Contacts of the helix formed by residues 467 - 483 (chain B) in PDB entry 2A1A
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 LYS 467 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B HIS* 3.6 36.1 + - + +
411B ILE* 3.5 13.6 - - + +
439B LEU* 3.7 33.2 - - + +
466B GLY* 1.3 66.8 - - - -
468B GLU* 1.3 75.1 + - + +
469B VAL 3.0 2.9 - - - -
470B ASP* 2.9 17.2 + - - +
471B LEU* 3.3 17.9 + - + +
528B ASN* 3.9 27.4 - - - +
529B THR* 5.3 2.4 + - - -
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Residues in contact with GLU 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B GLU* 4.3 1.9 - - - +
465B TYR* 4.0 8.1 - - - +
466B GLY* 3.0 26.7 + - - +
467B LYS* 1.3 101.8 + - + +
469B VAL* 1.3 53.4 + - - +
471B LEU* 3.0 17.8 + - + +
472B TYR 2.7 32.1 + - - -
523B PRO* 3.6 40.4 - - + +
526B ARG* 3.0 25.7 + - - +
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Residues in contact with VAL 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ILE* 4.9 4.3 - - + -
413B ARG* 3.7 30.5 - - + -
454B TYR 5.1 0.7 - - - +
455B MET* 5.8 0.2 - - - -
456B SER* 2.9 31.1 + - - +
458B GLU* 4.2 4.2 + - - +
459B GLN* 3.4 28.7 - - + +
465B TYR* 3.8 22.9 - - + -
466B GLY 3.4 16.7 + - - +
468B GLU* 1.3 79.9 + - - +
470B ASP* 1.3 67.6 + - - +
472B TYR* 3.7 3.5 - - - +
473B ALA* 3.4 18.5 + - - +
526B ARG* 4.0 0.4 - - - +
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Residues in contact with ASP 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B VAL* 4.1 2.5 - - + +
405B ILE* 5.4 0.2 - - - +
406B HIS* 2.7 33.3 + - + +
411B ILE* 3.5 7.4 - - - +
412B ASN* 2.1 48.7 + - - +
413B ARG* 3.7 6.1 - - - -
414B ASP 4.6 0.2 + - - -
415B LEU* 3.5 20.8 - - + +
467B LYS 2.9 9.1 + - - +
469B VAL* 1.3 74.3 - - - +
471B LEU* 1.3 56.3 + - - +
472B TYR 3.2 1.6 - - - -
473B ALA* 3.0 6.9 + - - +
474B LEU* 2.8 37.0 + - - +
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Residues in contact with LEU 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B HIS* 3.7 28.9 - - + +
467B LYS* 3.3 11.0 + - + +
468B GLU* 3.0 28.6 + - + +
470B ASP* 1.3 78.1 - - - +
472B TYR* 1.3 61.8 + - - +
474B LEU* 3.2 19.9 + - + +
475B GLY 3.1 16.6 + - - -
518B LEU* 3.4 19.9 - - + +
526B ARG* 4.1 14.8 - - + +
527B PRO 3.1 31.2 - - - +
528B ASN* 3.9 19.7 - - + -
529B THR* 4.2 7.4 - - + +
532B ILE* 4.8 0.4 - - + -
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Residues in contact with TYR 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B MET 4.0 10.8 - - - -
456B SER* 3.5 20.2 - - - -
457B PRO* 3.5 25.5 - - + +
468B GLU 2.7 19.8 + - - +
469B VAL 3.7 6.1 - - - +
471B LEU* 1.3 72.4 - - - +
473B ALA* 1.3 63.0 + - - +
475B GLY* 2.9 12.8 + - - -
476B LEU* 3.2 36.5 + - + +
499B ARG* 3.8 27.4 + - - -
518B LEU 3.7 14.5 + - - -
519B LEU* 3.6 39.3 + - + +
520B SER 4.4 1.1 - - - -
521B LYS* 5.4 0.2 - - - -
526B ARG* 3.4 30.0 - - - +
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Residues in contact with ALA 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B LEU* 3.7 36.8 - - + +
454B TYR* 3.8 19.2 + - + +
469B VAL 3.4 9.8 + - - +
470B ASP* 3.0 12.0 + - - +
472B TYR* 1.3 78.3 - - - +
474B LEU* 1.3 61.9 + - - +
476B LEU* 3.0 8.1 + - - +
477B ILE* 2.9 27.6 + - - +
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Residues in contact with LEU 474 (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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395B PHE* 3.3 16.0 - - + -
398B ILE* 3.6 31.0 - - + -
399B THR* 4.2 14.1 - - + +
402B VAL* 3.8 31.9 - - + -
415B LEU* 4.8 2.5 - - + -
470B ASP 2.8 22.9 + - - +
471B LEU* 3.2 18.1 + - + +
473B ALA* 1.3 71.2 - - - +
475B GLY* 1.3 53.0 - - - +
477B ILE* 4.4 7.9 - - + -
478B LEU* 2.8 36.4 + - - +
518B LEU* 4.9 1.8 - - + -
529B THR* 4.3 6.1 - - + -
532B ILE* 4.0 25.8 - - + -
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Residues in contact with GLY 475 (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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471B LEU 3.1 8.3 + - - -
472B TYR 2.9 10.8 + - - -
474B LEU* 1.3 75.6 - - - +
476B LEU* 1.3 55.8 + - - +
478B LEU 3.4 0.3 + - - -
479B ALA* 2.8 28.2 + - - +
515B LEU* 3.4 12.4 - - - +
518B LEU* 4.1 21.9 - - - +
519B LEU* 3.7 15.9 - - - -
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Residues in contact with LEU 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B TYR* 3.2 57.2 - - + +
472B TYR* 3.2 27.5 + - + +
473B ALA 3.0 7.7 + - - +
475B GLY* 1.3 75.5 - - - +
477B ILE* 1.3 58.3 + - - +
479B ALA* 3.8 3.2 - - - +
480B GLU* 2.9 31.4 + - - +
495B PHE* 3.7 26.6 - - + +
498B LEU* 3.8 29.6 - - + -
499B ARG* 4.2 8.5 - - - +
519B LEU* 3.8 7.6 - - + +
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Residues in contact with ILE 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 4.5 9.0 - - + -
378B ILE* 6.5 0.2 - - + -
395B PHE* 4.4 5.2 - - + -
398B ILE* 4.3 17.5 - - + -
415B LEU* 4.1 11.7 - - + -
416B LYS* 4.1 30.1 - - - +
417B PRO* 4.5 10.1 - - + -
420B ILE* 4.2 11.7 - - + -
454B TYR* 4.6 4.3 - - + -
473B ALA 2.9 24.5 + - - +
474B LEU* 3.8 15.0 - - + +
476B LEU* 1.3 73.8 - - - +
478B LEU* 1.3 61.1 + - - +
480B GLU* 3.7 6.6 - - - +
481B LEU* 2.8 50.4 + - + +
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Residues in contact with LEU 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 4.3 15.9 - - + -
395B PHE* 3.6 32.0 - - + -
474B LEU 2.8 23.1 + - - +
475B GLY 3.6 3.1 - - - +
477B ILE* 1.3 70.0 - - - +
479B ALA* 1.3 67.2 + - - +
481B LEU* 3.0 14.1 + - + -
482B LEU* 3.0 38.4 + - + +
511B GLU 5.3 0.2 - - - +
514B LEU* 3.6 32.3 - - + -
515B LEU* 3.6 22.2 - - + -
518B LEU* 4.3 7.9 - - + -
536B LEU* 6.3 0.2 - - + -
539B TRP* 4.8 6.5 - - + -
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Residues in contact with ALA 479 (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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475B GLY 2.8 22.0 + - - +
476B LEU 3.8 2.7 - - - +
478B LEU* 1.3 73.9 - - - +
480B GLU* 1.3 63.7 + - - +
482B LEU* 3.1 10.6 + - - +
483B HIS 3.2 10.4 + - - -
494B PHE* 3.7 13.2 - - + -
498B LEU* 3.7 31.2 - - + -
507B PHE* 3.9 10.0 - - + -
515B LEU* 3.6 21.0 - - + +
519B LEU* 5.5 1.6 - - + -
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Residues in contact with GLU 480 (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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378B ILE* 3.7 36.6 - - + +
381B ARG* 3.6 9.4 + - - -
417B PRO* 3.4 8.1 - - - +
453B ARG* 3.9 9.2 + - - -
454B TYR* 2.3 38.4 + - - -
476B LEU 2.9 15.9 + - - +
477B ILE* 3.8 4.2 - - - +
479B ALA* 1.3 76.8 - - - +
481B LEU* 1.3 61.9 + - - +
483B HIS 3.3 17.5 - - - +
485B CYS* 6.3 1.1 - - - -
491B THR* 4.3 7.7 - - + +
494B PHE* 3.9 11.4 - - + -
495B PHE* 3.4 19.8 - - + -
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Residues in contact with LEU 481 (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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374B LEU* 4.2 19.3 - - + -
377B TRP* 4.0 27.6 - - + -
378B ILE* 4.6 9.2 - - + -
381B ARG* 3.3 16.9 + - - +
386B LEU* 3.9 4.9 - - - +
391B ALA* 3.4 33.2 - - + +
392B LEU* 6.1 0.2 - - + -
394B LEU* 4.9 2.9 - - + -
395B PHE* 3.9 33.2 - - + +
398B ILE* 4.6 6.1 - - + -
477B ILE* 2.8 42.1 + - + +
478B LEU* 3.0 6.3 + - + +
480B GLU* 1.3 73.1 - - - +
482B LEU* 1.3 61.1 + - + +
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Residues in contact with LEU 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B LEU* 3.4 30.6 - - + +
388B LYS* 3.8 27.1 - - + -
391B ALA* 5.0 1.6 - - + -
392B LEU* 3.6 26.0 - - + -
478B LEU* 3.0 38.5 + - + +
479B ALA 3.1 3.8 + - - +
481B LEU* 1.3 82.6 - - + +
483B HIS* 1.3 58.8 + - - +
484B VAL 4.1 0.6 + - - -
506B ILE* 6.0 0.2 - - - -
507B PHE* 4.2 17.0 - - + -
511B GLU* 3.6 40.2 - - + +
515B LEU* 4.9 5.2 - - + -
539B TRP* 4.9 1.1 - - + -
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Residues in contact with HIS 483 (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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79A LYS* 4.3 9.0 - - - -
381B ARG* 4.7 1.5 + - - -
479B ALA 3.2 11.2 + - - +
480B GLU* 3.3 17.6 - - - +
482B LEU* 1.3 76.7 - - - +
484B VAL* 1.3 77.4 + - - +
485B CYS* 3.5 17.9 + - - -
490B GLU* 3.3 21.0 + - - -
494B PHE* 4.0 29.8 - + + -
504B SER* 6.1 0.2 - - - -
506B ILE* 3.6 41.5 - - + +
507B PHE* 4.1 4.3 - - + -
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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
------------------------------------------------------------
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