Contacts of the helix formed by residues 486 - 502 (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 HIS 486 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444B ARG* 4.8 10.8 - - + -
447B TYR* 4.1 29.6 - + + -
448B VAL* 4.7 17.4 - - + +
482B PHE 3.1 5.4 + - - +
483B THR 3.3 4.4 + - - -
485B VAL* 1.3 86.1 - - + +
487B PRO* 1.3 73.8 - - + +
488B ASP* 2.9 54.0 + - + +
489B TYR* 2.7 33.8 + - + +
490B GLY 3.3 1.2 + - - -
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Residues in contact with PRO 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B THR* 3.3 28.3 - - + +
486B HIS* 1.3 94.5 - - + +
488B ASP* 1.3 54.1 + - - +
490B GLY 4.1 0.2 - - - -
491B SER* 2.6 39.0 + - - -
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Residues in contact with ASP 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B TYR* 3.8 13.0 + - + +
456B ARG* 6.1 0.9 - - - -
486B HIS* 2.8 33.4 + - + +
487B PRO* 1.3 77.5 - - - +
489B TYR* 1.3 67.3 + - - +
491B SER* 3.3 7.0 + - - -
492B HIS* 2.9 29.5 + - - +
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Residues in contact with TYR 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B SER* 2.7 30.1 + - - -
443B VAL* 4.6 3.8 - - + -
447B TYR* 3.4 44.0 + + + -
459B LEU* 3.5 23.2 - - + +
460B CYS* 4.1 6.6 - - - -
463B ILE* 3.6 18.0 - - + +
482B PHE* 3.4 25.7 - + + +
485B VAL* 3.8 29.2 - - + -
486B HIS* 2.7 21.0 + - + +
488B ASP* 1.3 75.2 - - - +
490B GLY* 1.3 63.2 + - - +
493B ILE* 3.2 48.6 + - + +
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Residues in contact with GLY 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B VAL* 3.7 12.6 - - - +
482B PHE* 3.8 20.3 + - - -
483B THR* 3.8 15.7 - - - -
486B HIS 3.3 6.1 + - - -
487B PRO 4.1 0.4 - - - -
489B TYR* 1.3 81.1 - - - +
491B SER* 1.3 50.6 + - - +
493B ILE* 3.1 6.2 + - - +
494B GLN* 2.7 35.0 + - - +
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Residues in contact with SER 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B THR* 4.7 1.6 + - - -
487B PRO 2.6 27.1 + - - -
488B ASP* 3.3 12.3 + - - -
490B GLY* 1.3 72.4 - - - +
492B HIS* 1.3 59.4 + - - +
494B GLN* 3.3 9.3 + - - +
495B ALA* 2.9 26.7 + - - +
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Residues in contact with HIS 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B TYR* 5.3 1.6 + - - +
456B ARG* 5.1 1.8 + - - +
457B LYS* 4.0 32.0 - - + +
460B CYS* 3.7 25.9 - - + -
461B GLU* 5.3 0.6 - - - +
488B ASP 2.9 19.5 + - - +
489B TYR 4.1 1.8 - - - +
491B SER* 1.3 74.4 + - - +
493B ILE* 1.3 68.0 + - - +
495B ALA* 3.1 16.8 + - + +
496B LEU* 3.2 33.9 + - + +
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Residues in contact with ILE 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B CYS* 4.0 25.8 - - + +
463B ILE* 4.0 13.5 - - + -
464B ALA* 4.7 7.0 - - + -
467B LEU* 4.4 10.1 - - + -
479B VAL* 4.4 8.3 - - + -
482B PHE* 3.6 25.8 - - + -
489B TYR* 3.2 40.3 + - + +
490B GLY* 3.1 8.6 + - - +
492B HIS* 1.3 76.1 - - - +
494B GLN* 1.3 64.1 + - - +
495B ALA 3.2 0.2 + - - -
496B LEU* 3.2 9.8 + - - +
497B LEU* 2.9 41.2 + - + +
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Residues in contact with GLN 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B GLN* 5.0 2.5 + - - +
476B LYS* 5.5 4.5 - - - +
479B VAL* 3.5 29.5 - - + +
490B GLY 2.7 19.4 + - - +
491B SER* 3.5 11.0 - - - +
492B HIS 3.2 0.2 - - - -
493B ILE* 1.3 76.1 - - - +
495B ALA* 1.3 56.1 + - - +
497B LEU* 3.3 14.8 + - - +
498B ASP* 2.7 58.8 + - - +
501B ASN* 5.4 2.0 - - - +
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Residues in contact with ALA 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B SER 2.9 13.4 + - - +
492B HIS* 3.1 19.3 + - + +
494B GLN* 1.3 74.2 - - - +
496B LEU* 1.3 70.0 + - + +
498B ASP* 3.1 12.8 + - - +
499B LYS* 3.0 25.3 + - - +
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Residues in contact with LEU 496 (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* 3.8 6.1 - - + +
461B GLU* 3.6 46.7 - - + +
464B ALA* 3.5 19.5 - - + -
492B HIS* 3.5 33.7 - - + +
493B ILE* 3.2 2.2 + - - +
495B ALA* 1.3 78.3 - - + +
497B LEU* 1.3 64.4 + - - +
499B LYS* 2.9 29.2 + - + +
500B TYR* 2.9 32.5 + - + -
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Residues in contact with LEU 497 (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* 3.7 14.6 - - - +
467B LEU* 3.6 30.5 - - + -
468B LYS* 3.6 35.2 - - - +
475B GLN* 3.8 24.5 - - + +
479B VAL* 3.8 22.2 - - + -
493B ILE* 2.9 21.3 + - + +
494B GLN* 3.5 16.4 - - - +
496B LEU* 1.3 75.9 - - - +
498B ASP* 1.3 53.0 + - - +
500B TYR* 2.9 6.6 + - - +
501B ASN* 2.7 40.4 + - - +
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Residues in contact with ASP 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B GLN* 2.7 50.1 + - - +
495B ALA* 3.3 10.5 - - - +
497B LEU* 1.3 74.0 - - - +
499B LYS* 1.3 64.5 + - - +
501B ASN* 3.7 7.5 + - - +
502B ALA* 2.8 25.9 + - - +
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Residues in contact with LYS 499 (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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495B ALA* 3.0 14.0 + - - +
496B LEU* 2.9 29.4 + - + +
498B ASP* 1.3 79.2 - - - +
500B TYR* 1.3 63.7 + - + +
502B ALA* 3.1 18.9 + - + +
503B GLU* 3.2 19.9 - - - +
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Residues in contact with TYR 500 (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 4.7 2.5 + - - -
464B ALA* 3.8 24.5 - - + -
465B GLY* 3.5 20.0 + - - -
468B LYS* 3.6 48.9 - - + -
496B LEU* 2.9 31.1 + - + -
497B LEU* 2.9 7.1 + - - +
499B LYS* 1.3 78.4 - - + +
501B ASN* 1.3 62.1 + - - +
502B ALA 3.0 0.2 - - - -
503B GLU* 3.1 35.4 + - - +
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Residues in contact with ASN 501 (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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468B LYS 3.8 8.3 - - - +
472B ILE* 4.8 18.1 - - + +
475B GLN* 2.7 42.2 + - - -
494B GLN* 5.4 1.4 - - - +
497B LEU* 2.7 30.1 + - - +
498B ASP* 4.1 8.2 + - - +
500B TYR* 1.3 69.9 - - - +
502B ALA* 1.3 60.8 + - - +
503B GLU 3.0 15.4 + - - +
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Residues in contact with ALA 502 (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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498B ASP 2.8 12.9 + - - +
499B LYS* 3.1 18.6 - - + +
500B TYR 3.0 0.4 - - - -
501B ASN* 1.3 77.6 - - - +
503B GLU* 1.3 59.7 + - + +
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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