Contacts of the helix formed by residues 451 - 470 (chain B) in PDB entry 1IGN
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 451 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B SER* 1.3 71.0 - - - +
452B ASP* 1.3 63.0 + - - +
454B ASP 4.4 0.4 - - - +
455B TYR* 2.8 32.6 + - - +
557B TYR* 3.2 24.1 + - - +
561B TYR* 3.8 15.3 - - + -
572B GLU* 3.3 34.3 - - + +
573B PRO* 3.6 9.7 - - - +
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Residues in contact with ASP 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B SER* 3.2 10.2 - - - +
451B ALA* 1.3 78.7 - - - +
453B GLU* 1.3 57.0 + - + +
455B TYR* 3.8 1.9 - - - +
456B THR* 2.8 35.3 + - - +
561B TYR* 2.9 29.7 + - - -
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Residues in contact with GLU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B ARG* 3.4 11.8 + - - -
448B LYS 3.3 2.6 - - - +
449B PHE* 3.1 6.9 - - + -
450B SER* 2.9 38.0 + - - +
452B ASP* 1.3 76.1 - - + +
454B ASP* 1.3 65.6 + - - +
456B THR* 3.4 5.6 + - - -
457B LEU* 3.1 23.7 + - - +
535B ALA* 3.4 18.0 - - - +
536B HIS* 2.9 37.7 + - - -
541B TRP* 3.5 26.1 - - + -
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Residues in contact with ASP 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B PHE* 3.8 6.9 - - - -
450B SER 3.1 12.0 + - - +
451B ALA 3.2 5.1 + - - +
453B GLU* 1.3 75.2 - - - +
455B TYR* 1.3 58.3 + - - +
457B LEU* 3.3 7.9 + - - +
458B ALA* 2.8 28.4 + - - +
544B ARG* 2.8 52.4 + - - +
549B LEU* 4.7 3.8 - - - +
557B TYR* 3.9 19.1 - - + +
573B PRO* 3.9 3.1 - - - +
574B MET* 3.2 34.7 + - + +
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Residues in contact with TYR 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B ALA 2.8 21.6 + - - +
452B ASP* 3.8 4.0 - - - +
454B ASP* 1.3 69.9 - - - +
456B THR* 1.3 62.4 + - - +
458B ALA* 2.9 3.3 + - - +
459B ILE* 2.8 60.8 + - + +
557B TYR* 3.6 6.4 - + + -
558B ILE* 4.0 20.2 - - + -
561B TYR* 3.5 55.0 - + + -
562B GLU* 2.9 38.3 + - + +
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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
----------------------------------------------------------
452B ASP* 2.8 25.1 + - - +
453B GLU* 3.7 7.3 - - - -
454B ASP 3.4 0.2 - - - -
455B TYR* 1.3 78.5 - - - +
457B LEU* 1.3 56.3 + - - +
459B ILE* 4.1 5.1 - - - +
460B ALA* 2.9 33.0 + - + +
529B PHE* 3.5 13.9 - - + -
533B HIS* 3.4 36.3 + - + +
541B TRP* 5.8 0.7 - - - -
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Residues in contact with LEU 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B GLU 3.1 13.7 + - - +
454B ASP* 3.5 10.3 - - - +
455B TYR 3.1 0.2 - - - -
456B THR* 1.3 76.3 - - - +
458B ALA* 1.3 59.5 + - - +
461B VAL* 2.9 47.1 + - + +
525B PHE* 4.4 2.2 - - + -
526B PHE* 4.2 20.0 - - + -
529B PHE* 3.6 31.3 - - + -
541B TRP* 4.1 29.6 - - + +
544B ARG* 4.3 11.2 - - + -
545B PHE* 4.1 13.9 - - + +
549B LEU* 3.6 22.4 - - + -
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Residues in contact with ALA 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B ASP 2.8 15.1 + - - +
455B TYR* 2.9 11.0 + - - +
457B LEU* 1.3 77.3 - - - +
459B ILE* 1.3 63.1 + - - +
461B VAL* 3.4 0.5 + - - +
462B LYS* 3.0 19.1 + - - +
549B LEU* 3.7 26.4 - - + +
554B ILE* 3.5 16.5 - - + +
557B TYR* 4.5 6.7 - - + -
558B ILE* 3.7 24.5 - - + -
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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
----------------------------------------------------------
455B TYR* 2.8 58.4 + - + +
456B THR* 4.1 4.9 - - - +
458B ALA* 1.3 72.3 - - - +
460B ALA* 1.3 59.9 + - - +
462B LYS* 2.9 11.2 + - + +
463B LYS* 2.8 49.0 + - + +
558B ILE* 3.7 24.2 - - + -
562B GLU* 4.7 1.8 - - - +
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Residues in contact with ALA 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B THR* 2.9 22.3 + - + +
457B LEU 3.9 1.1 - - - +
459B ILE* 1.3 80.2 - - - +
461B VAL* 1.3 61.0 + - - +
463B LYS* 3.6 13.6 + - - +
464B GLN* 3.3 20.1 + - - +
467B ARG* 4.7 2.4 + - - -
525B PHE* 3.9 11.3 - - + -
529B PHE* 3.4 28.3 - - + -
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Residues in contact with VAL 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B LEU* 2.9 34.0 + - + +
458B ALA 3.8 3.4 - - - +
460B ALA* 1.3 74.2 - - - +
462B LYS* 1.3 60.5 + - - +
464B GLN* 3.2 5.9 + - - +
465B PHE* 3.0 43.6 + - + -
521B ILE* 4.1 7.6 - - + -
525B PHE* 3.7 26.0 - - + -
545B PHE* 3.8 27.6 - - + -
549B LEU* 4.2 2.0 - - + -
554B ILE* 3.5 26.0 - - + -
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Residues in contact with LYS 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B ALA 3.0 12.3 + - - +
459B ILE* 2.9 14.8 + - + +
461B VAL* 1.3 76.8 - - - +
463B LYS* 1.3 60.4 + - + +
465B PHE* 3.2 1.2 + - - +
466B TYR* 2.8 35.2 + - + +
513B ARG* 3.1 54.4 + - - +
515B GLN* 3.9 31.6 - - - +
554B ILE* 4.5 1.8 - - + +
555B ASP* 5.0 2.3 + - - +
558B ILE* 3.8 30.0 - - + +
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Residues in contact with LYS 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ILE* 2.8 36.5 + - + +
460B ALA* 4.0 13.0 - - - +
461B VAL 3.4 0.2 - - - -
462B LYS* 1.3 74.8 - - + +
464B GLN* 1.3 62.2 + - - +
466B TYR* 3.7 3.2 - - - +
467B ARG* 3.0 40.9 + - - +
474B PRO* 4.1 31.5 - - + +
475B ASP* 4.4 21.2 + - - +
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Residues in contact with GLN 464 (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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460B ALA 3.3 14.0 + - - +
461B VAL* 3.2 11.9 + - + +
462B LYS 3.1 0.8 - - - -
463B LYS* 1.3 77.7 - - - +
465B PHE* 1.3 67.7 + - + +
467B ARG* 3.0 36.9 + - - +
468B ASP* 3.1 56.9 + - - +
520B PRO 5.5 0.4 - - - +
521B ILE* 5.1 4.9 - - + -
522B ALA* 3.1 40.8 - - + +
525B PHE* 4.4 16.6 - - + -
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Residues in contact with PHE 465 (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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461B VAL* 3.0 37.3 + - + +
462B LYS 3.7 1.1 - - - +
464B GLN* 1.3 73.9 - - + +
466B TYR* 1.3 64.7 + - - +
468B ASP* 3.3 9.2 + - - +
469B LEU* 2.9 29.5 + - - +
513B ARG* 2.9 21.5 - - - +
515B GLN* 2.8 23.1 - - - +
517B ARG* 3.5 42.8 - - + +
518B ARG 3.7 8.3 - - - -
519B GLY* 3.5 35.4 - - - -
520B PRO 3.8 9.6 - - - -
521B ILE* 4.1 13.2 - - + -
545B PHE* 4.8 1.1 - + - -
554B ILE* 4.0 8.3 - - + -
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Residues in contact with TYR 466 (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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462B LYS* 2.8 24.0 + - + +
463B LYS* 3.7 7.2 - - - +
465B PHE* 1.3 71.1 - - - +
467B ARG* 1.3 56.6 + - - +
469B LEU* 4.6 0.2 - - - -
470B PHE* 2.8 67.5 + + + +
471B GLN 3.9 0.2 + - - -
472B ILE* 3.4 41.4 - - + +
473B ASP 4.1 1.9 + - - -
474B PRO* 3.5 35.4 - - + -
513B ARG* 3.7 28.6 - - + +
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Residues in contact with ARG 467 (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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460B ALA 4.7 2.2 + - - -
463B LYS* 3.0 29.1 + - - +
464B GLN* 3.0 55.8 + - - +
465B PHE 3.2 0.2 - - - -
466B TYR* 1.3 77.4 - - - +
468B ASP* 1.3 59.3 + - - +
471B GLN* 2.8 37.6 + - - +
472B ILE 3.8 13.7 - - - +
474B PRO* 4.1 12.5 - - + +
480B LEU* 3.6 28.8 - - + +
525B PHE* 5.9 1.0 - - - -
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Residues in contact with ASP 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B GLN* 3.1 47.3 + - - +
465B PHE* 3.8 8.9 - - - +
467B ARG* 1.3 80.2 + - - +
469B LEU* 1.3 64.6 + - + +
471B GLN* 4.2 14.4 - - - +
517B ARG* 4.2 18.1 + - - +
520B PRO 4.7 5.4 - - - +
522B ALA 5.7 0.2 + - - -
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Residues in contact with LEU 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B PHE 2.9 17.8 + - - +
466B TYR 3.8 2.0 - - - +
468B ASP* 1.3 83.2 - - - +
470B PHE* 1.3 83.8 + - + +
471B GLN* 5.3 1.4 - - - +
513B ARG* 3.0 35.9 - - - +
517B ARG* 4.5 31.0 - - - +
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Residues in contact with PHE 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B TYR* 2.8 55.6 + + + +
469B LEU* 1.3 96.6 - - + +
471B GLN* 1.3 71.7 + - - +
472B ILE* 3.0 35.0 + - + +
513B ARG* 3.8 28.5 - - + -
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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