Contacts of the helix formed by residues 477 - 488 (chain B) in PDB entry 1JPP
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 GLU 477 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436B MET* 4.2 27.3 - - + +
439B CYS* 4.6 11.5 - - + +
440B GLN* 5.5 6.4 - - - +
475B HIS* 2.8 22.1 + - + -
476B GLN* 1.3 79.2 - - + +
478B ALA* 1.3 64.9 + - - +
479B GLU 3.0 3.5 + - - -
480B MET* 3.0 35.8 + - + +
481B ALA* 2.9 22.9 + - - +
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Residues in contact with ALA 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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471B LEU 4.2 1.6 - - - -
472B THR* 4.3 2.5 - - - -
473B SER* 3.9 23.1 - - - +
474B ARG 4.3 0.9 - - - +
475B HIS* 3.1 36.9 + - - +
477B GLU* 1.3 77.7 - - - +
479B GLU* 1.3 58.7 + - - +
481B ALA* 3.4 7.4 - - - +
482B GLN* 3.2 33.1 + - - +
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Residues in contact with GLU 479 (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 GLN 4.9 6.3 + - - +
477B GLU 3.0 0.8 - - - -
478B ALA* 1.3 75.6 - - - +
480B MET* 1.3 68.4 + - - +
481B ALA 3.0 1.3 - - - -
482B GLN* 3.1 25.3 + - - +
483B ASN* 3.1 28.6 + - - +
520B CYS* 6.2 1.1 - - - -
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Residues in contact with MET 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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439B CYS* 4.0 40.2 - - + +
444B ILE* 4.1 17.5 - - + -
477B GLU* 3.0 36.6 + - + +
479B GLU* 1.3 82.1 - - - +
481B ALA* 1.3 57.2 + - - +
483B ASN* 3.3 8.0 + - - +
484B ALA* 2.9 36.8 + - + +
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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
----------------------------------------------------------
439B CYS* 4.8 6.5 - - - -
444B ILE* 4.5 13.7 - - + +
471B LEU 3.7 22.7 - - - +
472B THR* 3.7 12.8 - - + -
477B GLU 2.9 11.9 + - - +
478B ALA 3.4 11.2 - - - +
479B GLU 3.0 0.2 - - - -
480B MET* 1.3 86.4 - - - +
482B GLN* 1.3 62.9 + - - +
484B ALA* 3.3 9.5 + - - +
485B VAL* 3.3 21.0 + - - +
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Residues in contact with GLN 482 (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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472B THR* 3.9 30.0 - - + +
478B ALA* 3.2 20.6 + - - +
479B GLU* 3.1 15.3 + - - +
481B ALA* 1.3 76.5 - - - +
483B ASN* 1.3 62.4 + - - +
485B VAL* 3.8 11.8 + - - +
486B ARG* 4.1 2.6 + - - +
516B ASN 3.6 21.8 - - - +
517B LEU* 4.2 11.7 - - + +
519B LEU* 3.9 16.2 + - - +
520B CYS* 3.6 33.2 - - + +
523B ASN* 3.7 17.1 + - - +
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Residues in contact with ASN 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 GLU* 3.1 33.9 + - - +
480B MET* 3.7 9.5 - - - +
482B GLN* 1.3 75.8 - - - +
484B ALA* 1.3 63.8 + - - +
486B ARG* 3.1 38.1 + - - +
487B LEU* 3.0 34.4 + - + +
520B CYS* 3.2 21.1 - - - -
522B ALA* 4.3 1.7 - - - +
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Residues in contact with ALA 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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444B ILE* 4.0 19.3 - - + -
480B MET* 2.9 30.0 + - + +
481B ALA 3.3 4.7 + - - +
483B ASN* 1.3 72.0 - - - +
485B VAL* 1.3 65.6 + - - +
486B ARG 2.9 3.6 + - - -
487B LEU* 3.0 10.8 + - - +
488B HIS* 3.0 40.8 + - + +
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Residues in contact with VAL 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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444B ILE* 3.9 20.1 - - + +
448B VAL* 4.6 15.1 - - + +
468B LEU* 5.3 15.9 - - + -
472B THR* 4.4 8.1 - - + -
481B ALA 3.3 17.7 + - - +
482B GLN 4.0 1.8 - - - +
483B ASN 3.4 0.4 - - - -
484B ALA* 1.3 75.7 - - - +
486B ARG* 1.3 57.1 + - - +
488B HIS* 3.9 3.7 + - - +
490B GLY* 3.2 30.5 + - - -
491B LEU* 4.1 11.1 + - + -
494B VAL* 5.1 7.0 - - + -
513B LEU* 5.8 2.5 - - + -
517B LEU* 3.9 34.1 - - + -
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Residues in contact with ARG 486 (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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482B GLN 4.1 1.3 + - - +
483B ASN* 3.1 43.9 + - - +
484B ALA 2.9 0.6 - - - -
485B VAL* 1.3 76.7 - - - +
487B LEU* 1.3 75.3 + - - +
488B HIS 2.8 14.5 + - - -
489B TYR* 3.0 16.8 + - - -
491B LEU* 3.7 24.6 - - + +
522B ALA* 3.5 35.0 + - - +
523B ASN* 2.9 35.8 + - - +
526B PRO* 4.2 12.1 - - + -
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Residues in contact with LEU 487 (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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483B ASN* 3.0 34.9 + - + +
484B ALA* 3.0 9.2 + - - +
486B ARG* 1.3 91.1 - - - +
488B HIS* 1.3 70.4 + - + +
489B TYR* 3.6 13.3 - - - -
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Residues in contact with HIS 488 (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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444B ILE* 4.9 1.5 - - + +
445B GLU* 3.8 59.1 + - + +
448B VAL* 4.1 16.3 - - + +
452B LEU* 6.1 0.3 - - - +
484B ALA* 3.0 33.7 + - + +
485B VAL 4.5 2.9 - - - +
486B ARG 2.8 1.8 + - - -
487B LEU* 1.3 89.5 - - + +
489B TYR* 1.3 80.6 + + - +
490B GLY 3.3 2.7 + - - -
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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