Contacts of the helix formed by residues 428 - 443 (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 ASN 428 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A TYR* 3.4 28.1 - - - -
205A ASP* 4.9 10.2 + - - +
421A HIS 3.5 3.2 - - - +
422A LEU* 3.5 33.5 - - + +
423A ASP 4.5 3.0 - - - +
424A THR 3.5 10.8 + - - +
425A VAL 3.1 5.3 + - - -
427A GLU* 1.3 99.8 + - - +
429A ALA* 1.3 62.7 + - - +
430A ILE* 3.2 4.7 - - - -
431A ASP* 3.2 28.8 + - - +
432A VAL* 3.4 12.4 + - - +
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Residues in contact with ALA 429 (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* 3.0 19.0 + - + +
426A GLU* 4.4 8.7 - - - +
427A GLU 3.7 2.2 - - - -
428A ASN* 1.3 76.5 - - - +
430A ILE* 1.3 57.0 + - - +
432A VAL* 3.3 3.4 + - - +
433A ASP* 2.9 35.5 + - - +
483A ARG* 3.6 34.7 + - - +
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Residues in contact with ILE 430 (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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200A ALA* 4.4 10.1 - - + +
255A ALA* 6.0 2.9 - - + -
428A ASN* 4.8 1.6 - - - -
429A ALA* 1.3 77.5 - - - +
431A ASP* 1.3 75.9 + - - +
433A ASP* 3.2 10.5 + - + +
434A VAL* 2.9 48.0 + - + +
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Residues in contact with ASP 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A TYR* 3.4 19.7 - - - +
200A ALA* 2.8 33.3 + - - +
418A TYR* 2.6 34.8 + - - +
420A ALA* 3.8 22.4 - - + -
421A HIS 5.7 0.7 - - - -
422A LEU* 5.1 0.2 - - + -
428A ASN* 3.2 33.1 + - + +
430A ILE* 1.3 85.2 - - - +
432A VAL* 1.3 62.4 + - - +
435A GLY 3.3 7.8 + - - -
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Residues in contact with VAL 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ILE* 5.3 5.5 - - + +
404A VAL* 4.9 11.0 - - + -
418A TYR* 5.4 1.1 - - - -
420A ALA* 5.5 1.1 - - - -
422A LEU* 3.9 23.3 - - + -
425A VAL* 4.4 22.9 - - + -
428A ASN 3.4 11.0 + - - +
429A ALA* 3.3 8.5 + - - +
430A ILE 3.2 0.6 - - - -
431A ASP* 1.3 75.1 - - - +
433A ASP* 1.3 65.3 + - - +
435A GLY* 3.3 2.9 + - - -
436A ILE* 3.1 25.8 + - + +
480A ILE* 4.5 21.3 - - + -
483A ARG* 4.9 4.0 - - - -
484A PHE* 3.9 22.9 - - + -
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Residues in contact with ASP 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ALA 2.9 22.2 + - - +
430A ILE* 3.2 11.0 + - + +
432A VAL* 1.3 76.6 - - - +
434A VAL* 1.3 57.9 + - + +
436A ILE* 3.4 1.9 + - - +
437A THR* 2.8 33.6 + - - +
483A ARG* 2.6 45.5 + - - -
484A PHE* 3.2 20.6 - - + -
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Residues in contact with VAL 434 (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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200A ALA* 4.2 11.9 - - + -
254A ALA* 6.3 3.4 - - + -
255A ALA* 5.7 9.2 - - + +
418A TYR* 3.5 27.6 - - + +
430A ILE* 2.9 38.9 + - + +
433A ASP* 1.3 75.3 - - + +
435A GLY* 1.3 64.4 + - - +
437A THR* 3.4 7.4 + - - -
438A ILE* 3.1 32.2 + - + +
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Residues in contact with GLY 435 (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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402A ILE* 3.7 12.1 - - - -
418A TYR* 3.5 33.4 - - - -
431A ASP 3.3 11.5 + - - -
432A VAL 3.3 2.7 + - - -
434A VAL* 1.3 74.8 - - - +
436A ILE* 1.3 57.3 + - - +
438A ILE* 3.3 2.7 + - - +
439A PHE* 2.9 34.0 + - - -
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Residues in contact with ILE 436 (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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402A ILE* 3.9 18.2 - - + -
432A VAL* 3.1 20.6 + - + +
433A ASP 3.8 6.1 - - - +
435A GLY* 1.3 72.8 - - - +
437A THR* 1.3 61.4 + - - +
439A PHE* 3.1 1.6 + - - +
440A THR* 2.8 41.4 + - - +
450A ILE* 4.1 19.9 - - + +
452A ILE* 4.5 12.6 - - + -
480A ILE* 5.2 1.3 - - + -
484A PHE* 3.6 49.8 - - + -
487A LEU* 4.1 13.9 - - + -
493A LEU* 4.5 5.8 - - + -
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Residues in contact with THR 437 (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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433A ASP* 2.8 18.2 + - - +
434A VAL* 3.5 11.2 - - - -
436A ILE* 1.3 76.1 - - - +
438A ILE* 1.3 65.8 + - + +
440A THR* 3.1 22.0 + - - -
441A LYS* 3.5 28.9 + - + +
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Residues in contact with ILE 438 (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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397A HIS* 3.4 42.6 - - + +
399A GLU* 3.7 14.4 - - - +
418A TYR* 3.7 26.7 - - + -
434A VAL* 3.1 24.2 + - + +
435A GLY* 3.6 7.0 - - - +
437A THR* 1.3 80.9 - - + +
439A PHE* 1.3 64.0 + - + +
441A LYS* 3.3 12.9 + - + +
442A LEU* 3.1 49.0 + - + +
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Residues in contact with PHE 439 (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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399A GLU* 3.4 39.5 - - + -
400A ARG 3.6 14.8 - - - -
401A TYR* 3.4 28.0 - - - -
402A ILE* 3.5 19.5 - - + -
418A TYR* 4.4 7.0 - - + -
435A GLY* 2.9 22.2 + - - +
436A ILE 3.1 1.1 + - - +
438A ILE* 1.3 81.3 - - + +
440A THR* 1.3 58.9 + - - +
441A LYS 3.3 0.2 - - - -
442A LEU* 3.8 7.9 - - + -
443A ASN* 2.8 52.5 + - - +
444A LEU* 3.1 9.2 + - - +
450A ILE* 3.7 37.2 - - + +
451A PRO* 4.3 2.0 - - + -
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Residues in contact with THR 440 (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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436A ILE* 2.8 28.2 + - - +
437A THR* 3.1 13.4 + - - -
439A PHE* 1.3 75.0 - - - +
441A LYS* 1.3 60.6 + - + +
444A LEU* 3.6 29.8 - - + +
445A SER* 3.0 29.6 + - - -
487A LEU* 5.2 0.5 - - - +
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Residues in contact with LYS 441 (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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437A THR* 3.7 32.8 - - + +
438A ILE* 3.3 10.7 + - + +
440A THR* 1.3 78.2 - - + +
442A LEU* 1.3 66.1 + - + +
445A SER* 2.5 28.4 + - - -
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Residues in contact with LEU 442 (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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397A HIS* 3.9 21.5 - - + +
398A ALA* 4.3 3.6 - - - -
399A GLU* 3.5 45.8 - - - +
438A ILE* 3.1 35.2 + - + +
439A PHE* 4.1 12.8 - - + -
441A LYS* 1.3 87.7 - - + +
443A ASN* 1.3 61.5 + - - +
445A SER* 4.3 0.7 + - - -
446A ARG* 2.7 37.9 + - - +
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Residues in contact with ASN 443 (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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127A PHE* 3.8 13.3 - - - -
399A GLU 4.9 2.3 - - - +
400A ARG 4.7 2.4 + - - -
439A PHE* 2.8 33.6 + - + +
442A LEU* 1.3 81.3 - - - +
444A LEU* 1.3 60.0 + - - +
445A SER 3.3 1.8 - - - -
446A ARG* 2.9 44.9 + - - +
448A LEU* 3.0 25.1 + - + +
449A PRO 3.0 30.4 + - - +
450A ILE* 4.7 1.1 - - + -
451A PRO* 3.6 17.6 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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