Contacts of the helix formed by residues 455 - 473 (chain B) in PDB entry 4LT6
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 455 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ILE* 3.6 30.5 - - + -
404B LEU* 4.1 6.5 - - + -
407B ASN* 4.4 2.0 - - - +
410B ILE* 3.6 27.8 - - + -
440B ILE* 3.8 17.9 - - + -
442B PHE* 4.2 14.8 - - + -
454B ASP* 1.3 91.3 + - - +
456B THR* 1.3 61.3 + - - -
457B TYR 3.3 2.5 - - - -
458B ASP* 3.6 11.2 + - - +
459B ILE* 3.2 26.0 + - + +
486B HIS* 3.4 43.2 + - + +
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Residues in contact with THR 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B ASP* 3.0 32.4 - - - +
455B LEU* 1.3 73.3 - - - +
457B TYR* 1.3 59.8 + - - +
459B ILE* 3.7 8.1 - - - +
460B GLN* 3.0 35.3 + - - +
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Residues in contact with TYR 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 3.5 35.2 - - + +
26A SER* 3.4 31.9 + - - -
28A ALA* 5.4 3.3 - - + +
259A TYR* 3.6 7.6 - - - -
270A LYS* 3.3 26.3 + - - -
403B ASN* 6.4 0.7 - - - -
454B ASP* 5.4 0.4 + - - -
455B LEU 3.3 0.8 - - - -
456B THR* 1.3 80.0 + - - +
458B ASP* 1.3 86.8 + - - +
460B GLN* 3.4 6.3 + - + +
461B SER* 3.1 30.7 + - - -
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Residues in contact with ASP 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LEU* 4.1 3.5 - - + +
403B ASN* 3.3 45.1 + - + +
404B LEU* 4.1 21.5 - - + -
407B ASN* 3.3 30.0 + - - +
454B ASP 4.4 1.2 - - - +
455B LEU* 3.6 16.6 + - - +
456B THR 3.5 0.4 - - - -
457B TYR* 1.3 96.0 + - - +
459B ILE* 1.3 64.4 + - - +
461B SER* 3.5 1.3 + - - -
462B PHE* 3.1 20.1 + - - +
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Residues in contact with ILE 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ILE* 4.3 23.8 - - + -
400B LEU* 4.6 5.4 - - + -
455B LEU 3.2 21.9 + - - +
456B THR* 3.7 6.7 - - - +
458B ASP* 1.3 75.8 - - + +
460B GLN* 1.3 68.4 + - + +
462B PHE* 3.2 8.9 + - + +
463B THR* 2.9 34.6 + - + +
484B ALA* 3.1 48.2 - - + +
486B HIS* 4.1 18.4 - - + +
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Residues in contact with GLN 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B THR* 3.0 24.9 + - - +
457B TYR* 3.4 7.6 + - + +
459B ILE* 1.3 75.9 - - + +
461B SER* 1.3 57.9 + - - +
463B THR* 3.2 9.7 + - - -
464B ASP* 2.8 65.3 + - - +
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Residues in contact with SER 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LYS* 4.6 13.0 + - - -
273A LEU* 6.5 0.9 - - - -
399B VAL* 5.4 0.3 - - - +
403B ASN* 3.0 24.7 + - - -
457B TYR* 3.1 32.1 + - - -
458B ASP* 3.7 1.8 - - - -
460B GLN* 1.3 75.2 - - - +
462B PHE* 1.3 57.2 + - - +
464B ASP* 3.6 8.5 - - - +
465B THR* 2.8 38.5 + - - -
468B ARG* 4.9 0.8 + - - +
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Residues in contact with PHE 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B LEU* 3.8 23.8 - - + -
393B VAL* 4.9 2.9 - - + -
396B LYS* 3.1 27.4 - - + -
397B ILE* 4.3 10.8 - - + -
399B VAL* 4.1 7.2 - - + -
400B LEU* 3.5 44.6 - - + -
403B ASN* 3.6 7.8 - - - +
458B ASP 3.1 11.7 + - - +
459B ILE* 3.2 10.3 + - - +
461B SER* 1.3 79.6 + - - +
463B THR* 1.3 70.8 + - + +
465B THR* 3.2 6.8 + - - -
466B VAL* 3.0 44.8 + - + +
482B ILE* 3.7 25.6 - - + -
484B ALA* 5.0 5.2 - - + -
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Residues in contact with THR 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ILE* 2.9 30.9 + - + +
460B GLN* 3.2 13.5 + - - -
462B PHE* 1.3 83.0 - - + +
464B ASP* 1.3 73.9 + - - +
466B VAL* 3.1 9.1 + - - +
467B TYR* 2.9 46.7 + - - -
482B ILE* 4.2 17.9 - - + +
483B GLU* 5.5 0.2 - - - -
484B ALA* 5.1 7.2 - - + +
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Residues in contact with ASP 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LYS* 5.0 10.8 + - - +
460B GLN* 2.8 47.7 + - - +
461B SER* 3.6 7.6 + - - +
463B THR* 1.3 80.0 + - - +
465B THR* 1.3 64.1 + - - +
467B TYR* 3.4 6.2 + - - +
468B ARG* 2.9 45.6 + - - +
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Residues in contact with THR 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A HIS* 5.6 2.3 + - - -
348A ASP* 4.2 11.5 + - - +
352A GLN* 3.7 27.4 - - - +
396B LYS* 5.8 2.2 - - + -
399B VAL* 4.5 16.7 - - + +
461B SER* 2.8 22.2 + - - -
462B PHE 3.2 8.5 + - - -
464B ASP* 1.3 77.4 - - - +
466B VAL* 1.3 65.5 + - + +
468B ARG* 3.6 17.6 + - - +
469B GLN* 2.9 40.7 + - + +
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Residues in contact with VAL 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B TRP* 3.9 17.0 - - + -
392B LEU* 3.7 23.9 - - + +
393B VAL* 4.2 13.9 - - + -
396B LYS* 4.5 14.4 - - + -
462B PHE* 3.0 49.9 + - + +
463B THR* 3.1 5.8 + - - +
465B THR* 1.3 78.5 - - + +
467B TYR* 1.3 57.5 + - - +
469B GLN* 3.7 4.8 - - - +
470B ALA* 2.8 27.5 + - - +
482B ILE* 4.3 11.2 - - + -
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Residues in contact with TYR 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B TRP* 4.0 12.6 - + - -
463B THR* 2.9 33.8 + - - +
464B ASP* 4.1 5.4 - - - +
466B VAL* 1.3 76.0 - - - +
468B ARG* 1.3 54.9 + - - +
470B ALA* 3.0 6.0 + - - +
471B ASN* 2.7 47.6 + - - +
476B LEU* 4.0 14.9 - - + +
480B MET 4.0 18.6 - - - -
481B LYS* 3.7 9.0 - - - +
482B ILE* 2.8 51.7 + - + -
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Residues in contact with ARG 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A HIS* 4.4 3.6 + - - -
273A LEU* 3.6 24.2 - - - +
277A LYS* 4.9 2.4 - - - +
344A LEU* 3.5 36.0 - - + +
345A ALA* 5.8 1.3 - - - +
348A ASP* 2.7 42.4 + - - +
461B SER* 4.9 1.4 + - - +
464B ASP* 2.9 41.9 + - - +
465B THR* 3.6 17.3 + - - +
467B TYR* 1.3 78.1 - - - +
469B GLN* 1.3 57.1 + - - +
471B ASN* 3.3 9.6 + - - +
472B ASN* 2.9 29.2 + - + +
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Residues in contact with GLN 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ALA 4.8 0.8 + - - -
348A ASP* 3.5 40.1 + - + +
349A GLU* 4.0 16.6 + - - +
352A GLN* 3.1 24.9 + - - +
392B LEU* 5.3 0.9 - - + -
396B LYS* 2.9 41.7 + - - +
465B THR* 2.9 24.0 + - + +
466B VAL* 3.9 3.1 - - - +
468B ARG* 1.3 73.8 - - - +
470B ALA* 1.3 68.1 + - - +
472B ASN* 3.4 8.3 + - - +
473B ILE* 3.2 28.2 + - + +
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Residues in contact with ALA 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B TRP* 3.8 13.9 - - + -
392B LEU* 4.1 7.7 - - + +
466B VAL 2.8 18.2 + - - +
467B TYR 3.4 4.7 - - - +
469B GLN* 1.3 79.3 - - - +
471B ASN* 1.3 63.6 + - - +
473B ILE* 3.3 19.3 + - - +
474B ASN 3.3 5.7 + - - -
475B MET* 3.5 18.8 + - - -
476B LEU* 3.8 27.1 - - + -
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Residues in contact with ASN 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B TYR* 2.7 35.1 + - - +
468B ARG* 3.6 8.2 - - - +
470B ALA* 1.3 71.4 - - - +
472B ASN* 1.3 65.3 + - - +
474B ASN* 2.9 21.4 + - - +
476B LEU* 3.4 30.1 - - - +
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Residues in contact with ASN 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A GLN* 5.4 3.2 + - - -
345A ALA* 3.9 25.4 - - + +
349A GLU* 4.4 12.8 - - - +
468B ARG* 2.9 18.1 + - + +
469B GLN* 3.6 9.6 - - - +
470B ALA 3.2 0.2 - - - -
471B ASN* 1.3 77.9 - - - +
473B ILE* 1.3 66.5 + - + +
474B ASN* 3.3 13.7 + - - -
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Residues in contact with ILE 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A GLU* 6.0 1.1 - - - +
392B LEU* 3.6 30.3 - - + -
396B LYS* 6.2 1.1 - - - +
469B GLN* 3.2 15.7 - - + +
470B ALA 3.3 7.6 - - - +
472B ASN* 1.3 83.8 - - - +
474B ASN* 1.3 70.3 + - - +
475B MET* 3.5 15.8 + - + +
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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
------------------------------------------------------------
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