A GLY* 1.3 77.6 - - - +
331A LEU* 1.3 56.6 + - - +
333A LEU* 3.1 9.9 + - + +
334A ILE* 3.0 32.2 + - - +
342A ILE* 3.8 28.8 - - + +
344A PHE* 4.2 14.8 - - + -
351A LEU* 4.9 9.0 - - + +
353A LEU* 3.7 29.2 - - + +
424A LEU* 6.3 0.4 - - + -
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Residues in contact with LEU 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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327A ILE* 2.8 35.6 + - + +
328A GLU* 3.6 10.5 - - + +
330A LEU* 1.3 72.3 - - - +
332A LYS* 1.3 63.6 + - - +
334A ILE* 3.0 43.0 - - + +
335A LYS* 3.1 11.8 + - - +
353A LEU* 4.5 11.2 - - + -
410A PHE* 6.4 0.2 - - + -
419A ILE* 4.3 28.5 - - + +
420A GLU* 4.2 19.7 - - + +
422A TYR* 6.2 0.2 - - + -
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Residues in contact with LYS 332 (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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303A VAL* 5.4 2.7 - - + -
306A MET* 3.9 23.9 + - - +
308A GLU* 4.1 36.6 - - + -
311A LEU* 5.1 3.8 - - + -
328A GLU 3.0 12.9 + - - +
329A GLY* 3.5 11.2 - - - +
330A LEU 3.2 0.2 - - - -
331A LEU* 1.3 76.9 - - - +
333A LEU* 1.3 62.8 + - - +
335A LYS* 3.3 20.3 + - + +
336A GLU* 3.1 49.6 + - - +
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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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270A PHE* 6.0 0.2 - - + -
283A VAL* 4.4 3.6 - - + -
286A LEU* 3.9 25.1 - - + -
292A VAL* 4.9 4.7 - - + -
294A LEU* 5.7 6.3 - - + -
299A LEU* 5.8 3.6 - - + -
302A VAL* 3.7 30.3 - - + -
306A MET* 4.0 18.8 - - + -
329A GLY 3.1 11.3 + - - +
330A LEU* 3.1 15.7 + - + +
332A LYS* 1.3 79.0 - - - +
334A ILE* 1.3 61.2 + - - +
336A GLU* 3.3 1.9 + - - -
337A THR* 2.9 43.8 + - + +
339A VAL* 3.8 15.7 - - + -
342A ILE* 4.3 8.5 - - + -
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Residues in contact with ILE 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 LEU 3.0 13.2 + - - +
331A LEU* 3.0 48.9 - - + +
333A LEU* 1.3 75.7 - - - +
335A LYS* 1.3 60.0 + - + +
337A THR* 4.1 4.9 - - - -
338A GLY* 2.6 30.7 + - - +
339A VAL* 4.3 5.2 - - - +
342A ILE* 3.4 23.1 - - + -
353A LEU* 4.9 6.1 - - + -
420A GLU* 4.3 11.2 - - + +
422A TYR* 4.0 48.9 - - + +
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Residues in contact with LYS 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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331A LEU 3.1 13.8 + - - +
332A LYS* 3.5 21.3 - - + +
333A LEU 3.2 0.2 - - - -
334A ILE* 1.3 85.3 - - + +
336A GLU* 1.3 59.5 + - - +
337A THR 3.9 0.2 + - - -
338A GLY 4.9 0.3 + - - -
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Residues in contact with GLU 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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280A LEU* 4.5 4.7 - - - +
283A VAL* 3.7 11.8 - - - +
284A LYS* 4.0 24.7 - - + +
287A LYS* 3.8 13.9 - - - +
306A MET* 3.0 47.3 - - + +
332A LYS* 3.1 24.1 + - - +
333A LEU 4.1 0.2 - - - +
334A ILE 3.2 0.2 - - - -
335A LYS* 1.3 77.9 - - - +
337A THR* 1.3 61.2 + - + +
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Residues in contact with THR 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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283A VAL* 3.2 38.4 - - + +
284A LYS* 4.7 1.1 - - - -
286A LEU* 3.8 12.3 - - + -
287A LYS* 3.3 38.3 - - + +
333A LEU* 2.9 36.6 + - + +
336A GLU* 1.3 85.2 - - + +
338A GLY* 1.3 63.5 + - - +
339A VAL* 3.0 14.7 + - - +
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Residues in contact with GLY 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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287A LYS* 5.6 0.4 - - - -
334A ILE 2.6 24.0 + - - -
335A LYS 4.7 0.4 + - - -
336A GLU 4.0 0.2 - - - -
337A THR* 1.3 72.7 + - - +
339A VAL* 1.3 67.1 + - - +
340A LYS* 3.1 18.9 + - - +
422A TYR* 3.6 9.8 + - - -
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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