Contacts of the helix formed by residues 330 - 348 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A HIS 5.6 0.2 - - - -
302A LYS 4.0 13.2 + - - -
303A LEU* 3.2 27.5 + - - +
326A ALA* 4.7 0.4 - - - -
327A ASP* 3.0 29.4 + - - +
329A LEU* 1.3 80.1 - - - +
331A ILE* 1.3 64.9 + - - +
332A ASP 3.3 2.7 - - - -
333A ASP* 3.6 8.6 + - - +
334A MET* 3.2 24.8 + - - +
430A GLN* 3.8 0.7 - - - -
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Residues in contact with ILE 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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251A ALA* 3.8 18.4 - - + -
253A VAL* 4.3 6.1 - - + -
324A PHE* 4.0 21.2 - - + -
326A ALA* 4.7 6.7 - - + -
327A ASP 3.6 9.8 + - - +
328A PRO* 3.3 20.2 - - + +
330A SER* 1.3 78.8 - - - +
332A ASP* 1.3 65.4 + - - +
334A MET* 3.7 4.3 - - - +
335A MET* 3.1 20.6 + - - +
427A PRO 3.8 6.5 - - - +
428A ILE* 3.8 35.4 - - + -
430A GLN* 3.4 2.5 + - - +
431A LEU* 3.4 31.4 - - + +
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Residues in contact with ASP 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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331A ILE* 1.3 78.6 - - - +
333A ASP* 1.3 63.9 + - - +
334A MET 3.2 0.2 + - - -
335A MET* 3.2 8.8 + - - +
336A PHE* 2.8 30.6 + - - +
430A GLN* 2.9 38.7 + - + +
431A LEU* 5.2 5.1 - - - +
432A LEU 5.5 2.3 + - - -
4C ASN* 5.5 0.7 - - - +
6C ARG* 5.5 2.4 + - - -
7C LYS* 3.2 28.6 + - - +
21C ASP* 4.4 7.3 - - - +
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Residues in contact with ASP 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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303A LEU* 3.7 21.3 - - + -
329A LEU 4.5 12.0 - - - +
330A SER* 3.6 6.6 + - - +
331A ILE 3.5 0.6 - - - -
332A ASP* 1.3 77.3 - - - +
334A MET* 1.3 62.8 + - - +
336A PHE* 3.3 6.8 - - - +
337A CYS* 3.0 29.1 + - - -
430A GLN* 4.8 2.1 + - - +
3C PRO* 3.1 29.8 - - + +
4C ASN* 3.6 7.3 - - - +
7C LYS* 3.5 27.0 + - - +
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Residues in contact with MET 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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294A LEU* 3.4 45.3 - - + -
298A ALA* 4.9 1.1 - - - -
303A LEU* 3.8 29.8 - - - +
304A CYS* 3.7 24.9 - - + -
307A PHE* 4.1 19.7 - - + -
322A PHE* 6.1 0.7 - - + -
324A PHE* 3.7 33.2 - - + -
326A ALA* 5.1 0.4 - - + -
330A SER 3.2 17.0 + - - +
331A ILE 3.7 4.0 - - - +
332A ASP 3.2 0.6 - - - -
333A ASP* 1.3 77.8 - - - +
335A MET* 1.3 59.0 + - - +
337A CYS* 3.1 3.6 + - - +
338A ALA* 2.8 36.0 + - + +
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Residues in contact with MET 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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253A VAL* 3.6 31.4 - - + -
255A LEU* 4.7 5.6 - - + -
322A PHE* 4.3 14.8 - - + -
324A PHE* 3.9 14.1 - - + -
331A ILE 3.1 15.5 + - - +
332A ASP* 3.6 7.4 - - - +
334A MET* 1.3 78.9 - - - +
336A PHE* 1.3 63.8 + - - +
338A ALA* 4.3 1.3 - - - -
339A GLN* 3.0 62.1 + - - +
422A LEU* 4.2 12.6 - - + -
431A LEU* 3.7 27.4 - - + -
437A ILE* 4.4 12.3 - - + -
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Residues in contact with PHE 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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332A ASP* 2.8 19.6 + - - +
333A ASP* 3.3 12.1 - - - +
335A MET* 1.3 79.2 - - - +
337A CYS* 1.3 71.7 + - - +
339A GLN* 4.0 8.0 - - - +
340A GLY* 3.0 24.0 + - - -
3C PRO* 4.5 4.5 - - + -
4C ASN* 3.1 53.4 - - + +
6C ARG* 4.7 14.8 - - - -
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Residues in contact with CYS 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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294A LEU* 3.9 16.2 - - + -
297A LEU* 4.1 21.5 - - + -
303A LEU* 3.7 20.2 - - + -
333A ASP 3.0 23.7 + - - -
334A MET 3.6 5.8 - - - +
336A PHE* 1.3 80.8 - - - +
338A ALA* 1.3 68.6 + - - +
340A GLY* 3.0 4.1 + - - -
341A GLU* 2.9 26.9 + - - +
3C PRO* 3.9 23.6 - - - -
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Residues in contact with ALA 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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277A ILE* 5.6 0.2 - - - +
294A LEU* 3.9 26.6 - - + +
322A PHE* 3.7 33.2 - - + -
324A PHE* 5.1 0.4 - - + -
334A MET* 2.8 22.2 + - + +
335A MET* 3.6 5.8 - - - +
337A CYS* 1.3 75.7 - - - +
339A GLN* 1.3 56.3 + - - +
341A GLU* 2.6 28.3 + - - +
342A TRP* 3.2 9.7 + - - +
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Residues in contact with GLN 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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255A LEU* 4.3 4.6 - - + +
322A PHE* 4.3 10.0 - - + -
335A MET* 3.0 48.5 + - - +
336A PHE* 4.0 6.5 - - - +
338A ALA* 1.3 78.7 - - - +
340A GLY* 1.3 62.8 + - - +
342A TRP* 3.1 13.8 + - + +
343A MET* 3.1 26.5 + - - +
436A ARG 4.8 1.0 + - - -
437A ILE* 2.9 42.1 + - - +
440A GLY* 3.7 26.8 - - - +
441A MET* 3.9 9.9 - - - +
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Residues in contact with GLY 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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336A PHE* 3.0 13.6 + - - -
337A CYS* 3.0 8.5 + - - -
338A ALA 2.9 1.6 - - - -
339A GLN* 1.3 78.6 - - - +
341A GLU* 1.3 65.2 + - - +
343A MET* 3.1 11.1 + - - +
344A ARG* 3.0 22.7 + - - +
444A ILE 5.6 3.0 - - - -
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Residues in contact with GLU 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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277A ILE* 4.3 21.4 - - + +
293A ARG* 3.0 48.9 + - - +
294A LEU* 4.0 25.6 - - + +
297A LEU* 4.5 9.9 - - + +
337A CYS 2.9 15.3 + - - +
338A ALA* 2.6 16.9 + - - +
340A GLY* 1.3 70.2 - - - -
342A TRP* 1.3 64.9 + - - +
344A ARG* 3.1 26.8 + - - +
345A LEU* 3.0 24.9 + - - +
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Residues in contact with TRP 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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255A LEU* 3.8 34.5 - - + -
256A ALA* 4.3 4.0 - - - -
257A VAL* 4.2 7.2 - - + -
274A ASN* 5.3 1.6 - - - +
277A ILE* 3.5 25.4 - - + +
309A THR* 5.9 1.0 - - - +
320A PHE* 4.0 26.9 - + - -
321A GLY* 3.4 22.9 + - - -
322A PHE* 3.4 37.0 - + - +
338A ALA 3.2 6.7 + - - -
339A GLN* 3.1 14.2 + - - +
341A GLU* 1.3 76.8 - - - +
343A MET* 1.3 72.2 + - + +
345A LEU* 3.0 28.2 + - + +
346A CYS* 3.2 12.1 + - - -
415A ILE* 3.4 31.1 - - + +
441A MET* 4.0 19.5 - - + -
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Residues in contact with MET 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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339A GLN 3.1 14.0 + - - +
340A GLY* 3.1 12.2 + - - +
342A TRP* 1.3 91.8 - - + +
344A ARG* 1.3 60.2 + - - +
346A CYS* 3.4 6.9 + - - +
347A THR* 2.8 32.0 + - - +
415A ILE* 4.1 17.0 - - + -
416A TYR* 3.9 15.7 - - + -
440A GLY 3.8 11.7 - - - +
441A MET* 3.6 42.2 - - - +
442A TYR* 3.6 9.2 - - - -
443A TRP 4.1 13.2 - - - +
444A ILE* 3.6 20.9 - - - -
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Residues in contact with ARG 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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276A ILE* 5.1 5.7 - - - +
293A ARG* 3.1 54.2 - - - +
340A GLY 3.0 13.2 + - - +
341A GLU* 3.2 23.8 + - - +
342A TRP 3.1 0.4 - - - -
343A MET* 1.3 75.3 - - - +
345A LEU* 1.3 64.7 + - - +
347A THR* 3.9 5.4 - - - -
348A SER* 2.7 54.7 + - - +
349A THR* 3.5 4.0 + - - -
350A THR* 4.4 3.6 + - - -
353A GLU* 2.7 39.9 + - - -
444A ILE* 5.5 4.5 - - - +
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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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273A ALA* 4.3 28.5 - - + +
276A ILE* 4.2 29.4 - - + -
277A ILE* 3.4 30.5 - - + -
320A PHE* 5.3 2.7 - - + -
341A GLU 3.0 14.7 + - - +
342A TRP* 3.2 20.4 - - + +
344A ARG* 1.3 79.6 - - - +
346A CYS* 1.3 59.9 + - - +
349A THR* 2.9 26.2 + - + +
407A VAL* 4.3 3.7 - - + +
408A ARG* 3.4 16.1 + - - +
411A CYS* 4.0 16.3 - - + +
415A ILE* 4.7 5.6 - - + -
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Residues in contact with CYS 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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342A TRP 3.2 16.8 + - - -
343A MET* 3.9 11.7 - - - +
344A ARG 3.2 0.8 - - - -
345A LEU* 1.3 80.5 - - - +
347A THR* 1.3 66.4 + - + +
408A ARG* 3.7 17.9 - - - +
411A CYS* 3.8 28.5 - - - -
412A SER* 3.3 30.3 + - - +
415A ILE* 4.1 16.2 - - - -
416A TYR* 4.3 15.3 - - + -
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Residues in contact with THR 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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343A MET* 2.8 22.2 + - - +
344A ARG* 3.9 0.2 - - - -
346A CYS* 1.3 88.5 - - + +
348A SER* 1.3 69.3 + - - +
408A ARG* 3.6 13.2 + - - +
416A TYR* 5.0 11.7 - - + -
443A TRP* 5.6 7.6 - - + -
444A ILE* 3.3 31.9 + - - +
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Residues in contact with SER 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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344A ARG* 2.7 49.3 + - - +
347A THR* 1.3 83.0 + - - +
349A THR* 1.3 67.4 + - - +
350A THR* 3.6 5.2 + - - -
408A ARG* 4.2 2.5 - - - +
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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