Contacts of the helix formed by residues 471 - 486 (chain A) in PDB entry 1F4J
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 GLN 471 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A ASP* 2.9 37.6 + - - +
469A ASP 3.9 1.0 + - - -
470A ALA* 1.3 75.3 - - - +
472A ILE* 1.3 60.6 + - - +
473A PHE* 3.4 29.9 - - + -
474A ILE* 3.0 7.0 + - + +
475A GLN 2.9 22.5 + - - -
409B PHE* 3.9 22.7 - - - -
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Residues in contact with ILE 472 (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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470A ALA 3.6 0.2 + - - -
471A GLN* 1.3 70.1 - - - +
473A PHE* 1.3 56.1 + - - +
475A GLN* 2.9 22.9 + - + +
476A LYS* 2.6 57.0 + - + +
501A ASN* 4.9 14.6 - - + +
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Residues in contact with PHE 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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184A ASP* 4.3 0.9 - - - -
471A GLN* 3.6 30.3 - - + -
472A ILE* 1.3 78.2 - - - +
474A ILE* 1.3 86.8 + - + +
476A LYS* 3.4 10.6 + - - +
477A LYS* 3.2 37.6 + - - +
408B SER* 3.6 32.3 - - - -
409B PHE* 3.8 22.9 - + - -
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Residues in contact with ILE 474 (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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180A ASP* 3.4 50.3 - - + +
183A TRP* 3.3 43.3 - - + +
184A ASP* 3.9 13.2 - - + +
187A SER* 4.3 4.8 - - - +
470A ALA* 3.9 5.8 - - + -
471A GLN* 3.0 10.6 + - + +
473A PHE* 1.3 111.6 - - + +
475A GLN* 1.3 63.4 + - - +
477A LYS* 3.5 4.0 + - - +
478A ALA* 3.2 19.9 + - - +
409B PHE* 4.5 3.4 - - + -
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Residues in contact with GLN 475 (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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467A LEU* 3.6 28.7 - - + +
468A LYS* 3.6 11.7 + - - +
470A ALA 2.9 21.5 + - - +
471A GLN 2.9 15.3 + - - +
472A ILE* 2.9 20.2 + - + +
474A ILE* 1.3 76.9 - - - +
476A LYS* 1.3 66.7 + - + +
478A ALA* 3.0 3.5 + - - +
479A VAL* 2.9 25.8 + - + +
494A GLN* 5.1 2.0 + - - +
497A LEU* 3.4 27.2 - - + +
501A ASN* 3.2 40.3 + - - +
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Residues in contact with LYS 476 (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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472A ILE* 2.6 40.2 + - + +
473A PHE* 3.5 11.4 - - - +
475A GLN* 1.3 74.0 - - - +
477A LYS* 1.3 64.6 + - - +
479A VAL* 3.0 7.2 + - - +
480A LYS* 2.9 30.3 + - - +
494A GLN* 5.2 9.2 - - - +
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Residues in contact with LYS 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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184A ASP* 5.7 0.6 + - - -
187A SER* 3.9 32.1 + - - +
188A LEU* 4.1 25.3 - - + +
473A PHE* 3.2 33.0 + - - +
474A ILE* 4.0 1.9 - - - +
476A LYS* 1.3 78.7 - - - +
478A ALA* 1.3 64.5 + - - +
480A LYS* 3.1 37.9 - - + +
481A ASN* 3.2 17.1 + - - +
408B SER* 4.9 2.4 + - - -
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Residues in contact with ALA 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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183A TRP* 4.4 12.3 - - + +
187A SER* 4.0 11.8 - - - +
467A LEU* 3.9 28.5 - - + -
474A ILE 3.2 12.9 + - - +
475A GLN 3.0 9.7 + - - +
477A LYS* 1.3 76.0 - - - +
479A VAL* 1.3 58.1 + - - +
481A ASN* 2.9 23.8 + - - +
482A PHE* 3.1 22.5 + - + -
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Residues in contact with VAL 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A LEU* 4.4 5.6 - - + -
475A GLN 2.9 16.0 + - - +
476A LYS* 3.6 6.3 - - - +
478A ALA* 1.3 75.0 - - - +
480A LYS* 1.3 56.8 + - - +
482A PHE* 3.9 9.2 - - - +
483A THR* 2.9 37.3 + - - +
490A GLY* 3.2 29.8 - - - +
491A SER* 5.2 0.2 - - - -
493A ILE* 4.4 4.7 - - + -
494A GLN* 3.6 32.5 - - + +
497A LEU* 3.6 23.8 - - + -
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Residues in contact with LYS 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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476A LYS* 2.9 14.5 + - - +
477A LYS* 3.1 46.7 - - + +
478A ALA 3.0 0.4 - - - -
479A VAL* 1.3 79.9 - - - +
481A ASN* 1.3 61.6 + - - +
483A THR* 3.6 7.5 + - - +
484A GLU* 3.3 24.7 + - + +
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Residues in contact with ASN 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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186A TRP 4.3 2.2 + - - -
187A SER* 3.2 35.3 + - - +
190A PRO* 3.8 22.2 - - - +
193A LEU* 4.0 24.3 - - + +
477A LYS* 3.4 17.4 + - - +
478A ALA* 2.9 7.7 + - - +
480A LYS* 1.3 78.0 - - - +
482A PHE* 1.3 66.1 + - - +
483A THR 3.1 1.8 - - - -
484A GLU* 2.9 26.6 + - - +
485A VAL* 3.2 10.4 + - - +
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Residues in contact with PHE 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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183A TRP* 4.2 20.9 - + - -
193A LEU* 3.9 19.3 - - + -
196A VAL* 4.4 12.8 - - + -
197A SER* 4.9 1.1 - - - -
463A ILE* 3.8 27.8 - - + -
467A LEU* 4.7 3.1 - - + -
478A ALA* 3.1 34.7 + - + -
479A VAL* 3.9 7.0 - - - +
481A ASN* 1.3 76.4 - - - +
483A THR* 1.3 61.5 + - - +
485A VAL* 3.0 18.4 + - - +
486A HIS 3.1 12.5 + - - +
489A TYR* 3.4 42.2 - + + +
490A GLY* 3.7 22.1 + - - +
493A ILE* 3.6 18.4 - - + -
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Residues in contact with THR 483 (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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479A VAL* 2.9 24.9 + - - +
480A LYS* 3.6 7.8 - - - +
481A ASN 3.1 0.2 - - - -
482A PHE* 1.3 76.3 - - - +
484A GLU* 1.3 62.2 + - + +
486A HIS* 3.1 23.4 + - - -
487A PRO* 3.4 18.5 + - + +
490A GLY* 3.3 16.9 - - - -
491A SER* 4.0 1.4 + - - -
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Residues in contact with GLU 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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193A LEU* 5.5 0.2 - - + -
440A VAL* 3.8 24.4 - - + +
444A ARG* 3.2 17.7 + - - -
480A LYS* 3.3 16.9 + - + +
481A ASN* 2.9 20.8 + - - +
483A THR* 1.3 79.5 - - - +
485A VAL* 1.3 58.8 + - - +
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Residues in contact with VAL 485 (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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193A LEU* 3.7 29.2 - - + -
440A VAL* 4.1 10.8 - - + +
443A VAL* 3.8 21.3 - - + +
444A ARG* 2.9 58.0 + - - +
447A TYR* 4.7 2.0 - - + -
481A ASN 3.4 14.1 - - - +
482A PHE* 3.0 10.0 + - - +
484A GLU* 1.3 78.9 - - - +
486A HIS* 1.3 64.3 + - + +
489A TYR* 3.9 17.5 - - + -
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Residues in contact with HIS 486 (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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444A ARG* 4.9 9.0 - - + +
447A TYR* 4.4 12.7 - + + -
448A VAL* 3.8 27.1 - - + +
482A PHE 3.1 11.8 + - - +
483A THR 3.1 6.9 + - - +
484A GLU 4.7 0.2 - - - -
485A VAL* 1.3 84.9 - - + +
487A PRO* 1.3 87.7 - - + +
488A ASP* 2.7 56.7 + - + +
489A TYR* 3.1 20.8 + - + -
490A GLY 3.2 3.6 + - - -
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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