Contacts of the helix formed by residues 468 - 485 (chain B) in PDB entry 3IAD
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 ASN 468 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B ASP* 1.3 80.8 - - + +
469B TYR* 1.3 66.5 + - - +
470B SER* 3.3 27.2 + - - +
471B ASP* 3.0 32.1 + - - +
472B ARG* 3.4 17.4 + - - +
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Residues in contact with TYR 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLU* 5.8 2.9 - - - -
428B LYS* 3.6 25.0 - - + +
429B MET* 3.6 43.0 - - + +
432B ASP* 2.8 28.6 + - - -
468B ASN* 1.3 74.0 - - - +
470B SER* 1.3 67.9 + - - +
472B ARG* 2.9 14.1 + - + +
473B ILE* 2.9 48.0 + - + +
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Residues in contact with SER 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ASN* 3.3 20.4 + - - +
469B TYR* 1.3 83.0 - - - +
471B ASP* 1.3 66.0 + - - +
473B ILE* 3.1 9.9 - - - +
474B GLN* 3.0 40.2 + - - +
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Residues in contact with ASP 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B MET* 3.1 38.6 - - - +
466B LEU* 4.3 20.2 - - + -
467B ASP* 4.7 8.8 + - - +
468B ASN* 3.0 24.0 + - - +
469B TYR 3.3 0.6 - - - -
470B SER* 1.3 82.6 + - - +
472B ARG* 1.3 62.0 + - - +
474B GLN* 3.6 4.2 + - - +
475B VAL* 3.3 28.9 + - - +
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Residues in contact with ARG 472 (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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350B VAL* 2.7 31.7 + - - +
351B PHE* 3.8 9.7 - - + +
352B THR* 4.3 9.1 - - - +
355B GLU* 2.8 42.5 + - - +
466B LEU* 3.0 53.6 + - + +
467B ASP 4.8 2.5 - - - -
468B ASN 3.4 20.0 - - - +
469B TYR* 2.9 13.8 + - + +
471B ASP* 1.3 77.1 - - - +
473B ILE* 1.3 62.0 + - - +
475B VAL* 3.4 5.5 + - - +
476B LEU* 3.2 27.6 + - + +
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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
----------------------------------------------------------
429B MET* 3.7 30.3 - - + +
432B ASP* 3.6 21.5 - - + +
433B ILE* 3.8 17.5 - - + -
469B TYR* 2.9 50.2 + - + +
470B SER* 3.1 16.4 - - - +
472B ARG* 1.3 74.4 - - - +
474B GLN* 1.3 60.4 + - + +
476B LEU* 3.2 9.6 + - + +
477B GLN* 2.7 49.3 + - - +
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Residues in contact with GLN 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B LEU* 6.3 1.3 - - + -
448B ASP* 3.5 44.6 + - + +
449B LEU* 6.1 0.2 - - - -
452B MET* 3.2 33.8 - - - +
470B SER* 3.0 35.1 + - - +
471B ASP* 3.6 7.3 + - - +
473B ILE* 1.3 78.5 - - + +
475B VAL* 1.3 56.7 + - - +
477B GLN* 3.4 16.2 + - - +
478B ASN* 3.0 41.8 + - - +
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Residues in contact with VAL 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 4.6 11.0 - - + -
351B PHE* 3.8 23.8 - - + -
449B LEU* 5.5 2.9 - - + -
452B MET* 4.6 11.4 - - + -
464B LEU* 4.9 0.9 - - + -
466B LEU* 4.2 19.1 - - + -
471B ASP 3.3 15.5 + - - +
472B ARG 3.7 7.2 - - - +
473B ILE 3.3 0.2 - - - -
474B GLN* 1.3 76.4 - - + +
476B LEU* 1.3 59.4 + - - +
478B ASN* 3.6 3.8 + - - +
479B MET* 3.0 28.7 + - + +
550B TRP* 3.7 21.7 - - + -
553B LEU* 4.3 20.2 - - + -
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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
----------------------------------------------------------
342B LEU* 4.6 3.1 - - + -
351B PHE* 3.7 34.5 - - + -
355B GLU* 4.2 34.8 - - + +
359B ALA* 4.2 17.9 - - + -
429B MET* 4.7 5.8 - - - -
433B ILE* 4.1 25.1 - - + -
472B ARG* 3.2 17.6 + - + +
473B ILE* 3.5 17.0 - - + +
475B VAL* 1.3 74.5 - - - +
477B GLN* 1.3 65.6 + - - +
479B MET* 3.1 13.9 + - + +
480B VAL* 3.0 27.9 + - - +
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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
----------------------------------------------------------
432B ASP* 2.8 34.9 + - - +
433B ILE* 4.1 13.9 - - - +
436B ALA* 3.6 27.5 - - + +
437B THR* 5.9 0.5 - - - +
445B LEU* 4.2 16.4 - - + +
473B ILE* 2.7 33.2 + - + +
474B GLN* 3.5 26.0 + - - +
476B LEU* 1.3 74.3 - - - +
478B ASN* 1.3 56.4 + - - +
480B VAL* 3.5 1.7 + - - +
481B HIS* 3.0 30.0 + - - +
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Residues in contact with ASN 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B LEU* 3.0 47.9 + - - +
446B LEU 4.1 0.7 + - - -
449B LEU* 3.8 38.3 - - + +
474B GLN* 3.0 36.2 + - - +
475B VAL 4.0 3.6 - - - +
477B GLN* 1.3 74.0 - - - +
479B MET* 1.3 60.0 + - - +
481B HIS* 3.7 5.4 - - - +
482B CYS* 2.8 37.3 + - - -
546B LEU* 4.2 9.0 - - - +
550B TRP* 4.2 5.8 - - + -
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Residues in contact with MET 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B THR* 4.1 15.5 - - + +
341B LEU* 3.8 23.1 - - + +
342B LEU* 3.7 42.4 - - + -
347B LEU* 3.6 31.6 - - + -
351B PHE* 4.2 11.0 - - + -
359B ALA* 5.3 1.3 - - - -
475B VAL* 3.0 18.1 + - + +
476B LEU* 3.1 12.5 + - + +
478B ASN* 1.3 76.3 - - - +
480B VAL* 1.3 58.7 + - + +
482B CYS* 3.2 6.2 + - - +
483B ALA* 2.9 26.3 + - - +
550B TRP* 3.6 20.6 - - + -
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Residues in contact with VAL 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B VAL* 4.1 9.1 - - + +
338B THR* 4.1 9.6 - - + +
359B ALA* 4.1 14.4 - - + +
363B SER* 3.5 31.6 - - - +
366B HIS* 5.2 4.3 - - + -
433B ILE* 3.6 33.4 - - + -
437B THR* 4.1 16.8 - - + -
476B LEU 3.0 11.9 + - - +
477B GLN 4.1 1.6 - - - +
479B MET* 1.3 72.6 - - + +
481B HIS* 1.3 60.0 + - - +
483B ALA* 3.1 7.5 + - - +
484B ASP* 2.8 27.7 + - + +
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Residues in contact with HIS 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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436B ALA 4.3 10.6 + - - +
437B THR* 4.7 10.8 - - - +
438B ASP 5.6 0.4 - - - -
439B MET* 3.5 24.5 - - + +
442B HIS* 2.8 35.3 + - + +
445B LEU* 3.7 26.0 - - + -
477B GLN 3.0 18.0 + - - +
478B ASN* 3.7 4.0 - - - +
480B VAL* 1.3 77.1 - - - +
482B CYS* 1.3 56.2 + - - +
484B ASP* 3.0 11.1 + - - +
485B LEU* 2.8 50.3 + - + +
546B LEU* 3.4 28.3 - - + -
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Residues in contact with CYS 482 (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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341B LEU* 4.4 4.7 - - + -
478B ASN* 2.8 29.5 + - - +
479B MET* 3.4 6.3 - - - +
481B HIS* 1.3 72.4 - - - +
483B ALA* 1.3 61.6 + - - +
485B LEU 3.2 14.9 - - - -
486B SER 3.2 0.3 + - - -
546B LEU* 3.7 36.6 - - - -
547B TRP* 3.1 39.3 - - + +
550B TRP* 4.0 30.5 - - + -
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Residues in contact with ALA 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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268B TRP* 5.5 0.2 - - - -
333B ASP* 5.4 1.0 - - - +
334B VAL* 3.6 24.9 - - + +
337B SER* 3.9 14.8 - - - -
338B THR* 3.5 25.8 - - - +
341B LEU* 4.6 4.9 - - + +
479B MET 2.9 12.2 + - - +
480B VAL 3.1 8.5 + - - +
482B CYS* 1.3 76.5 - - - +
484B ASP* 1.3 60.4 + - - +
486B SER* 2.9 27.3 + - - -
487B ASN* 5.5 0.9 + - - -
547B TRP* 4.9 0.2 - - - -
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Residues in contact with ASP 484 (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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325B TYR* 4.2 13.3 + - - -
330B HIS* 3.1 11.3 + - - -
334B VAL* 3.9 8.6 - - + +
366B HIS* 3.3 13.1 + - + -
437B THR* 4.0 19.6 - - + +
439B MET* 4.4 11.4 - - - +
480B VAL* 2.8 13.5 + - + +
481B HIS* 3.0 15.9 + - - +
483B ALA* 1.3 77.3 - - - +
485B LEU* 1.3 64.1 + - + +
486B SER 3.4 2.2 + - - -
487B ASN* 5.0 2.8 + - - +
620B ZN 2.2 35.5 - - - -
621B MG 4.3 4.5 - - - -
901B 15X 4.9 4.8 - - - +
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Residues in contact with LEU 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B MET* 3.6 17.9 - - + -
442B HIS* 4.1 0.2 - - - +
481B HIS* 2.8 46.4 + - + +
482B CYS 3.2 5.2 - - - +
484B ASP* 1.3 79.6 - - + +
486B SER* 1.3 56.3 + - - +
487B ASN 3.6 2.2 - - - -
488B PRO* 4.1 4.2 - - - +
538B PHE* 3.7 13.5 - - + -
542B ILE* 3.9 24.5 - - + -
543B VAL* 3.9 17.6 - - + +
546B LEU* 3.8 15.9 - - + -
547B TRP* 3.0 18.2 + - - -
901B 15X 3.6 33.7 - - + -
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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