Contacts of the helix formed by residues 484 - 495 (chain j) in PDB entry 5JPQ
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 484 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23j LYS* 4.5 21.3 - - - -
24j ARG* 4.6 5.4 - - + +
480j TYR* 4.2 14.4 - - + -
481j ALA 3.4 15.2 + - - +
482j GLN 3.1 3.2 + - - -
483j GLY* 1.3 77.3 - - - +
485j ASN* 1.3 65.9 + - - +
486j VAL* 4.5 2.5 - - + +
487j GLU* 3.2 18.8 + - + +
488j LYS* 3.1 19.2 + - - +
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Residues in contact with ASN 485 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23j LYS* 5.0 2.6 - - - +
24j ARG 4.2 8.2 + - - +
25j SER* 6.0 1.3 - - - -
198j SER* 3.5 34.1 - - - +
483j GLY 3.0 7.7 + - - +
484j ASP* 1.3 69.6 - - - +
486j VAL* 1.3 66.3 + - - +
488j LYS* 3.6 8.6 - - + +
489j TRP* 3.0 23.4 + - - +
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Residues in contact with VAL 486 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24j ARG* 3.5 38.6 + - + +
25j SER* 4.3 10.9 - - - +
26j PHE* 4.8 7.9 - - + +
140j ILE* 5.6 12.3 - - + +
149j VAL* 6.2 3.1 - - + -
484j ASP* 3.2 1.7 - - + -
485j ASN* 1.3 77.2 - - - +
487j GLU* 1.3 61.2 + - - +
489j TRP* 3.1 9.6 - - - +
490j LEU* 3.0 21.1 + - - +
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Residues in contact with GLU 487 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140j ILE* 6.1 3.4 - - - -
484j ASP* 3.2 21.0 + - + +
486j VAL* 1.3 76.2 - - - +
488j LYS* 1.3 65.9 + - - +
490j LEU* 3.3 5.2 + - - +
491j ASN* 3.0 23.6 + - - +
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Residues in contact with LYS 488 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483j GLY 5.6 2.2 - - - +
484j ASP 3.1 12.5 + - - +
485j ASN* 3.6 12.1 - - + +
486j VAL 3.3 0.2 - - - -
487j GLU* 1.3 74.5 - - - +
489j TRP* 1.3 64.3 + - - +
491j ASN* 3.2 7.8 + - - +
492j THR* 3.0 24.6 + - - -
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Residues in contact with TRP 489 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26j PHE* 5.4 11.0 - - + -
192j SER* 5.2 6.5 - - - -
199j CYS* 6.3 2.2 - - + -
485j ASN 3.0 13.3 + - - +
486j VAL* 3.1 14.1 - - - +
488j LYS* 1.3 77.5 - - - +
490j LEU* 1.3 65.0 + - - +
492j THR* 3.6 4.3 - - - -
493j LEU* 2.8 24.3 + - - +
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Residues in contact with LEU 490 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136j LEU 6.1 0.2 - - - -
137j ALA* 4.9 21.1 - - + -
140j ILE* 5.3 9.6 - - + -
486j VAL 3.0 10.2 + - - +
487j GLU* 3.3 6.0 + - - +
489j TRP* 1.3 79.8 - - - +
491j ASN* 1.3 62.9 + - - +
493j LEU* 3.7 6.0 - - - +
494j LEU* 2.8 30.5 + - + +
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Residues in contact with ASN 491 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487j GLU 3.0 14.3 + - - +
488j LYS* 3.2 11.4 + - - +
490j LEU* 1.3 74.8 - - - +
492j THR* 1.3 59.0 + - - +
494j LEU* 4.8 0.9 - - - -
495j CYS* 2.8 25.8 + - - -
496j LEU* 3.1 29.8 + - + -
497j ASP 4.9 0.2 + - - -
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Residues in contact with THR 492 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192j SER* 4.7 14.4 - - - -
488j LYS 3.0 16.2 + - - -
489j TRP* 3.7 3.8 - - - -
491j ASN* 1.3 74.9 - - - +
493j LEU* 1.3 66.5 + - - +
494j LEU 3.4 0.2 + - - -
495j CYS* 3.5 11.2 + - - +
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Residues in contact with LEU 493 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188j ARG* 5.4 10.6 - - - +
189j PHE* 5.8 7.9 - - + +
192j SER* 5.0 10.7 - - - -
489j TRP 2.8 20.8 + - - +
490j LEU* 3.7 6.7 - - - +
492j THR* 1.3 74.8 - - - +
494j LEU* 1.3 60.1 + - + +
495j CYS* 3.6 1.4 + - - +
556j LEU* 6.1 0.3 - - - +
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Residues in contact with LEU 494 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133j PRO* 6.5 0.9 - - + -
137j ALA* 5.6 8.5 - - + -
490j LEU* 2.8 19.5 + - + +
491j ASN* 4.1 3.1 - - - +
493j LEU* 1.3 76.3 - - + +
495j CYS* 1.3 66.8 + - - +
496j LEU* 4.6 4.9 - - + +
553j PRO* 5.0 17.2 - - + +
556j LEU* 4.7 14.8 - - - +
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Residues in contact with CYS 495 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491j ASN 2.8 13.7 + - - -
492j THR* 3.5 6.8 + - - +
493j LEU 3.4 4.5 - - - +
494j LEU* 1.3 77.0 - - - +
496j LEU* 1.3 60.6 + - - +
497j ASP* 3.3 9.8 + - + +
538j GLN* 6.1 5.4 - - + +
541j VAL* 6.0 7.0 - - + -
545j VAL* 6.0 1.9 - - - +
556j LEU* 6.2 1.1 - - + -
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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