Contacts of the helix formed by residues 468 - 490 (chain B) in PDB entry 1X11
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 ALA 468 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421B ASP* 3.1 18.0 - - + +
423B GLY 4.4 5.4 - - - +
424B ASN* 3.8 26.2 - - - +
425B ILE 4.2 4.0 - - - +
426B VAL* 3.9 23.8 - - + +
465B SER* 3.4 22.4 + - - +
466B GLU 3.3 3.4 + - - +
467B ASP* 1.3 76.3 - - - +
469B GLN* 1.3 60.2 + - - +
471B ILE* 4.0 1.3 - - - -
472B ALA* 3.4 12.0 + - - +
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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
----------------------------------------------------------
421B ASP* 2.7 36.1 + - - +
423B GLY 5.5 2.0 + - - +
466B GLU 5.2 0.6 + - - -
467B ASP 3.1 0.8 + - - -
468B ALA* 1.3 76.4 - - - +
470B LEU* 1.3 61.2 + - - +
471B ILE 3.3 0.2 - - - -
472B ALA 3.4 0.7 + - - -
473B GLN* 2.8 53.1 + - - +
2D ASN* 3.3 20.4 + - - +
4D TYR* 3.2 20.0 + - - -
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Residues in contact with LEU 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A GLN* 4.3 14.6 - - + -
361A VAL* 4.0 11.7 - - + -
365A LYS* 3.3 36.1 - - - +
422A ILE* 3.7 31.2 - - + -
425A ILE* 4.9 5.6 - - + -
332B PHE* 3.5 20.6 - - + -
467B ASP* 2.9 14.1 + - + +
469B GLN* 1.3 76.8 - - - +
471B ILE* 1.3 58.1 + - - +
473B GLN* 4.2 9.4 - - + +
474B SER* 2.6 44.8 + - - +
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Residues in contact with ILE 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B PHE* 3.6 39.3 - - + -
333B ALA 4.4 0.4 - - - +
334B ALA* 4.4 5.8 - - + -
390B LEU* 3.9 32.8 - - + -
392B ILE* 4.5 3.5 - - + +
426B VAL* 4.0 20.6 - - + -
465B SER* 3.7 30.7 - - - +
467B ASP 2.9 15.8 + - - +
468B ALA* 4.0 4.5 - - - +
470B LEU* 1.3 75.6 - - - +
472B ALA* 1.3 59.9 + - - +
474B SER* 3.4 2.3 + - - -
475B ILE* 2.9 45.4 + - + +
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Residues in contact with ALA 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ILE* 3.9 28.4 - - + +
421B ASP* 3.4 35.4 - - + +
426B VAL* 4.6 1.1 - - + +
468B ALA 3.4 10.3 + - - +
469B GLN 3.4 0.8 + - - +
471B ILE* 1.3 77.7 - - - +
473B GLN* 1.3 55.3 + - - +
475B ILE* 3.1 2.9 + - - +
476B GLY* 2.7 33.3 + - - -
4D TYR* 4.0 14.7 - - + -
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Residues in contact with GLN 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A GLN* 3.6 6.1 - - - +
422A ILE* 3.3 26.0 - - - +
469B GLN* 2.8 58.9 + - - +
470B LEU* 3.9 7.1 - - + +
472B ALA* 1.3 71.7 - - - +
474B SER* 1.3 56.9 + - - +
476B GLY* 3.3 1.2 + - - -
477B GLN* 2.9 32.6 + - - +
1C GLN* 3.3 45.8 + - + +
4D TYR* 4.0 15.6 - - + +
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Residues in contact with SER 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A MSE 4.7 1.7 - - - +
358A GLN* 3.5 33.6 + - - +
330B ILE* 4.2 14.1 - - - -
332B PHE* 3.4 21.3 - - - -
392B ILE* 4.1 8.7 - - - +
470B LEU* 2.6 26.5 + - - +
471B ILE 3.6 4.7 - - - -
472B ALA 3.2 0.2 - - - -
473B GLN* 1.3 76.5 - - - +
475B ILE* 1.3 57.4 + - - +
477B GLN* 3.3 3.3 + - - +
478B ALA* 2.9 27.5 + - - +
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Residues in contact with ILE 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B LEU* 5.4 3.4 - - + -
392B ILE* 4.0 21.5 - - + -
397B ILE* 4.2 33.9 - - + -
413B LEU* 4.8 0.2 - - + -
416B ILE* 5.3 1.8 - - + -
419B ILE* 4.0 29.6 - - + -
426B VAL* 5.6 0.4 - - + -
428B LEU* 4.4 8.1 - - + -
471B ILE* 2.9 33.2 + - + +
472B ALA 3.7 3.4 - - - +
474B SER* 1.3 73.4 - - - +
476B GLY* 1.3 59.8 + - - +
478B ALA* 3.3 7.4 + - - +
479B PHE* 2.9 51.6 + - + -
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Residues in contact with GLY 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ILE* 4.7 0.4 - - - +
472B ALA 2.7 19.8 + - - -
473B GLN 3.7 1.6 - - - -
475B ILE* 1.3 70.4 - - - +
477B GLN* 1.3 64.6 + - - +
479B PHE* 3.1 19.5 - - - +
480B SER* 3.0 23.3 + - - -
4D TYR* 4.5 21.1 - - - -
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Residues in contact with GLN 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ASN* 3.2 38.3 + - - +
354A MSE 3.6 15.8 - - + +
355A MSE 3.8 10.3 - - + -
358A GLN* 3.1 41.3 - - - +
473B GLN 2.9 13.1 + - - +
474B SER 3.5 0.7 - - - +
475B ILE 3.3 0.2 - - - -
476B GLY* 1.3 72.1 - - - +
478B ALA* 1.3 68.0 + - - +
480B SER* 2.9 15.9 + - - -
481B VAL* 3.0 16.5 + - - +
1C GLN* 2.8 29.6 + - - +
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Residues in contact with ALA 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A MSE 3.8 22.1 - - + -
392B ILE* 4.2 5.2 - - + -
393B LEU 3.5 26.0 - - - +
394B THR* 4.2 2.2 - - - +
413B LEU* 3.9 10.0 - - + +
474B SER 2.9 14.7 + - - +
475B ILE* 3.3 13.7 - - - +
476B GLY 3.2 0.2 - - - -
477B GLN* 1.3 77.1 - - - +
479B PHE* 1.3 63.3 + - - +
481B VAL* 3.3 1.2 + - - +
482B ALA* 2.9 25.5 + - - +
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Residues in contact with PHE 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B LEU* 3.6 32.8 - - + -
416B ILE* 3.6 25.1 - - + -
417B SER 4.1 3.8 - - - -
419B ILE* 4.2 9.9 - - + -
475B ILE* 2.9 31.7 + - + -
476B GLY* 3.1 17.0 + - - +
478B ALA* 1.3 76.3 - - - +
480B SER* 1.3 58.0 + - - +
482B ALA* 3.1 1.8 + - - +
483B TYR* 2.8 32.9 + - - +
4D TYR* 3.9 20.0 - - + -
5D GLU 3.7 17.7 - - - +
6D ASN* 3.5 44.5 - - + +
7D PRO* 4.6 4.5 - - + -
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Residues in contact with SER 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ASN* 3.4 29.4 + - - -
476B GLY 3.0 11.7 + - - -
477B GLN* 2.9 11.5 + - - -
479B PHE* 1.3 75.9 - - - +
481B VAL* 1.3 62.3 + - - +
483B TYR* 3.3 8.9 + - - +
484B GLN* 3.0 29.8 + - - +
7D PRO* 5.5 3.3 - - - +
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Residues in contact with VAL 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ASN* 3.5 29.2 - - + -
352A VAL* 3.5 33.2 - - + +
355A MSE 3.8 11.0 - - - -
394B THR* 3.8 15.9 - - + -
477B GLN 3.0 10.3 + - - +
478B ALA 3.9 4.9 - - - +
480B SER* 1.3 74.4 - - - +
482B ALA* 1.3 64.7 + - - +
484B GLN* 2.9 23.1 + - + +
485B GLU* 2.9 35.7 + - + +
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Residues in contact with ALA 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B THR* 3.5 25.9 - - - +
413B LEU* 3.9 12.6 - - + -
478B ALA 2.9 16.9 + - - +
479B PHE* 3.5 4.0 - - - +
481B VAL* 1.3 76.5 - - - +
483B TYR* 1.3 57.9 + - - +
485B GLU* 3.4 14.9 + - - +
486B PHE* 2.9 28.4 + - - +
6D ASN* 5.7 1.3 - - - +
8D THR* 4.2 8.6 - - + +
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Residues in contact with TYR 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B PHE 2.8 15.7 + - - +
480B SER* 3.6 7.4 - - - +
481B VAL 3.1 0.2 - - - -
482B ALA* 1.3 74.5 - - - +
484B GLN* 1.3 56.9 + - + +
486B PHE* 3.1 9.5 + + - +
487B LEU* 2.8 78.7 + - + +
7D PRO* 3.6 46.7 - - + +
8D THR* 3.1 26.9 + - - +
10D LYS* 4.7 6.1 + - - -
11D PHE* 4.1 15.9 - + - -
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Residues in contact with GLN 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A SER* 3.1 27.2 + - - -
351A ASN* 2.6 31.7 + - - -
352A VAL* 5.1 0.3 - - - +
480B SER* 3.0 17.4 + - - +
481B VAL* 2.9 17.3 + - + +
483B TYR* 1.3 76.3 - - + +
485B GLU* 1.3 58.0 + - + +
487B LEU* 3.4 4.0 + - + -
488B ARG* 2.8 36.0 + - - +
494B PRO* 2.9 42.6 - - + +
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Residues in contact with GLU 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B THR* 4.0 18.4 + - - +
395B GLN* 4.8 6.5 + - - +
481B VAL* 2.9 36.1 + - + +
482B ALA* 3.6 16.1 - - - +
484B GLN* 1.3 73.9 - - + +
486B PHE* 1.3 65.7 + - - +
488B ARG* 3.2 27.9 + - - +
489B ALA* 2.9 25.5 + - - +
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Residues in contact with PHE 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ALA 2.9 15.3 + - - +
483B TYR* 3.1 28.5 + + - +
485B GLU* 1.3 76.4 - - - +
487B LEU* 1.3 71.6 + - + +
489B ALA* 3.4 4.8 + - + +
490B ASN* 2.9 56.0 + - + -
492B ILE* 6.1 1.6 - - + -
8D THR* 4.1 12.6 - - + -
11D PHE* 3.6 49.1 - + + -
12D PHE* 3.5 28.7 - + - -
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Residues in contact with LEU 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B TYR* 2.8 70.8 + - + +
484B GLN* 3.6 6.5 - - + +
486B PHE* 1.3 78.6 - - + +
488B ARG* 1.3 66.4 + - - +
490B ASN* 2.8 17.8 + - - +
492B ILE* 3.1 46.3 + - + +
494B PRO* 3.9 23.1 - - + -
11D PHE* 5.7 2.5 - - + -
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Residues in contact with ARG 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A SER* 6.2 1.0 - - - -
484B GLN* 2.8 28.0 + - - +
485B GLU* 3.3 37.5 - - - +
487B LEU* 1.3 75.3 - - - +
489B ALA* 1.3 64.7 + - - +
490B ASN 3.0 1.4 + - - -
491B GLY* 3.1 14.6 + - - -
492B ILE 3.3 11.9 + - - +
494B PRO* 3.5 32.0 + - + +
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Residues in contact with ALA 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B GLU 2.9 16.0 + - - +
486B PHE* 3.8 7.6 - - + +
487B LEU 3.2 0.4 - - - -
488B ARG* 1.3 76.8 - - - +
490B ASN* 1.3 62.3 + - - +
491B GLY 3.2 3.4 + - - -
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Residues in contact with ASN 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B PHE* 2.9 51.5 + - + +
487B LEU* 2.8 15.6 + - - +
489B ALA* 1.3 77.7 - - - +
491B GLY* 1.3 57.9 + - - +
492B ILE* 3.2 24.8 + - + +
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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