Contacts of the helix formed by residues 464 - 484 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A VAL 3.2 1.0 + - - -
463A PRO* 1.3 70.5 - - - +
465A SER* 1.3 63.7 + - - +
466A ARG 3.4 2.0 - - - -
467A GLU* 3.3 27.8 + - - +
468A ARG* 3.0 39.7 + - - +
273B LYS* 6.1 5.6 - - - -
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Residues in contact with SER 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A TYR* 3.5 4.2 - - - +
459A ASP* 2.9 36.6 + - - +
462A VAL* 3.0 29.6 + - - -
463A PRO 3.3 2.2 + - - -
464A GLY* 1.3 76.6 - - - +
466A ARG* 1.3 58.9 + - - +
468A ARG* 3.4 13.4 + - - +
469A THR* 2.7 33.7 + - - -
207B GLU* 4.8 4.9 + - - +
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Residues in contact with ARG 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A TYR* 3.7 42.7 + - + -
459A ASP 4.9 0.2 + - - -
462A VAL 4.6 1.4 + - - -
464A GLY 3.4 0.8 - - - -
465A SER* 1.3 79.2 + - - +
467A GLU* 1.3 74.1 + - - +
469A THR* 3.2 2.4 + - - -
470A VAL* 3.0 41.1 + - + +
499A VAL* 3.8 12.0 - - + +
509A GLU* 2.7 41.6 + - - +
510A GLU 5.1 1.6 + - - -
511A VAL* 4.2 10.7 - - - +
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Residues in contact with GLU 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A GLY* 3.4 34.4 + - - +
466A ARG* 1.3 89.3 + - - +
468A ARG* 1.3 55.3 + - + +
470A VAL* 3.3 8.5 + - - +
471A VAL* 2.9 36.0 + - + +
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Residues in contact with ARG 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A VAL* 4.1 12.9 - - - +
463A PRO 3.8 10.3 + - - -
464A GLY* 3.0 28.2 + - - +
465A SER* 3.7 19.9 - - - +
467A GLU* 1.3 75.7 - - + +
469A THR* 1.3 57.6 + - - +
471A VAL* 3.4 9.2 + - - +
472A LYS* 2.9 27.9 + - - +
475A ARG* 5.0 1.7 + - - -
206B ILE* 3.7 45.7 - - - +
207B GLU* 2.9 44.1 + - + +
210B LEU* 6.1 1.0 - - - +
273B LYS* 5.0 8.5 + - - +
277B ALA* 4.4 4.0 - - - +
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Residues in contact with THR 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A TYR* 3.4 31.7 - - + -
457A ARG 3.8 13.6 + - - +
458A TYR* 3.4 17.5 - - + +
465A SER* 2.7 23.2 + - - -
466A ARG* 3.5 4.7 - - - -
468A ARG* 1.3 78.4 - - - +
470A VAL* 1.3 56.4 + - - +
472A LYS* 3.3 14.7 + - - +
473A ALA* 2.9 27.2 + - - +
499A VAL* 3.7 14.8 - - + -
207B GLU* 5.5 1.6 + - - -
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Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ARG* 3.0 42.1 + - + +
467A GLU* 3.3 8.9 + - - +
469A THR* 1.3 73.5 - - - +
471A VAL* 1.3 67.1 + - + +
473A ALA* 3.2 8.3 + - - +
474A ARG* 3.0 60.3 + - - +
499A VAL* 4.3 15.5 - - + -
511A VAL* 4.3 17.5 - - + -
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Residues in contact with VAL 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A GLU* 2.9 24.5 + - + +
468A ARG* 3.6 8.1 - - - +
470A VAL* 1.3 76.7 - - + +
472A LYS* 1.3 62.0 + - - +
474A ARG* 3.3 10.5 + - - +
475A ARG* 3.0 45.8 + - + +
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Residues in contact with LYS 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ASP* 5.0 2.6 + - - -
423A ASP* 2.9 51.8 + - + +
456A TYR* 3.5 38.1 - - + +
457A ARG 5.4 2.4 + - - -
468A ARG 2.9 13.4 + - - +
469A THR* 3.4 16.8 + - - +
470A VAL 3.2 0.2 - - - -
471A VAL* 1.3 76.8 - - - +
473A ALA* 1.3 63.5 + - - +
475A ARG* 3.0 32.8 + - - +
476A ILE* 3.0 22.9 + - - +
427B GLU* 5.9 0.2 - - - +
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Residues in contact with ALA 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A ILE* 3.9 10.6 - - + +
456A TYR* 4.0 22.9 - - + -
469A THR 2.9 14.2 + - - +
470A VAL* 3.5 12.6 - - - +
472A LYS* 1.3 75.4 - - - +
474A ARG* 1.3 61.3 + - - +
476A ILE* 3.4 4.7 + - - +
477A TYR* 3.2 16.8 + - - +
497A LEU* 3.5 26.4 - - + +
498A SER 4.9 2.9 - - - +
499A VAL* 4.9 7.0 - - + -
511A VAL* 4.8 5.2 - - + -
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Residues in contact with ARG 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A VAL* 3.0 43.7 + - + +
471A VAL* 3.7 7.9 - - - +
472A LYS 3.2 0.2 - - - -
473A ALA* 1.3 74.8 - - - +
475A ARG* 1.3 63.4 + - - +
477A TYR* 3.5 3.2 + - - +
478A ASN* 2.8 35.8 + - - +
497A LEU* 3.8 14.1 - - + -
511A VAL* 4.5 3.0 - - - +
512A ALA* 2.8 35.5 + - - +
513A SER 3.6 18.6 - - - +
514A ALA* 3.7 27.5 + - - +
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Residues in contact with ARG 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ASP 4.9 3.2 + - - -
468A ARG 5.0 1.6 + - - -
471A VAL* 3.0 40.2 + - + +
472A LYS* 3.0 40.3 + - - +
474A ARG* 1.3 73.2 - - - +
476A ILE* 1.3 67.0 + - + +
478A ASN* 3.3 4.9 + - - +
479A ALA* 2.9 26.9 + - - +
426B GLU* 3.3 40.8 + - + +
427B GLU* 3.8 39.7 + - - +
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Residues in contact with ILE 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A VAL* 3.9 19.1 - - + -
422A LEU* 3.6 10.1 - - + -
423A ASP 3.4 24.2 - - - +
424A THR* 3.6 16.4 - - - -
425A VAL* 3.8 7.6 - - + +
454A ILE* 4.0 8.3 - - + -
456A TYR* 3.3 25.1 - - + +
472A LYS 3.0 15.0 + - - +
473A ALA 3.7 6.3 - - - +
474A ARG 3.3 0.2 - - - -
475A ARG* 1.3 76.3 - - + +
477A TYR* 1.3 58.7 + - - +
479A ALA* 3.7 0.5 - - - +
480A ILE* 2.8 57.9 + - + +
426B GLU* 3.6 8.1 - - - +
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Residues in contact with TYR 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A ILE* 3.7 14.1 - - + +
473A ALA 3.2 11.0 + - - +
474A ARG* 3.5 9.0 - - - +
476A ILE* 1.3 80.0 - - - +
478A ASN* 1.3 79.1 + - - +
480A ILE* 3.5 1.6 + - - +
481A LYS* 3.0 60.3 + - + +
495A PHE* 3.5 47.1 - + + -
497A LEU* 4.2 6.3 - - + -
513A SER* 3.5 45.3 + - - -
514A ALA* 6.0 0.4 - - + -
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Residues in contact with ASN 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A ARG* 2.8 30.1 + - - +
475A ARG* 4.0 4.8 - - - +
477A TYR* 1.3 90.0 - - - +
479A ALA* 1.3 57.5 - - - +
481A LYS* 3.2 26.9 + - - +
482A GLU* 2.9 45.9 + - - +
513A SER 4.9 2.4 + - - -
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Residues in contact with ALA 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A VAL* 3.8 19.7 - - + +
475A ARG 2.9 18.6 + - - +
478A ASN* 1.3 74.1 - - - +
480A ILE* 1.3 65.4 + - - +
482A GLU* 3.7 10.4 + - - +
483A ARG* 3.1 24.4 + - - +
426B GLU* 3.7 27.4 - - + +
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Residues in contact with ILE 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A VAL* 4.3 18.2 - - + -
425A VAL* 3.6 17.0 - - + -
432A VAL* 4.5 19.5 - - + -
436A ILE* 5.2 1.6 - - + -
452A ILE* 4.1 19.5 - - + -
454A ILE* 4.7 0.9 - - + -
476A ILE* 2.8 42.0 + - + +
479A ALA* 1.3 73.5 - - - +
481A LYS* 1.3 64.6 + - - +
483A ARG* 3.3 4.7 + - - -
484A PHE* 3.1 37.5 + - + +
493A LEU* 4.3 4.0 - - + +
495A PHE* 3.9 31.0 - - + -
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Residues in contact with LYS 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477A TYR* 3.0 56.8 + - + +
478A ASN* 3.2 27.8 + - - +
479A ALA 3.4 0.2 - - - -
480A ILE* 1.3 77.2 - - - +
482A GLU* 1.3 61.7 + - + +
484A PHE 3.4 1.9 - - - +
485A SER* 3.3 26.3 + - - -
488A ASP* 3.4 39.7 - - - +
493A LEU* 4.4 4.5 - - - -
495A PHE* 3.7 13.7 - - + -
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Residues in contact with GLU 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A ASN* 2.9 40.2 + - - +
479A ALA* 3.7 9.0 + - - +
481A LYS* 1.3 72.9 - - + +
483A ARG* 1.3 64.5 + - - +
484A PHE 3.6 0.2 + - - -
485A SER* 3.8 16.9 + - - -
483B ARG* 5.0 9.2 + - - -
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Residues in contact with ARG 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A VAL* 4.1 20.4 - - + +
429A ALA* 3.6 26.6 + - - +
432A VAL* 4.9 2.0 - - - -
433A ASP* 2.6 41.9 + - - -
479A ALA 3.1 17.8 + - - +
480A ILE* 3.3 4.7 + - - +
482A GLU* 1.3 77.9 - - - +
484A PHE* 1.3 79.5 + - + +
485A SER* 3.9 1.2 + - - -
482B GLU* 4.9 10.9 + - - -
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Residues in contact with PHE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A VAL* 3.9 11.7 - - + -
433A ASP* 3.2 27.4 - - - -
436A ILE* 3.6 48.7 - - + -
480A ILE* 3.1 25.0 + - + +
481A LYS 3.4 4.3 - - - -
483A ARG* 1.3 98.8 - - + +
485A SER* 1.3 58.1 + - - +
486A SER* 3.4 2.5 - - - -
487A LEU* 3.3 21.2 + - + +
488A ASP* 2.9 27.5 + - - +
493A LEU* 3.8 11.8 - - + +
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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