Contacts of the helix formed by residues 477 - 488 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436A MET* 4.2 26.2 - - + -
439A CYS* 4.5 14.8 - - + +
440A GLN* 5.5 6.5 - - - +
475A HIS* 2.9 21.5 + - + -
476A GLN* 1.3 78.0 - - + +
478A ALA* 1.3 58.6 + - - +
479A GLU 3.0 3.8 + - - +
480A MET* 3.1 32.0 + - + +
481A ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A LEU 4.2 1.1 - - - -
472A THR* 4.4 1.9 - - - -
473A SER* 4.0 20.4 - - - +
474A ARG 4.2 4.0 - - - +
475A HIS* 3.0 37.2 + - - +
476A GLN 3.4 0.4 - - - -
477A GLU* 1.3 77.5 - - - +
479A GLU* 1.3 58.5 + - - +
481A ALA* 3.5 5.9 - - - +
482A GLN* 3.1 34.8 + - - +
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Residues in contact with GLU 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476A GLN 4.8 7.0 + - - +
477A GLU 3.0 1.0 - - - -
478A ALA* 1.3 75.4 - - - +
480A MET* 1.3 67.8 + - - +
481A ALA 3.1 1.6 - - - -
482A GLN* 3.1 17.3 + - - +
483A ASN* 3.1 36.9 + - - +
520A CYS* 6.4 0.4 - - - -
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Residues in contact with MET 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A CYS* 3.9 39.0 - - + +
444A ILE* 4.1 18.2 - - + -
477A GLU* 3.1 36.6 + - + +
479A GLU* 1.3 80.9 - - - +
481A ALA* 1.3 57.2 + - - +
483A ASN* 3.2 7.9 + - - +
484A ALA* 2.9 37.0 + - + +
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Residues in contact with ALA 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A CYS* 4.7 6.3 - - - -
444A ILE* 4.5 13.9 - - + +
471A LEU 3.7 22.7 - - - +
472A THR* 3.8 11.7 - - + -
477A GLU 2.9 16.4 + - - +
478A ALA 3.5 7.6 - - - +
479A GLU 3.1 0.2 - - - -
480A MET* 1.3 89.3 - - - +
482A GLN* 1.3 63.5 + - - +
484A ALA* 3.3 7.7 + - - +
485A VAL* 3.2 20.8 + - - +
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Residues in contact with GLN 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A THR* 3.8 31.7 - - + +
478A ALA* 3.1 20.9 + - - +
479A GLU* 3.1 14.0 + - - +
481A ALA* 1.3 75.9 - - - +
483A ASN* 1.3 62.0 + - - +
485A VAL* 3.8 9.0 + - - +
486A ARG 4.1 4.9 + - - -
491A LEU* 6.2 0.2 - - - +
516A ASN 3.6 22.7 - - - +
517A LEU* 4.2 10.6 - - + +
519A LEU* 4.0 15.9 + - - +
520A CYS* 3.6 33.3 - - + +
523A ASN* 3.8 17.1 + - - +
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Residues in contact with ASN 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A GLU* 3.1 31.7 + - - +
480A MET* 3.7 10.0 - - - +
482A GLN* 1.3 76.5 - - - +
484A ALA* 1.3 58.6 + - - +
486A ARG* 3.0 39.3 + - - +
487A LEU* 3.0 38.0 + - + +
520A CYS* 3.2 19.1 - - - -
522A ALA* 4.2 1.9 - - - +
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Residues in contact with ALA 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A ILE* 4.0 18.2 - - + -
480A MET* 2.9 30.0 + - + +
481A ALA 3.3 4.7 + - - +
483A ASN* 1.3 72.7 - - - +
485A VAL* 1.3 66.9 + - - +
486A ARG 2.9 3.5 + - - -
487A LEU* 3.0 11.7 + - + +
488A HIS* 2.9 41.6 + - + +
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Residues in contact with VAL 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A ILE* 3.9 20.8 - - + +
448A VAL* 4.5 16.7 - - + +
468A LEU* 5.3 14.8 - - + -
472A THR* 4.5 7.6 - - + -
481A ALA 3.2 17.9 + - - +
482A GLN 4.1 5.4 - - - +
483A ASN 3.4 0.4 - - - -
484A ALA* 1.3 76.2 - - - +
486A ARG* 1.3 57.8 + - - +
488A HIS* 3.8 3.6 + - - +
490A GLY* 3.2 32.4 + - - -
491A LEU* 4.1 9.1 + - + -
494A VAL* 5.1 7.0 - - + -
513A LEU* 5.9 2.9 - - + -
517A LEU* 4.1 29.4 - - + -
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Residues in contact with ARG 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A GLN 4.1 1.7 + - - +
483A ASN* 3.0 46.4 + - - +
484A ALA 3.0 0.6 - - - -
485A VAL* 1.3 76.6 - - - +
487A LEU* 1.3 72.6 + - - +
488A HIS 2.7 15.7 + - - -
489A TYR* 2.9 16.6 + - - -
491A LEU* 3.7 25.6 - - + +
522A ALA* 3.5 36.8 + - - +
523A ASN* 2.9 35.9 + - - +
526A PRO* 4.2 11.7 - - + -
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Residues in contact with LEU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483A ASN* 3.0 33.3 + - + +
484A ALA* 3.0 10.4 + - - +
486A ARG* 1.3 90.7 - - - +
488A HIS* 1.3 70.7 + - + +
489A TYR* 3.6 12.5 - - - -
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Residues in contact with HIS 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A ILE* 4.8 1.5 - - + +
445A GLU* 3.7 55.6 + - + +
448A VAL* 4.1 18.1 - - + +
484A ALA* 2.9 33.1 + - + +
485A VAL 4.4 2.5 - - - +
486A ARG 2.7 7.5 + - - -
487A LEU* 1.3 84.8 + - + +
489A TYR* 1.3 78.7 + + - +
490A GLY 3.4 3.0 + - - -
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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