Contacts of the helix formed by residues 477 - 485 (chain B) in PDB entry 2JAZ
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 PRO 477 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458B LYS 3.3 8.5 - - - +
460B VAL* 3.9 23.1 - - + -
464B TRP* 3.5 36.8 - - + +
475B PRO 3.3 4.7 - - - +
476B VAL* 1.3 88.9 - - + +
478B ASP* 1.3 63.0 + - - +
479B ARG* 4.5 4.5 - - + +
480B ILE* 3.0 24.9 + - + +
481B ALA* 2.9 23.7 + - - +
499B PHE* 4.6 2.9 - - + -
509B LEU* 4.1 16.6 - - + -
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Residues in contact with ASP 478 (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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456B LYS 3.2 21.8 - - - +
457B GLY 4.2 1.3 - - - +
458B LYS* 2.9 21.9 + - - +
459B PRO* 3.4 25.3 - - + +
460B VAL 4.8 0.7 + - - -
476B VAL 3.4 0.8 + - - -
477B PRO* 1.3 72.8 - - - +
479B ARG* 1.3 94.1 + - - +
481B ALA* 3.0 3.1 + - - +
482B ASN* 3.0 30.5 + - - +
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Residues in contact with ARG 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B VAL* 4.6 20.3 + - - +
477B PRO* 3.3 2.4 - - + -
478B ASP* 1.3 96.3 + - - +
480B ILE* 1.3 64.1 + - + +
482B ASN* 3.4 15.8 + - - +
483B LYS* 3.4 22.8 - - + +
506B ASP* 2.9 42.3 + - - +
508B GLU* 3.5 24.6 - - - +
509B LEU* 3.6 22.6 - - - +
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Residues in contact with ILE 480 (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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476B VAL* 4.4 1.6 - - + -
477B PRO* 3.0 22.9 + - + +
479B ARG* 1.3 75.8 - - - +
481B ALA* 1.3 63.8 - - - +
483B LYS* 3.2 15.0 + - + +
484B LEU* 3.2 35.1 + - + +
499B PHE* 3.9 21.5 - - + +
502B GLU* 3.8 37.5 - - + +
503B VAL* 3.9 4.7 - - + -
506B ASP* 4.1 10.5 - - + +
509B LEU* 3.6 33.0 - - + -
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Residues in contact with ALA 481 (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 GLY 3.8 5.4 - - - +
456B LYS 3.3 35.4 - - - +
457B GLY* 4.0 3.8 - - - +
476B VAL* 4.3 1.1 - - + -
477B PRO 2.9 10.3 + - - +
478B ASP 3.0 2.2 + - - +
480B ILE* 1.3 77.9 - - - +
482B ASN* 1.3 56.8 + - - +
484B LEU* 4.2 0.2 - - - +
485B ARG* 2.8 41.4 + - - +
558B MET* 3.5 23.0 - - + +
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Residues in contact with ASN 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B LYS* 4.8 3.2 + - - +
478B ASP* 3.0 22.3 + - - +
479B ARG* 3.6 11.3 - - - +
480B ILE 3.2 0.2 - - - -
481B ALA* 1.3 77.0 - - - +
483B LYS* 1.3 67.7 + - + +
484B LEU 3.6 0.2 + - - -
485B ARG* 2.8 49.8 + - - +
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Residues in contact with LYS 483 (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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479B ARG* 3.4 16.2 - - + +
480B ILE* 3.2 11.3 + - + +
482B ASN* 1.3 85.4 - - + +
484B LEU* 1.3 61.7 + - - +
485B ARG 5.0 0.4 - - - -
487B LYS* 3.2 25.5 - - - -
498B LYS* 4.4 1.0 + - - -
502B GLU* 3.5 32.8 + - + +
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Residues in contact with LEU 484 (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 ALA* 3.2 12.1 - - + +
480B ILE* 3.2 25.1 + - + +
481B ALA 3.2 1.6 + - - -
483B LYS* 1.3 76.8 - - - +
485B ARG* 1.3 68.9 + - - +
487B LYS* 3.0 22.0 + - - +
489B PHE* 4.1 12.6 - - + -
495B PHE* 4.0 11.7 - - + -
498B LYS* 3.5 42.8 - - + +
499B PHE* 4.0 16.6 - - + -
502B GLU* 3.7 13.5 - - + -
558B MET* 3.4 33.7 - - + -
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Residues in contact with ARG 485 (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 ALA* 3.5 11.7 - - - +
454B THR* 4.5 4.9 - - - -
455B GLY 2.7 31.0 + - - +
456B LYS* 3.2 47.4 - - - +
481B ALA* 2.8 20.4 + - - +
482B ASN* 2.8 52.3 + - - +
483B LYS 3.6 1.5 - - - +
484B LEU* 1.3 78.5 - - - +
486B ASP* 1.3 87.3 + - - +
487B LYS* 3.0 11.3 + - - +
558B MET* 4.7 2.0 - - - -
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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