Contacts of the helix formed by residues 452 - 456 (chain B) in PDB entry 2JI8
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 ASP 452 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ARG* 2.7 27.5 + - - -
451B GLY* 1.3 69.2 - - - -
453B SER* 1.3 57.6 + - - +
455B PHE* 3.5 5.1 + - - +
456B GLY 3.5 6.4 + - - -
476B ILE* 3.9 24.5 - - + -
477B MET 3.8 10.4 + - - +
478B ASN* 3.8 6.6 - - - +
479B ASN* 2.9 6.9 - - - +
480B GLY* 3.1 12.2 + - - -
481B GLY 3.0 24.6 + - - +
500B LEU* 3.8 7.9 - - - +
501B THR 4.9 0.7 - - - +
505B TYR* 4.1 14.6 + - + +
1563B TPP 2.8 3.2 + - - -
1564B MG 2.2 32.5 - - - -
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Residues in contact with SER 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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31A VAL* 5.4 1.0 - - - +
54A ARG* 4.2 5.0 + - - +
452B ASP* 1.3 76.6 + - - +
454B ALA* 1.3 68.3 + - - +
456B GLY* 3.0 13.9 + - - -
457B PHE* 3.2 23.2 - - - -
482B ILE* 3.8 16.6 - - - +
500B LEU* 3.6 21.1 - - - +
1563B TPP 2.9 39.8 + - - +
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Residues in contact with ALA 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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399B GLU* 3.7 28.4 - - + +
400B GLY 3.6 12.3 - - - +
428B MET* 3.6 26.2 - - - -
429B GLY 4.2 0.3 + - - -
451B GLY 3.6 7.0 - - - +
453B SER* 1.3 74.2 + - - +
455B PHE* 1.3 63.0 + - - +
456B GLY 3.2 0.3 + - - -
457B PHE* 3.3 24.6 + - - +
458B SER 4.4 0.5 + - - -
1563B TPP 2.8 23.3 + - - +
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Residues in contact with PHE 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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460A MET* 4.1 9.0 - - - -
399B GLU* 4.6 0.4 - - - -
432B MET* 4.0 23.3 - - + -
450B GLU* 3.8 15.9 - - + -
451B GLY 2.9 18.3 + - - +
452B ASP* 3.7 5.8 - - - +
453B SER 3.0 0.4 + - - -
454B ALA* 1.3 77.3 - - - +
456B GLY* 1.3 61.4 + - - +
457B PHE 3.0 2.5 + - - -
458B SER* 3.1 5.6 + - - -
459B GLY* 2.9 51.5 + - - -
462B LEU* 3.5 40.8 - - + -
474B VAL* 4.3 1.6 - - + -
476B ILE* 3.5 24.2 - - + -
505B TYR* 3.6 38.6 - + - -
508B MET* 4.6 1.3 - - - -
540B LEU* 4.6 0.9 - - + -
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Residues in contact with GLY 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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54A ARG* 3.4 40.7 - - - +
55A HIS* 4.8 1.7 - - - +
460A MET* 3.3 33.1 - - - +
461A GLU* 5.0 0.2 - - - +
452B ASP 3.5 3.8 + - - -
453B SER 3.0 8.2 + - - -
455B PHE* 1.3 79.9 - - - +
457B PHE* 1.3 58.6 + - - +
458B SER 3.4 0.8 + - - -
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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