Contacts of the helix formed by residues 450 - 459 (chain B) in PDB entry 5IJ7
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 450 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447B TYR* 4.3 15.0 - - + +
448B TYR 3.5 4.7 - - - +
449B ASP* 1.4 77.8 + - - +
451B PHE* 1.4 58.6 + - - +
452B CYS* 3.4 12.3 + - - +
453B ALA* 3.0 39.5 + - + +
454B ILE* 3.3 26.5 + - - +
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Residues in contact with PHE 451 (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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440B PHE* 4.6 5.6 - + - -
444B ILE* 5.0 2.2 - - + -
448B TYR 4.2 11.7 - - - -
449B ASP* 3.1 33.1 + - + -
450B ASN* 1.4 69.2 - - - +
452B CYS* 1.3 59.4 + - - +
453B ALA 3.4 0.2 - - - -
454B ILE* 3.8 8.3 - - + -
455B ALA* 3.0 30.3 + - - +
463B CYS* 4.0 18.8 - - - +
466B VAL* 3.6 31.2 - - + +
467B TYR* 3.7 37.2 - + + -
470B ARG* 3.6 49.1 - - + -
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Residues in contact with CYS 452 (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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450B ASN* 3.2 9.2 - - - +
451B PHE* 1.3 79.2 - - - +
453B ALA* 1.4 56.4 + - - +
455B ALA* 3.4 4.5 + - - +
456B ARG* 3.0 26.3 + - - +
463B CYS* 2.7 40.1 - - - -
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Residues in contact with ALA 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B TYR* 3.9 22.2 - - + -
450B ASN* 3.0 32.7 + - - +
452B CYS* 1.4 73.3 - - - +
454B ILE* 1.4 59.8 + - - +
456B ARG* 3.2 29.3 - - - +
457B LEU* 3.1 32.2 + - - +
675T ASP* 4.8 0.4 - - - +
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Residues in contact with ILE 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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440B PHE* 4.4 6.5 - - + -
443B LEU* 3.8 25.8 - - + +
444B ILE* 4.3 11.7 - - + -
447B TYR* 3.7 38.1 - - + +
448B TYR 4.1 9.0 - - - +
450B ASN 3.3 26.1 + - - +
451B PHE* 4.1 11.7 - - + +
452B CYS 3.4 0.4 - - - -
453B ALA* 1.4 72.6 - - - +
455B ALA* 1.3 59.8 + - - +
457B LEU* 3.3 7.0 + - - +
458B ILE* 2.9 48.1 + - + +
466B VAL* 3.8 14.4 - - + -
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Residues in contact with ALA 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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451B PHE 3.0 19.1 + - - +
452B CYS 3.4 6.1 - - - +
454B ILE* 1.3 75.8 - - - +
456B ARG* 1.4 53.0 + - - +
458B ILE* 3.2 1.4 + - - -
459B GLY* 2.8 33.3 + - - +
461B LYS 3.3 14.2 - - - +
462B THR* 3.5 34.3 - - - +
463B CYS* 3.5 4.0 - - + +
466B VAL* 3.9 7.1 - - + +
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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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452B CYS 3.0 14.6 + - - +
453B ALA* 3.2 29.4 - - - +
455B ALA* 1.4 73.2 - - - +
457B LEU* 1.3 58.7 + - - +
459B GLY* 4.1 5.7 + - - -
675T ASP* 3.4 43.7 + - - +
678T VAL* 5.3 0.9 - - - +
679T THR* 4.7 12.0 + - - +
682T ARG* 3.7 16.6 + - - -
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Residues in contact with LEU 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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443B LEU* 3.6 12.8 - - + -
447B TYR* 3.4 41.3 - - + +
453B ALA 3.1 21.7 + - - +
454B ILE 3.7 4.5 - - - +
455B ALA 3.1 0.2 - - - -
456B ARG* 1.3 79.3 - - - +
458B ILE* 1.3 60.4 + - - +
459B GLY 3.2 1.3 - - - -
657T MET* 3.4 34.5 - - + +
674T ILE* 4.1 11.4 - - + +
675T ASP* 4.1 8.3 - - - +
678T VAL* 3.7 36.6 - - + -
682T ARG* 2.7 21.3 + - - +
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Residues in contact with ILE 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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432B TRP* 4.0 16.8 - - + -
436B GLU* 4.0 22.7 - - + +
439B MET* 4.1 11.4 - - + -
440B PHE* 3.9 23.6 - - + +
443B LEU* 3.6 12.6 - - + -
454B ILE* 2.9 41.1 + - + +
455B ALA* 3.2 2.4 + - - +
457B LEU* 1.3 72.3 - - - +
459B GLY* 1.3 53.3 + - - +
460B THR* 2.8 35.9 + - - +
461B LYS* 4.3 14.4 - - + +
466B VAL* 4.4 6.1 - - + -
657T MET* 4.9 1.3 - - - -
682T ARG* 4.8 1.5 + - - -
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Residues in contact with GLY 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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455B ALA 2.8 12.6 + - - +
456B ARG* 4.4 7.6 - - - -
457B LEU 3.2 2.8 - - - -
458B ILE* 1.3 72.3 - - - +
460B THR* 1.4 63.1 + - - -
461B LYS 3.2 11.5 + - - +
462B THR* 5.5 1.6 - - - +
682T ARG* 4.9 9.2 - - - -
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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