Contacts of the helix formed by residues 387 - 401 (chain A) in PDB entry 1LSH
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 THR 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A ARG* 5.1 3.6 - - - +
386A LEU* 1.3 77.0 - - - +
388A SER* 1.3 59.5 + - - +
389A ALA* 3.5 7.9 + - - +
390A GLU* 3.0 38.3 + - - +
391A ALA* 2.9 28.1 + - - +
420A PHE* 4.2 2.5 - - - -
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Residues in contact with SER 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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387A THR* 1.3 73.2 - - - +
389A ALA* 1.3 57.9 + - - +
391A ALA* 3.4 6.2 + - - +
392A THR* 3.0 31.7 + - - +
420A PHE* 4.3 2.0 - - - -
424A ARG* 2.9 38.7 + - - +
427A LEU* 5.2 1.9 - - - +
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Residues in contact with ALA 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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387A THR* 3.2 7.0 + - - +
388A SER* 1.3 78.0 - - - +
390A GLU* 1.3 65.7 + - + +
392A THR* 3.1 16.5 - - - +
393A GLN* 2.9 26.6 - - - +
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Residues in contact with GLU 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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358A ARG* 2.9 47.4 + - - -
359A ARG* 6.0 0.7 - - - -
362A LEU* 3.8 22.4 - - + +
386A LEU* 3.6 8.6 - - + +
387A THR* 3.0 36.3 + - - +
389A ALA* 1.3 78.0 - - + +
391A ALA* 1.3 63.7 + - - +
393A GLN* 3.1 19.9 + - - +
394A ILE* 3.0 27.6 + - - +
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Residues in contact with ALA 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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381A LEU* 3.7 25.8 - - + -
386A LEU* 4.3 4.5 - - + +
387A THR 2.9 18.8 + - - +
388A SER 3.6 4.7 - - - +
389A ALA 3.3 0.2 - - - -
390A GLU* 1.3 77.2 - - - +
392A THR* 1.3 58.6 + - - +
394A ILE* 3.7 9.0 - - - -
395A VAL* 2.9 35.3 + - - +
420A PHE* 3.9 5.6 - - + -
427A LEU* 3.7 20.0 - - + -
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Residues in contact with THR 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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388A SER 3.0 15.7 + - - +
389A ALA* 3.1 21.3 - - - +
391A ALA* 1.3 74.7 - - - +
393A GLN* 1.3 66.3 + - + +
395A VAL* 4.8 0.7 - - - +
396A ALA* 3.3 17.2 + - - +
426A ILE* 4.2 22.6 + - + +
427A LEU* 4.0 15.7 - - - +
430A THR* 4.4 9.3 + - - +
2005A PLD 4.1 14.9 - - + +
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Residues in contact with GLN 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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389A ALA* 2.9 23.0 + - + +
390A GLU* 3.1 26.7 + - - +
392A THR* 1.3 81.4 - - + +
394A ILE* 1.3 61.2 + - + +
396A ALA* 3.4 3.7 - - - +
397A SER* 3.2 26.9 + - - -
798A LYS* 5.0 19.6 - - - +
2005A PLD 5.5 4.9 - - - +
2006A PLD 3.2 33.1 + - - -
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Residues in contact with ILE 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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362A LEU* 3.5 51.1 - - + +
365A VAL* 3.8 17.9 - - + -
366A PRO* 4.2 4.9 - - + -
376A PHE* 5.7 0.4 - - + -
377A LEU* 3.7 26.9 - - + -
386A LEU* 4.0 5.8 - - + -
390A GLU 3.0 18.2 + - - +
391A ALA* 3.4 13.2 - - - +
393A GLN* 1.3 77.1 - - + +
395A VAL* 1.4 58.5 + - + +
396A ALA 3.0 2.5 - - - -
397A SER* 4.2 3.4 - - - +
398A THR* 2.6 52.3 + - - +
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Residues in contact with VAL 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 4.2 11.7 - - + -
381A LEU* 3.9 29.8 - - + -
391A ALA 2.9 20.5 + - - +
394A ILE* 1.4 76.6 - - + +
396A ALA* 1.3 55.3 - - - +
398A THR* 3.9 0.7 - - - -
399A LEU* 3.0 56.6 + - + +
415A LEU* 4.5 7.2 - - + -
421A ILE* 4.9 2.0 - - + -
427A LEU* 3.7 20.9 - - + -
430A THR* 3.7 17.3 - - + -
431A ALA* 4.0 16.4 - - + -
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Residues in contact with ALA 396 (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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392A THR 3.3 22.0 - - - +
393A GLN 3.4 6.1 - - - +
395A VAL* 1.3 76.6 - - - +
397A SER* 1.3 71.2 + - - +
398A THR 3.1 0.5 + - - -
399A LEU* 3.6 4.2 + - - +
400A SER* 3.2 13.5 + - - -
430A THR* 3.8 9.5 - - + +
2005A PLD 3.1 52.8 - - + +
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Residues in contact with SER 397 (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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366A PRO* 3.0 35.3 - - - +
393A GLN 3.2 15.5 + - - -
394A ILE 3.2 2.5 + - - -
396A ALA* 1.3 83.0 - - - +
398A THR* 1.3 62.0 + - - +
400A SER* 3.0 5.5 + - - -
401A ASN* 3.0 25.2 + - - +
798A LYS* 5.8 1.4 + - - -
2005A PLD 3.9 36.5 - - - +
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Residues in contact with THR 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A VAL* 3.8 17.5 - - + +
366A PRO* 3.6 18.2 - - + +
374A LEU* 4.2 16.6 - - + +
377A LEU* 3.8 21.8 - - + +
394A ILE* 2.6 44.0 + - - +
395A VAL 3.9 0.2 - - - -
397A SER* 1.3 74.0 - - - +
399A LEU* 1.3 66.2 + - - +
400A SER 3.4 0.2 + - - -
401A ASN* 3.5 5.7 + - - +
402A GLN* 3.2 32.0 + - - +
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Residues in contact with LEU 399 (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 LEU* 4.3 16.2 - - + -
377A LEU* 6.0 0.2 - - + -
395A VAL* 3.0 29.2 + - + +
396A ALA* 4.4 1.8 - - - +
398A THR* 1.3 79.8 - - - +
400A SER* 1.3 61.8 + - - +
402A GLN* 3.5 19.6 - - - +
412A ALA* 3.8 30.5 - - + -
415A LEU* 4.7 8.5 - - + -
430A THR* 4.2 1.6 - - + +
431A ALA* 3.7 37.9 - - + +
434A GLY* 3.8 26.5 - - - +
435A TYR* 4.9 1.3 - - + +
438A LEU* 3.6 23.6 - - + +
441A ARG* 4.8 0.3 + - - -
2005A PLD 6.5 0.2 - - + -
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Residues in contact with SER 400 (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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396A ALA 3.2 6.1 + - - -
397A SER* 3.0 12.1 + - - -
399A LEU* 1.3 80.2 - - - +
401A ASN* 1.3 61.9 + - - +
402A GLN 3.2 5.6 - - - -
437A SER* 5.1 4.5 - - - -
441A ARG* 3.4 26.6 + - - +
2005A PLD 2.9 74.5 + - - +
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Residues in contact with ASN 401 (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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190A MET* 5.7 0.5 - - - +
337A ARG* 4.8 1.6 - - - +
366A PRO* 2.6 30.5 + - + +
367A ALA* 3.4 22.2 + - - +
369A ALA* 3.0 19.5 - - - +
397A SER 3.0 16.2 + - - +
398A THR 3.5 2.0 + - - +
399A LEU 3.4 0.4 - - - -
400A SER* 1.3 77.3 + - - +
402A GLN* 1.3 62.6 + - - +
441A ARG* 4.2 2.6 + - - -
801A VAL* 5.4 7.5 + - - +
804A GLU* 5.0 5.9 + - - +
2005A PLD 3.3 32.3 + - - +
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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