Contacts of the helix formed by residues 464 - 484 (chain B) in PDB entry 2FGY
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 GLY 464 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LYS* 6.1 6.1 - - - -
462B VAL 3.2 1.0 + - - -
463B PRO* 1.3 70.3 - - - +
465B SER* 1.3 64.0 + - - +
466B ARG 3.4 2.2 - - - -
467B GLU* 3.3 28.2 + - - +
468B ARG* 3.0 39.8 + - - +
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Residues in contact with SER 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLU* 4.8 5.2 + - - +
458B TYR* 3.5 3.9 - - - +
459B ASP* 3.0 45.2 + - - +
462B VAL* 3.0 20.9 + - - -
463B PRO 3.3 2.6 + - - -
464B GLY* 1.3 77.4 - - - +
466B ARG* 1.3 63.0 + - - +
468B ARG* 3.3 14.0 + - - +
469B THR* 2.8 30.2 + - - -
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Residues in contact with ARG 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B TYR* 3.7 41.5 - - + -
459B ASP 4.9 0.2 + - - -
462B VAL 4.6 1.0 + - - -
464B GLY 3.4 0.4 - - - -
465B SER* 1.3 77.7 + - - +
467B GLU* 1.3 76.0 + - - +
469B THR* 3.2 3.3 + - - -
470B VAL* 3.0 41.2 + - - +
499B VAL* 3.8 14.7 - - + +
509B GLU* 2.8 38.0 + - - +
510B GLU 5.0 2.0 + - - -
511B VAL* 4.2 11.3 - - - +
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Residues in contact with GLU 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B GLY* 3.3 37.3 + - - +
466B ARG* 1.3 88.7 + - - +
468B ARG* 1.3 57.2 + - + +
470B VAL* 3.4 7.7 + - - +
471B VAL* 3.0 36.4 + - + +
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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
----------------------------------------------------------
206A ILE* 3.7 44.3 - - - +
207A GLU* 2.8 46.1 + - + +
210A LEU* 6.1 0.2 - - - +
273A LYS* 5.0 8.3 + - - +
277A ALA* 4.4 4.4 - - - +
462B VAL* 4.0 13.7 - - - +
463B PRO 3.8 9.3 + - - -
464B GLY* 3.0 29.2 + - - +
465B SER* 3.6 20.8 - - - +
467B GLU* 1.3 77.7 - - + +
469B THR* 1.3 58.1 + - - +
471B VAL* 3.4 8.6 + - - +
472B LYS* 2.9 27.9 + - - +
475B ARG* 5.1 1.7 + - - -
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Residues in contact with THR 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLU* 5.6 0.9 + - - -
456B TYR* 3.3 32.8 - - + -
457B ARG 3.7 16.0 + - - +
458B TYR* 3.4 15.6 - - + +
465B SER* 2.8 18.9 + - - -
466B ARG 3.6 4.0 - - - -
467B GLU 3.2 0.2 - - - -
468B ARG* 1.3 76.5 - - - +
470B VAL* 1.3 59.9 + - - +
472B LYS* 3.4 14.6 + - - +
473B ALA* 3.0 27.4 + - - +
499B VAL* 3.8 13.9 - - + -
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Residues in contact with VAL 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B ARG* 3.0 47.4 + - + +
467B GLU* 3.8 7.4 - - - +
468B ARG 3.4 0.2 - - - -
469B THR* 1.3 74.1 - - - +
471B VAL* 1.3 66.0 + - + +
473B ALA* 3.3 7.7 + - - +
474B ARG* 3.1 59.3 + - - +
499B VAL* 4.2 16.2 - - + -
511B VAL* 4.3 15.9 - - + -
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Residues in contact with VAL 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B GLU* 3.0 24.9 + - + +
468B ARG* 3.6 8.7 - - - +
470B VAL* 1.3 75.7 - - + +
472B LYS* 1.3 62.3 + - - +
474B ARG* 3.3 10.0 + - - +
475B ARG* 3.0 44.8 + - + +
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Residues in contact with LYS 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A GLU* 5.9 0.2 - - - +
406B ASP* 5.1 2.2 + - - -
423B ASP* 2.8 52.8 + - + +
456B TYR* 3.6 39.1 - - + +
457B ARG 5.5 2.0 + - - -
468B ARG 2.9 12.6 + - - +
469B THR* 3.5 16.2 - - - +
470B VAL 3.2 0.2 - - - -
471B VAL* 1.3 77.5 - - - +
473B ALA* 1.3 62.2 + - - +
475B ARG* 3.1 32.3 + - - +
476B ILE* 3.1 21.8 + - - +
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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
----------------------------------------------------------
454B ILE* 3.9 18.7 - - + +
456B TYR* 4.1 14.1 - - + -
469B THR 3.0 17.3 + - - +
470B VAL* 3.3 9.6 + - - +
472B LYS* 1.3 74.0 - - - +
474B ARG* 1.3 56.5 + - - +
476B ILE* 3.4 4.7 + - - +
477B TYR* 3.2 25.8 + - - +
497B LEU* 3.6 23.1 - - + +
498B SER 5.0 2.9 - - - +
499B VAL* 4.9 6.7 - - + -
511B VAL* 4.8 4.5 - - + -
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Residues in contact with ARG 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B VAL* 3.1 42.0 + - + +
471B VAL* 3.7 7.8 - - - +
472B LYS 3.2 0.2 - - - -
473B ALA* 1.3 74.8 - - - +
475B ARG* 1.3 63.1 + - - +
477B TYR* 3.5 3.4 + - - +
478B ASN* 2.9 35.8 + - - +
497B LEU* 3.9 13.2 - - + -
511B VAL* 4.4 2.8 - - + +
512B ALA* 2.8 37.8 + - - +
513B SER 3.7 18.4 - - - +
514B ALA* 3.5 29.9 + - - +
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Residues in contact with ARG 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A GLU* 3.3 41.5 + - + +
427A GLU* 3.8 38.6 + - - +
423B ASP 5.0 2.6 + - - -
468B ARG 5.1 1.8 + - - -
471B VAL* 3.0 41.4 + - + +
472B LYS* 3.4 42.0 - - - +
474B ARG* 1.3 73.3 - - - +
476B ILE* 1.3 61.1 + - + +
478B ASN* 3.3 5.9 + - - +
479B ALA* 2.8 31.7 + - - +
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Residues in contact with ILE 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A GLU* 3.6 15.7 - - - +
404B VAL* 4.0 14.8 - - + -
422B LEU* 3.7 10.5 - - + -
423B ASP 3.5 23.8 - - - +
424B THR* 3.7 7.9 - - - -
425B VAL* 3.8 9.0 - - + +
454B ILE* 4.0 13.2 - - + -
456B TYR* 3.2 25.8 - - + +
472B LYS 3.1 13.7 + - - +
473B ALA 3.7 6.3 - - - +
474B ARG 3.3 0.2 - - - -
475B ARG* 1.3 74.4 - - + +
477B TYR* 1.3 57.4 + - - +
479B ALA* 3.2 1.0 + - - +
480B ILE* 2.9 58.1 + - + +
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Residues in contact with TYR 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B ILE* 3.6 14.0 - - + +
473B ALA 3.2 11.6 + - - +
474B ARG* 3.5 8.5 - - - +
476B ILE* 1.3 79.3 - - - +
478B ASN* 1.3 74.1 + - - +
480B ILE* 4.0 1.9 - - - +
481B LYS* 3.1 62.1 + - + +
495B PHE* 3.4 46.7 - + + -
497B LEU* 4.2 6.3 - - + -
513B SER* 3.5 49.0 + - - -
514B ALA* 6.0 1.1 - - + -
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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
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474B ARG* 2.9 33.7 + - - +
475B ARG* 3.9 5.5 - - - +
477B TYR* 1.3 86.6 - - - +
479B ALA* 1.3 58.1 + - - +
481B LYS* 3.2 27.0 + - - +
482B GLU* 3.0 43.4 + - - +
513B SER 5.0 2.4 + - - -
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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
----------------------------------------------------------
426A GLU* 3.7 27.8 - - + +
425B VAL* 3.7 19.8 - - + +
475B ARG 2.8 17.7 + - - +
478B ASN* 1.3 75.6 - - - +
480B ILE* 1.3 64.9 + - - +
482B GLU* 3.6 11.0 + - - +
483B ARG* 3.1 24.6 + - - +
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Residues in contact with ILE 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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404B VAL* 4.3 17.7 - - + -
425B VAL* 3.6 17.9 - - + -
432B VAL* 4.5 20.0 - - + -
436B ILE* 5.2 1.6 - - + -
452B ILE* 4.0 20.0 - - + -
454B ILE* 4.8 0.7 - - + -
476B ILE* 2.9 38.2 + - + +
479B ALA* 1.3 73.1 - - - +
481B LYS* 1.3 65.5 + - - +
483B ARG* 3.2 4.9 + - - -
484B PHE* 3.1 39.6 + - + +
493B LEU* 4.3 3.8 - - + +
495B PHE* 3.8 30.1 - - + -
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Residues in contact with LYS 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B TYR* 3.1 57.7 + - + +
478B ASN* 3.2 27.1 + - - +
479B ALA 3.4 0.2 - - - -
480B ILE* 1.3 76.3 - - - +
482B GLU* 1.3 61.2 + - + +
484B PHE 3.4 1.9 - - - +
485B SER* 3.2 26.0 + - - -
488B ASP* 3.5 37.2 - - - +
493B LEU* 4.4 6.7 - - - -
495B PHE* 3.8 12.6 - - + -
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Residues in contact with GLU 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ARG* 4.9 10.6 + - - -
478B ASN* 3.0 35.8 + - + +
479B ALA* 3.8 8.6 - - - +
481B LYS* 1.3 73.6 - - + +
483B ARG* 1.3 65.2 + - - +
485B SER* 3.8 17.6 + - - -
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Residues in contact with ARG 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A GLU* 5.0 9.5 + - - -
425B VAL* 4.2 20.3 - - + +
429B ALA* 3.5 28.1 + - - +
432B VAL* 5.0 1.6 - - - -
433B ASP* 2.7 43.5 + - - -
479B ALA 3.1 18.1 + - - +
480B ILE* 3.2 4.7 + - - +
482B GLU* 1.3 76.4 - - - +
484B PHE* 1.3 80.5 + - + +
485B SER 3.6 0.7 + - - -
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Residues in contact with PHE 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B VAL* 3.9 12.3 - - + -
433B ASP* 3.2 26.7 - - - -
436B ILE* 3.6 48.9 - - + -
480B ILE* 3.1 25.1 + - + +
481B LYS 3.4 3.3 - - - +
483B ARG* 1.3 100.3 - - + +
485B SER* 1.3 57.5 + - - +
486B SER* 3.4 3.1 - - - -
487B LEU* 3.4 19.5 + - + -
488B ASP* 3.0 26.5 + - - +
493B LEU* 3.6 11.6 - - + +
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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