Contacts of the helix formed by residues 375 - 392 (chain A) in PDB entry 4LBD
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 MET 375 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A PRO 4.5 12.6 - - - +
321A LEU* 3.9 34.1 - - - +
365A ALA* 4.7 11.0 - - + +
369A ARG* 3.9 26.0 - - + +
372A GLN* 3.3 44.1 + - + +
373A PRO 3.2 2.6 - - - -
374A TYR* 1.3 74.7 - - - +
376A PHE* 1.3 62.5 + - - +
378A ARG* 3.2 20.3 + - - +
379A MET* 2.9 47.0 + - + +
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Residues in contact with PHE 376 (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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358A LEU* 3.5 36.1 - - + -
361A LEU* 3.8 27.4 - - + -
362A ARG* 3.7 51.4 - - + -
365A ALA* 4.6 8.9 - - + +
366A ARG* 5.5 4.5 - - + +
373A PRO 4.4 2.8 + - - +
375A MET* 1.3 77.3 - - - +
377A PRO* 1.4 69.2 - - + +
379A MET* 2.9 24.8 + - - +
380A LEU* 3.0 44.6 + - + +
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Residues in contact with PRO 377 (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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373A PRO 3.8 11.2 - - - +
374A TYR* 3.5 28.5 - - + +
376A PHE* 1.4 101.5 - - + +
378A ARG* 1.3 55.2 + - + -
380A LEU* 3.9 8.3 - - + +
381A MET* 3.1 38.9 + - + +
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Residues in contact with ARG 378 (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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321A LEU* 4.6 20.0 - - + -
374A TYR* 2.8 57.0 + - + +
375A MET* 3.2 25.6 + - - +
376A PHE 3.1 0.6 - - - -
377A PRO* 1.3 76.1 - - + +
379A MET* 1.3 63.1 + - - +
381A MET* 3.6 8.4 + - - +
382A LYS* 3.2 28.4 + - - +
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Residues in contact with MET 379 (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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321A LEU* 4.4 5.6 - - + -
323A MET* 3.9 37.5 - - + -
327A GLU* 3.5 28.7 - - - +
331A LEU* 3.6 24.3 - - + +
361A LEU* 4.3 28.3 - - + -
365A ALA* 4.4 8.3 - - + -
369A ARG* 4.0 6.7 - - - +
375A MET* 2.9 39.9 + - + +
376A PHE* 2.9 7.8 + - - +
378A ARG* 1.3 76.2 - - - +
380A LEU* 1.3 65.4 + - - +
382A LYS* 3.1 23.2 + - - +
383A ILE 3.6 2.4 + - - -
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Residues in contact with LEU 380 (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* 4.6 0.9 - - + -
334A ILE* 4.7 2.5 - - + -
358A LEU* 3.9 27.1 - - + -
361A LEU* 4.5 10.5 - - + -
376A PHE* 3.0 52.8 + - + +
377A PRO* 4.1 7.0 - - + +
379A MET* 1.3 75.9 - - - +
381A MET* 1.3 57.5 + - + +
383A ILE* 2.8 47.5 + - + +
384A THR* 3.9 2.8 + - - -
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Residues in contact with MET 381 (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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377A PRO* 3.1 24.4 + - + +
378A ARG* 3.9 7.9 - - - +
380A LEU* 1.3 79.0 - - + +
382A LYS* 1.3 62.1 + - - +
384A THR* 3.1 24.8 + - - +
385A ASP* 3.5 11.9 + - - +
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Residues in contact with LYS 382 (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 LEU* 6.4 0.9 - - + -
314A PHE* 4.5 17.2 + - + -
317A GLN* 3.4 35.1 + - - +
318A LEU* 4.4 16.3 - - + +
321A LEU* 3.8 31.9 - - + -
323A MET* 5.8 1.6 - - - -
331A LEU* 5.0 7.9 - - + -
378A ARG* 3.2 16.5 + - - +
379A MET* 3.1 13.4 + - - +
380A LEU 3.0 0.8 + - - -
381A MET* 1.3 76.2 - - - +
383A ILE* 1.3 52.8 + - - +
385A ASP* 3.0 25.3 + - - +
386A LEU* 2.8 38.1 + - + +
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Residues in contact with ILE 383 (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 ASP* 4.5 2.3 - - - +
331A LEU* 3.8 28.9 - - + -
334A ILE* 3.7 29.6 - - + -
335A CYS* 3.6 31.9 - - + +
341A ARG* 6.3 0.7 - - - +
380A LEU* 2.8 25.8 + - + +
382A LYS* 1.3 76.9 - - - +
384A THR* 1.3 56.3 + - - +
386A LEU* 3.6 8.7 - - - +
387A ARG* 3.0 29.0 + - + +
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Residues in contact with THR 384 (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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380A LEU 4.3 1.6 + - - -
381A MET* 3.3 18.4 + - - +
382A LYS 3.1 0.6 - - - -
383A ILE* 1.3 77.0 - - - +
385A ASP* 1.3 69.1 + - - +
387A ARG* 3.2 46.3 + - - +
388A GLY* 3.1 17.8 + - - -
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Residues in contact with ASP 385 (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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314A PHE* 3.5 21.4 - - + -
381A MET* 3.5 13.5 - - - +
382A LYS* 3.0 32.6 + - - +
384A THR* 1.3 78.1 - - - +
386A LEU* 1.3 57.0 + - - +
388A GLY* 2.9 17.6 + - - -
389A ILE* 3.0 15.4 + - - +
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Residues in contact with LEU 386 (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 ASP* 3.4 34.5 - - + +
270A ILE* 5.6 0.2 - - - -
272A MET* 3.9 10.5 - - + -
273A LEU* 3.6 37.2 - - + +
314A PHE* 3.8 21.9 - - + -
331A LEU* 4.6 4.7 - - + -
335A CYS* 3.8 29.4 - - - -
382A LYS* 2.8 19.1 + - + +
383A ILE* 3.6 8.3 - - - +
385A ASP* 1.3 74.3 - - - +
387A ARG* 1.3 60.1 + - - +
389A ILE* 2.9 20.3 - - + +
390A SER* 2.9 18.6 + - - -
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Residues in contact with ARG 387 (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 ASP* 3.3 21.1 - - - +
341A ARG* 5.4 9.0 - - - +
383A ILE* 3.0 17.8 + - + +
384A THR* 3.2 46.8 + - - +
386A LEU* 1.3 79.5 - - - +
388A GLY* 1.3 60.2 - - - +
390A SER* 3.3 4.2 - - - -
391A THR* 3.1 30.8 + - + +
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Residues in contact with GLY 388 (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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384A THR 3.1 9.3 + - - -
385A ASP* 2.9 8.4 + - - -
387A ARG* 1.3 80.5 - - - +
389A ILE* 1.3 63.9 + - - +
390A SER 3.0 1.9 + - - -
391A THR* 3.3 10.4 + - - -
392A LYS* 3.3 27.6 + - - +
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Residues in contact with ILE 389 (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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272A MET* 3.6 30.5 - - + +
307A LEU* 3.9 11.9 - - + +
310A LEU* 3.7 47.6 - - + +
311A VAL* 3.9 19.1 - - + +
314A PHE* 4.7 19.7 - - + -
385A ASP 3.0 10.2 + - - +
386A LEU* 2.9 35.0 - - + +
388A GLY* 1.3 76.0 - - - +
390A SER* 1.3 56.5 + - - +
392A LYS* 3.5 6.7 + - + +
393A GLY 3.0 20.1 + - - -
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Residues in contact with SER 390 (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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268A LEU* 3.2 26.8 + - - +
269A ASP* 2.8 42.7 + - - -
272A MET* 4.0 6.1 - - - +
386A LEU 2.9 16.3 + - - -
387A ARG 3.3 9.2 - - - -
389A ILE* 1.3 74.1 - - - +
391A THR* 1.3 63.1 + - - +
392A LYS 3.1 1.8 - - - -
393A GLY 2.9 1.7 + - - -
394A ALA* 2.8 26.0 + - - +
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Residues in contact with THR 391 (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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387A ARG* 3.1 16.6 + - + +
388A GLY* 3.3 13.0 + - - -
390A SER* 1.3 78.9 - - - +
392A LYS* 1.3 57.5 + - - +
394A ALA* 3.3 8.3 + - + +
395A GLU* 2.9 41.4 + - - +
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Residues in contact with LYS 392 (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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307A LEU* 3.7 15.1 - - + +
310A LEU* 3.6 32.2 - - + +
388A GLY 3.3 16.7 + - - +
389A ILE* 3.7 12.1 - - + +
390A SER 3.1 0.6 - - - -
391A THR* 1.3 79.8 - - - +
393A GLY* 1.3 50.4 + - - +
395A GLU* 3.3 17.4 + - + +
396A ARG* 2.8 33.1 + - - +
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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