Contacts of the helix formed by residues 330 - 348 (chain N) in PDB entry 3L73
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 330 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301N HIS 5.7 0.4 - - - -
302N LYS 4.0 13.1 + - - -
303N LEU* 3.2 26.4 + - - +
326N ALA* 4.6 0.9 - - - -
327N ASP* 3.1 29.7 + - - +
329N LEU* 1.3 80.3 - - - +
331N ILE* 1.3 65.5 + - - +
332N ASP 3.4 1.8 - - - -
333N ASP* 3.7 8.8 + - - +
334N MET* 3.2 24.9 + - - +
430N GLN* 3.9 0.4 - - - -
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Residues in contact with ILE 331 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251N ALA* 3.8 18.4 - - + -
253N VAL* 4.3 5.6 - - + -
324N PHE* 4.0 22.3 - - + -
326N ALA* 4.7 5.8 - - + -
327N ASP 3.5 11.2 + - - +
328N PRO* 3.4 19.7 - - + +
330N SER* 1.3 79.7 - - - +
332N ASP* 1.3 63.2 + - - +
334N MET* 3.7 4.0 - - - +
335N MET* 3.1 22.3 + - - +
427N PRO 3.7 6.7 - - - +
428N ILE* 3.7 35.2 - - + -
430N GLN* 3.4 3.4 + - + +
431N LEU* 3.4 31.4 - - + +
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Residues in contact with ASP 332 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331N ILE* 1.3 76.5 - - - +
333N ASP* 1.3 60.9 + - - +
335N MET* 3.8 6.6 - - - +
336N PHE* 2.9 34.5 + - - +
430N GLN* 2.9 39.3 + - + +
431N LEU* 5.2 5.8 - - - +
432N LEU 5.4 1.9 + - - -
6P ARG* 5.5 2.3 + - - -
7P LYS* 3.2 27.4 + - - +
21P ASP* 4.5 7.3 - - - +
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Residues in contact with ASP 333 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303N LEU* 3.7 21.1 - - + -
329N LEU 4.5 11.6 - - - +
330N SER* 3.7 6.1 + - - +
331N ILE 3.5 0.4 - - - -
332N ASP* 1.3 76.9 - - - +
334N MET* 1.3 57.5 + - - +
336N PHE* 3.3 5.6 - - - +
337N CYS* 3.0 35.2 + - - -
430N GLN* 4.8 2.6 + - - +
3P PRO* 3.1 30.3 - - + +
4P ASN* 3.6 7.6 - - - +
7P LYS* 3.5 27.9 + - - +
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Residues in contact with MET 334 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294N LEU* 3.4 44.9 - - + -
298N ALA* 4.9 1.1 - - - -
303N LEU* 3.8 30.6 - - + +
304N CYS* 3.6 25.1 - - + -
307N PHE* 4.2 15.0 - - + -
322N PHE* 6.1 0.2 - - + -
324N PHE* 3.6 35.0 - - + -
330N SER 3.2 18.2 + - - +
331N ILE 3.7 3.8 - - - +
333N ASP* 1.3 75.3 - - - +
335N MET* 1.3 67.0 + - - +
337N CYS* 3.1 3.5 + - - +
338N ALA* 2.8 30.9 + - + +
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Residues in contact with MET 335 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253N VAL* 3.5 31.9 - - + -
255N LEU* 4.6 6.3 - - + -
322N PHE* 4.2 15.0 - - - -
324N PHE* 3.9 12.3 - - + -
331N ILE 3.1 15.1 + - - +
332N ASP* 3.8 6.5 - - - +
334N MET* 1.3 77.8 - - - +
336N PHE* 1.3 65.4 + - - +
338N ALA* 3.2 2.9 + - - +
339N GLN* 2.9 63.0 + - - +
422N LEU* 4.0 13.9 - - + -
431N LEU* 3.7 27.4 - - + -
437N ILE* 4.4 11.4 - - + -
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Residues in contact with PHE 336 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332N ASP* 2.9 23.6 + - - +
333N ASP* 3.3 7.4 - - - +
335N MET* 1.3 77.9 - - - +
337N CYS* 1.3 78.6 + - - +
339N GLN* 3.7 8.2 + - - +
340N GLY* 3.1 18.9 + - - -
3P PRO* 4.6 4.3 - - + -
4P ASN* 3.2 51.4 - - + +
6P ARG* 4.8 14.1 - - - -
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Residues in contact with CYS 337 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294N LEU* 3.9 17.3 - - + -
297N LEU* 4.1 22.8 - - + +
303N LEU* 3.8 19.3 - - + -
333N ASP 3.0 25.5 + - - +
334N MET 3.6 2.9 - - - +
336N PHE* 1.3 81.0 - - - +
338N ALA* 1.3 66.0 + - - +
340N GLY* 3.1 3.7 + - - -
341N GLU* 3.0 27.4 + - - +
3P PRO* 4.0 23.3 - - - -
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Residues in contact with ALA 338 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277N ILE* 5.5 0.2 - - - +
294N LEU* 3.9 26.6 - - + +
322N PHE* 3.8 32.1 - - + -
324N PHE* 5.2 0.2 - - + -
334N MET* 2.8 23.1 + - + +
335N MET* 3.4 5.8 - - - +
337N CYS* 1.3 71.7 - - - +
339N GLN* 1.3 58.0 + - - +
340N GLY 2.9 1.1 - - - -
341N GLU* 2.7 27.4 + - - +
342N TRP* 3.2 10.2 + - - +
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Residues in contact with GLN 339 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255N LEU* 4.4 3.7 - - + +
322N PHE* 4.5 9.4 - - + -
335N MET* 2.9 48.5 + - - +
336N PHE* 3.9 7.4 - - - +
338N ALA* 1.3 74.5 - - - +
340N GLY* 1.3 63.5 + - - +
342N TRP* 3.1 13.7 + - + +
343N MET* 3.1 26.3 + - - +
436N ARG 4.8 1.2 + - - -
437N ILE* 3.0 49.3 + - - +
440N GLY* 3.7 24.9 - - - +
441N MET* 4.0 9.8 - - - +
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Residues in contact with GLY 340 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336N PHE 3.1 14.5 + - - -
337N CYS* 3.3 7.0 - - - -
338N ALA 2.8 1.8 + - - -
339N GLN* 1.3 78.1 - - - +
341N GLU* 1.3 64.6 + - - +
343N MET* 3.1 10.6 + - - +
344N ARG* 3.0 23.1 + - - +
444N ILE* 5.6 3.1 - - - -
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Residues in contact with GLU 341 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277N ILE* 4.3 21.3 - - + +
293N ARG* 3.0 55.3 + - - +
294N LEU* 4.0 25.4 - - + +
297N LEU* 4.5 10.0 - - + +
337N CYS 3.0 17.5 + - - +
338N ALA* 2.7 15.0 + - - +
340N GLY* 1.3 70.6 - - - -
342N TRP* 1.3 64.8 + - - +
344N ARG* 3.2 14.3 + - - +
345N LEU* 3.0 25.9 + - - +
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Residues in contact with TRP 342 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255N LEU* 3.8 26.7 - - + -
256N ALA* 4.3 4.0 - - - -
257N VAL* 4.4 7.0 - - + -
274N ASN* 5.2 1.6 - - - +
277N ILE* 3.5 26.8 - - + +
309N THR* 5.8 1.0 - - - +
320N PHE* 4.1 26.3 - + - -
321N GLY* 3.4 29.2 + - - -
322N PHE* 3.3 37.6 - + - -
338N ALA 3.2 8.0 + - - -
339N GLN* 3.1 14.4 + - - +
341N GLU* 1.3 76.0 - - - +
343N MET* 1.3 72.0 + - + +
345N LEU* 2.9 30.4 + - + +
346N CYS* 3.2 11.3 + - - -
415N ILE* 3.5 26.0 - - + +
441N MET* 4.0 22.7 - - + -
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Residues in contact with MET 343 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339N GLN* 3.1 11.1 + - + +
340N GLY* 3.1 9.6 + - - +
342N TRP* 1.3 91.5 - - + +
344N ARG* 1.3 62.5 + - - +
346N CYS* 3.3 8.7 + - - +
347N THR* 3.0 29.9 + - - +
415N ILE* 4.2 16.6 - - + -
416N TYR* 3.9 14.6 - - + -
440N GLY 3.8 13.5 - - - +
441N MET* 3.5 41.1 - - - +
442N TYR* 3.6 10.5 - - - -
443N TRP 4.1 11.2 - - - +
444N ILE* 3.5 20.9 - - - +
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Residues in contact with ARG 344 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293N ARG* 3.1 51.0 - - - +
340N GLY 3.0 12.7 + - - +
341N GLU* 3.4 19.2 + - - +
342N TRP 3.1 0.2 - - - -
343N MET* 1.3 76.7 - - - +
345N LEU* 1.3 58.8 + - - +
347N THR* 3.9 5.8 - - - -
348N SER* 2.6 62.4 + - - +
349N THR* 3.5 4.5 + - - +
350N THR* 4.4 4.6 + - - -
353N GLU* 3.2 35.0 + - - -
444N ILE* 5.0 5.8 - - - +
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Residues in contact with LEU 345 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273N ALA* 4.3 28.3 - - + +
274N ASN* 5.7 0.2 - - - +
276N ILE* 4.2 31.0 - - + -
277N ILE* 3.5 30.1 - - + -
320N PHE* 5.3 2.7 - - + -
341N GLU 3.0 15.0 + - - +
342N TRP* 2.9 22.3 + - + +
344N ARG* 1.3 76.1 - - - +
346N CYS* 1.3 59.8 + - - +
349N THR* 2.9 25.6 + - - +
407N VAL* 4.3 3.4 - - + +
408N ARG* 3.4 15.9 + - - +
411N CYS* 4.0 16.9 - - + +
415N ILE* 4.7 4.9 - - + -
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Residues in contact with CYS 346 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342N TRP 3.2 18.7 + - - -
343N MET* 3.8 13.0 - - - +
344N ARG 3.2 0.2 - - - -
345N LEU* 1.3 76.2 - - - +
347N THR* 1.3 66.3 + - + +
408N ARG* 3.6 20.4 - - - +
411N CYS* 3.9 26.9 - - - -
412N SER* 3.3 29.9 + - - +
415N ILE* 4.2 13.7 - - - -
416N TYR* 4.4 14.6 - - + -
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Residues in contact with THR 347 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343N MET 3.0 18.9 + - - +
344N ARG* 3.9 0.2 - - - -
346N CYS* 1.3 86.6 - - + +
348N SER* 1.3 67.8 + - - +
408N ARG* 3.5 14.2 + - - +
416N TYR* 5.1 11.9 - - + -
443N TRP* 5.5 8.3 - - + -
444N ILE* 3.3 29.9 + - - +
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Residues in contact with SER 348 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344N ARG* 2.6 59.2 + - - +
347N THR* 1.3 85.6 + - - +
349N THR* 1.3 66.3 + - - +
350N THR* 3.6 5.4 + - - -
408N ARG* 4.2 2.2 - - - +
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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