Contacts of the helix formed by residues 379 - 395 (chain A) in PDB entry 3L6X
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 LEU 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A PHE* 3.2 6.0 - - + +
378A ARG* 1.3 79.2 - - + +
380A ASP* 1.3 67.2 + - - +
381A ALA* 4.3 5.8 - - + +
382A VAL* 2.9 41.1 + - + +
383A LYS* 3.2 10.1 + - - -
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Residues in contact with ASP 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ARG 3.3 4.3 + - - +
379A LEU* 1.3 71.1 - - - +
381A ALA* 1.3 56.4 + - - +
383A LYS* 3.1 22.7 + - - +
384A SER* 2.8 31.9 + - - -
419A HIS* 3.2 35.2 + - - -
421A LYS* 4.7 6.8 - - + +
424A VAL* 3.9 11.6 - - + +
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Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LEU* 3.1 8.6 + - + +
380A ASP* 1.3 78.8 - - - +
382A VAL* 1.3 61.1 + - + +
384A SER* 3.3 7.8 + - - -
385A ASN* 3.1 33.8 + - - +
423A GLU* 5.5 4.3 - - - +
773B GLN* 4.1 19.2 - - - +
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Residues in contact with VAL 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A MET* 3.7 39.7 - - + +
377A PHE* 3.8 22.7 - - + -
379A LEU* 2.9 33.8 + - + +
381A ALA* 1.3 77.2 - - + +
383A LYS* 1.3 67.4 + - - +
385A ASN* 4.0 3.0 - - - +
386A ALA* 2.8 23.6 + - - +
773B GLN* 4.0 17.9 - - + +
774B LEU* 4.2 3.9 - - + +
775B HIS 5.4 4.9 - - - +
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Residues in contact with LYS 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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374A MET 3.8 7.6 - - - +
375A LEU* 2.9 34.6 - - - +
376A GLY 4.9 1.9 + - - -
377A PHE 2.5 32.1 + - - +
378A ARG* 3.6 12.4 + - - +
379A LEU 3.2 5.7 + - - -
380A ASP* 3.1 35.9 + - - +
382A VAL* 1.3 78.5 - - - +
384A SER* 1.3 58.8 + - - +
386A ALA* 3.6 1.9 - - - +
387A ALA* 2.9 30.0 + - - +
416A LEU* 4.3 15.9 - - + -
419A HIS* 4.0 11.3 + - + -
424A VAL* 4.2 16.8 - - + -
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Residues in contact with SER 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ASP 2.8 17.9 + - - -
381A ALA* 3.3 11.1 + - - -
383A LYS* 1.3 77.8 - - - +
385A ASN* 1.3 60.9 + - - +
387A ALA* 3.3 6.0 + - - +
388A ALA* 2.9 29.9 + - - +
423A GLU* 3.4 49.8 + - - +
424A VAL* 4.0 7.2 - - - +
427A GLY* 4.9 1.0 - - - -
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Residues in contact with ASN 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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381A ALA* 3.1 24.2 + - - +
382A VAL* 4.8 0.4 - - - -
384A SER* 1.3 83.4 + - - +
386A ALA* 1.3 58.1 + - - +
388A ALA* 3.8 5.1 - - - +
389A TYR* 2.8 31.9 + - - +
769B PHE* 3.6 8.9 - - + +
770B ASP* 2.8 36.1 + - - +
773B GLN* 3.8 27.7 + - + +
774B LEU* 3.8 19.6 - - + +
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Residues in contact with ALA 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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371A VAL* 3.6 30.7 - - + +
374A MET* 3.8 15.0 - - + -
375A LEU* 4.1 9.9 - - + +
382A VAL 2.8 22.5 + - - +
383A LYS 3.6 3.4 - - - +
385A ASN* 1.3 71.7 - - - +
387A ALA* 1.3 59.9 + - - +
389A TYR* 4.4 2.9 - - - -
390A LEU* 2.8 31.9 + - - +
774B LEU* 3.6 11.3 - - + +
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU* 3.7 15.8 - - + +
383A LYS 2.9 17.5 + - - +
384A SER* 3.8 4.5 - - - +
386A ALA* 1.3 75.4 - - - +
388A ALA* 1.3 57.7 + - - +
390A LEU* 3.3 6.5 + - - +
391A GLN* 2.8 29.5 + - - +
413A LEU* 4.4 4.9 - - + -
416A LEU* 5.3 2.0 - - + -
424A VAL* 4.9 1.8 - - + +
427A GLY* 3.5 30.3 - - - +
428A ALA* 3.7 10.1 - - + +
431A ALA* 3.7 4.5 - - - +
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Residues in contact with ALA 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 SER 2.9 17.5 + - - +
385A ASN* 3.8 6.5 - - - +
387A ALA* 1.3 77.4 - - - +
389A TYR* 1.3 63.4 + - - +
391A GLN* 3.1 9.1 + - - +
392A HIS* 3.0 18.9 + - - +
427A GLY* 4.7 7.1 + - - -
767B GLN* 3.6 20.3 - - + +
768B ASP 3.1 24.2 - - - +
769B PHE* 4.1 4.4 - - + -
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Residues in contact with TYR 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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3A SO4 2.9 26.5 + - - -
365A GLN* 3.8 17.8 + - - +
366A PRO* 4.0 15.3 + - + -
371A VAL* 3.9 20.2 - - + -
385A ASN 2.8 20.1 + - - +
386A ALA 3.8 2.5 - - - +
388A ALA* 1.3 75.2 - - - +
390A LEU* 1.3 53.4 + - - +
392A HIS* 3.0 12.7 + + - +
393A LEU* 2.8 63.5 + - + +
769B PHE* 3.5 47.7 - + + +
771B LEU* 4.0 9.9 - - + -
774B LEU* 3.5 22.2 - - + -
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Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LEU* 3.6 31.9 - - + -
371A VAL* 3.8 14.8 - - + +
372A ILE* 4.6 6.3 - - + -
375A LEU* 4.2 15.0 - - + -
386A ALA 2.8 18.5 + - - +
387A ALA 3.3 5.4 - - - +
389A TYR* 1.3 74.5 - - - +
391A GLN* 1.3 66.6 + - - +
393A LEU* 3.0 9.1 + - + +
394A CYS* 2.9 31.7 + - - -
404A VAL* 4.1 22.4 - - + -
413A LEU* 3.9 36.6 - - + -
431A ALA* 4.6 2.2 - - + -
435A ILE* 5.0 0.4 - - + -
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Residues in contact with GLN 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 ALA 2.8 16.1 + - - +
388A ALA* 3.1 9.2 + - - +
390A LEU* 1.3 70.7 - - - +
392A HIS* 1.3 64.6 + - - +
394A CYS* 3.3 4.0 + - - +
395A TYR* 3.1 9.4 + - - +
426A LEU 5.3 0.6 + - - -
427A GLY* 4.3 6.1 + - - -
430A GLY* 3.2 39.2 - - - +
431A ALA* 3.6 13.9 - - - +
433A LYS* 6.2 0.2 - - - +
434A ASN* 3.0 38.3 + - - +
765B GLU* 3.1 25.5 - - - +
766B ASP 3.7 4.9 - - - +
767B GLN* 3.1 35.2 + - + +
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Residues in contact with HIS 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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3A SO4 3.2 33.2 + - - -
388A ALA 3.0 9.0 + - - +
389A TYR* 3.0 16.1 + + - +
391A GLN* 1.3 77.9 - - - +
393A LEU* 1.3 69.8 + - + +
395A TYR* 3.2 19.0 + + - +
766B ASP* 2.8 37.8 + - - +
767B GLN* 3.7 9.9 + - - +
769B PHE* 3.4 35.4 - + + -
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Residues in contact with LEU 393 (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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3A SO4 4.5 8.7 - - - +
366A PRO 5.5 2.2 - - - +
368A LEU* 4.3 23.3 - - + +
371A VAL* 4.5 5.8 - - + -
389A TYR* 2.8 62.6 + - + +
390A LEU* 3.5 11.4 - - + +
392A HIS* 1.3 82.5 - - + +
394A CYS* 1.3 61.0 + - - +
395A TYR 3.4 1.4 + - - +
397A ASN* 3.5 19.9 + - - +
400A VAL* 3.8 22.9 - - + +
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Residues in contact with CYS 394 (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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390A LEU* 2.9 22.4 + - - +
391A GLN* 3.7 6.3 - - - +
393A LEU* 1.3 76.4 - - - +
395A TYR* 1.3 65.7 + - - +
397A ASN 3.0 13.8 + - - +
400A VAL* 3.9 21.5 - - - -
401A LYS* 3.0 31.7 - - + -
404A VAL* 4.1 14.1 - - - -
431A ALA* 5.3 0.4 - - - -
434A ASN* 4.1 13.7 - - + -
435A ILE* 3.8 26.5 - - + -
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Residues in contact with TYR 395 (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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391A GLN 3.1 11.7 + - - +
392A HIS* 3.4 15.3 - + - +
393A LEU 3.2 3.1 - - - +
394A CYS* 1.3 74.5 - - - +
396A ARG* 1.3 111.8 + - + +
397A ASN* 3.1 5.5 + - - +
434A ASN* 3.7 7.4 - - - +
764B GLU* 3.7 30.0 + - + -
765B GLU* 3.6 5.6 - - - -
766B ASP* 3.6 52.0 - - + +
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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
------------------------------------------------------------
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