Contacts of the helix formed by residues 452 - 468 (chain B) 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 ASN 452 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451B LEU* 1.3 73.4 - - - +
453B GLU* 1.3 58.6 + - - +
454B GLU* 2.5 49.3 + - - +
455B GLN* 3.0 38.9 + - - +
456B ARG* 2.8 38.2 + - - +
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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
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452B ASN* 1.3 74.9 + - - +
454B GLU* 1.3 54.9 + - + +
456B ARG* 2.9 35.8 + - - +
457B LYS* 2.7 38.9 + - - +
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Residues in contact with GLU 454 (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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452B ASN* 2.5 24.8 + - - +
453B GLU* 1.3 73.0 - - + +
455B GLN* 1.3 55.1 + - + +
457B LYS* 2.9 19.2 + - - +
458B ARG* 2.8 59.5 + - - +
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Residues in contact with GLN 455 (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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201B SER* 5.5 3.8 - - - -
202B ASP* 4.0 23.2 + - - +
450B VAL 4.0 4.0 - - - +
451B LEU* 3.4 32.3 - - + +
452B ASN* 3.0 43.9 + - - +
454B GLU* 1.3 79.5 - - + +
456B ARG* 1.3 52.3 + - - +
458B ARG* 3.8 14.7 - - - +
459B LEU* 2.7 36.8 + - - +
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Residues in contact with ARG 456 (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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447B TYR* 3.2 67.3 + - + +
448B VAL* 3.6 17.3 + - - +
451B LEU* 3.3 28.6 + - + +
452B ASN* 2.8 18.4 + - - +
453B GLU* 2.9 62.1 + - - +
455B GLN* 1.3 77.8 - - - +
457B LYS* 1.3 63.7 + - - +
459B LEU* 3.4 7.9 + - - +
460B CYS* 3.2 23.4 + - - -
488B ASP* 6.1 0.9 - - - -
492B HIS* 5.9 1.3 - - - +
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Residues in contact with LYS 457 (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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453B GLU* 2.7 21.8 + - - +
454B GLU* 2.9 25.6 + - - +
456B ARG* 1.3 74.7 - - - +
458B ARG* 1.3 75.9 + - - +
460B CYS* 3.1 6.2 + - - +
461B GLU* 3.0 51.0 + - + +
492B HIS* 4.0 25.1 - - + +
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Residues in contact with ARG 458 (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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201B SER* 6.4 0.4 - - - -
202B ASP* 2.3 46.3 + - - +
454B GLU* 2.8 55.1 + - - +
455B GLN* 3.8 14.7 - - - +
457B LYS* 1.3 77.7 - - - +
459B LEU* 1.3 70.0 + - - +
461B GLU* 2.8 27.2 + - + +
462B ASN* 2.8 31.5 + - - +
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Residues in contact with LEU 459 (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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197B SER* 3.6 22.9 - - - +
200B PHE* 3.6 35.6 + - + +
201B SER* 4.1 4.4 - - - +
446B PHE* 4.8 0.9 - - + -
447B TYR* 4.0 12.8 - - + -
451B LEU* 3.6 26.5 - - + -
455B GLN 2.7 22.9 + - - +
456B ARG 3.4 4.9 - - - +
457B LYS 3.3 0.2 - - - -
458B ARG* 1.3 74.7 - - - +
460B CYS* 1.3 61.6 + - - +
462B ASN* 3.4 1.7 + - - +
463B ILE* 3.2 30.1 + - + +
489B TYR* 3.5 31.0 - - + +
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Residues in contact with CYS 460 (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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447B TYR* 4.1 18.2 - - - -
456B ARG 3.2 14.1 + - - -
457B LYS 3.1 9.5 + - - +
458B ARG 3.1 0.4 - - - -
459B LEU* 1.3 80.0 - - - +
461B GLU* 1.3 57.2 + - - +
463B ILE* 3.5 2.0 + - - +
464B ALA* 2.9 30.5 + - - +
489B TYR* 4.1 17.3 - - - -
492B HIS* 3.7 29.8 - - + +
493B ILE* 4.0 28.8 - - + +
496B LEU* 3.8 4.9 - - + +
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Residues in contact with GLU 461 (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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457B LYS* 3.2 48.3 - - + +
458B ARG* 2.8 22.6 + - + +
460B CYS* 1.3 69.7 - - - +
462B ASN* 1.3 62.8 + - - +
464B ALA* 3.7 0.7 - - - +
465B GLY* 2.8 27.7 + - - -
492B HIS* 5.3 1.3 - - - +
496B LEU* 3.6 24.9 - - + +
500B TYR* 4.7 3.1 + - - -
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Residues in contact with ASN 462 (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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127B ARG* 3.5 28.9 + - - +
200B PHE* 2.8 46.8 + - + +
201B SER 4.6 4.8 + - - -
202B ASP* 5.2 2.8 + - - +
247B VAL* 3.9 15.1 - - - +
458B ARG* 2.8 35.1 + - - +
459B LEU 3.9 0.9 - - - +
461B GLU* 1.3 71.8 - - - +
463B ILE* 1.3 67.0 + - - +
465B GLY* 3.6 2.1 + - - -
466B HIS* 3.5 13.7 + - - +
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Residues in contact with ILE 463 (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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183B TRP* 3.8 21.2 - - + -
196B VAL* 4.6 5.2 - - + +
200B PHE* 3.6 27.6 - - + -
459B LEU* 3.2 24.9 + - + +
460B CYS 3.8 3.4 - - - +
462B ASN* 1.3 74.9 - - - +
464B ALA* 1.3 61.9 + - - +
466B HIS* 3.0 4.0 + - - +
467B LEU* 2.8 36.2 + - + +
482B PHE* 3.7 30.7 - - + -
489B TYR* 3.6 31.9 - - + +
493B ILE* 4.0 9.2 - - + -
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Residues in contact with ALA 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 CYS 2.9 19.9 + - - +
461B GLU 3.7 3.4 - - - +
463B ILE* 1.3 79.6 - - - +
465B GLY* 1.3 62.5 + - - +
467B LEU* 4.6 0.7 - - - -
468B LYS* 3.0 29.6 + - - +
493B ILE* 4.4 12.8 - - + +
496B LEU* 3.5 33.2 - - + -
497B LEU* 3.7 11.0 - - - +
500B TYR* 3.9 8.3 - - + -
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Residues in contact with GLY 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 GLU 2.8 19.8 + - - -
462B ASN 3.6 2.4 + - - -
463B ILE 3.2 0.4 - - - -
464B ALA* 1.3 73.3 - - - +
466B HIS* 1.3 58.5 + - - +
468B LYS* 3.0 25.4 - - - -
469B ASP* 4.2 2.1 - - - +
500B TYR* 3.5 24.2 - - - -
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Residues in contact with HIS 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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179B PRO* 4.2 21.1 - - + +
182B VAL* 3.9 22.0 - - + +
183B TRP* 2.9 39.2 + + - -
186B TRP* 5.9 0.2 - + - -
200B PHE* 4.1 18.2 - + + -
462B ASN 3.5 10.6 + - - +
463B ILE 3.0 7.1 + - - +
465B GLY* 1.3 78.4 - - - +
467B LEU* 1.3 63.2 + - - +
468B LYS 3.2 1.9 + - - -
469B ASP* 3.5 20.4 + - - +
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Residues in contact with LEU 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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183B TRP* 3.5 50.0 - - + +
463B ILE* 2.8 22.8 + - + +
466B HIS* 1.3 73.2 - - - +
468B LYS* 1.3 54.0 + - - +
469B ASP 3.0 5.4 - - - -
470B ALA* 2.8 35.7 + - + +
475B GLN* 3.7 19.4 + - + +
478B ALA* 3.8 25.4 - - + -
479B VAL* 4.6 1.6 - - + -
482B PHE* 4.8 3.1 - - + -
493B ILE* 4.4 12.3 - - + -
497B LEU* 3.6 28.5 - - + -
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Residues in contact with LYS 468 (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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464B ALA 3.0 22.2 + - - +
465B GLY 3.0 22.7 - - - +
467B LEU* 1.3 77.1 - - - +
469B ASP* 1.3 92.8 + - - +
470B ALA 3.2 1.5 - - - +
475B GLN* 3.1 22.1 + - - +
497B LEU* 3.6 8.4 - - + +
500B TYR* 3.6 52.9 - - + -
501B ASN* 3.8 6.4 - - - +
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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