Contacts of the helix formed by residues 425 - 438 (chain B) in PDB entry 2JGN
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 425 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421B VAL* 3.8 10.5 - - + -
422B GLU* 2.9 27.8 + - - +
424B SER* 1.3 86.9 + - - +
426B LYS* 1.3 64.9 + - - +
427B ARG 3.3 3.1 + - - -
428B SER* 3.4 10.5 + - - -
429B PHE* 2.9 27.4 + - + +
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Residues in contact with LYS 426 (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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421B VAL* 3.7 28.9 - - + -
422B GLU 3.4 4.7 + - - +
423B GLU* 2.8 44.9 + - - +
424B SER 3.6 0.4 - - - -
425B ASP* 1.3 77.6 - - - +
427B ARG* 1.3 58.4 + - - +
429B PHE* 3.5 2.7 - - - +
430B LEU* 2.9 28.6 + - - +
515B PHE* 2.8 56.5 + - + +
516B ASP* 3.0 17.9 + - - +
543B PHE* 3.6 30.0 + - + -
545B ASN* 3.7 4.6 - - - +
547B ARG* 5.4 0.4 - - - +
548B ASN* 5.2 3.8 + - - +
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Residues in contact with ARG 427 (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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423B GLU 4.8 1.0 + - - +
424B SER 5.4 0.6 - - - -
425B ASP 3.3 0.4 - - - -
426B LYS* 1.3 75.9 - - - +
428B SER* 1.3 57.5 + - - +
430B LEU* 3.2 4.6 + - - +
431B LEU* 3.0 32.4 + - - +
452B GLY 5.2 0.2 + - - -
455B SER* 2.4 42.8 + - - -
456B LEU* 3.7 13.9 - - + +
459B PHE* 3.2 62.2 - - + +
515B PHE* 4.1 19.0 - - + -
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Residues in contact with SER 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B SER 5.6 0.9 + - - -
425B ASP* 3.4 14.9 + - - -
427B ARG* 1.3 78.8 - - - +
429B PHE* 1.3 61.7 - - - +
431B LEU* 3.2 10.3 + - - +
432B ASP* 3.0 34.8 + - - +
459B PHE* 4.9 0.9 - - - -
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Residues in contact with PHE 429 (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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419B VAL* 3.7 30.1 - - + -
420B TRP 4.7 5.2 - - - -
421B VAL* 4.0 23.6 - - + -
425B ASP* 2.9 20.1 + - + +
426B LYS 3.5 4.9 - - - +
428B SER* 1.3 73.0 - - - +
430B LEU* 1.3 59.6 + - - +
432B ASP* 3.4 10.0 + - + +
433B LEU* 2.7 41.2 + - + +
541B THR* 5.4 1.1 - - + -
543B PHE* 3.4 36.1 - + + -
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Residues in contact with LEU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B LYS 2.9 21.0 + - - +
427B ARG* 3.2 5.6 + - - +
429B PHE* 1.3 74.0 - - - +
431B LEU* 1.3 53.1 + - - +
433B LEU* 3.0 3.3 + - - +
434B LEU* 2.7 53.1 + - + +
445B VAL* 4.5 9.0 - - + -
456B LEU* 3.9 33.7 - - + -
459B PHE* 5.4 0.4 - - + -
460B LEU* 4.1 20.4 - - + -
513B ILE* 3.7 41.1 - - + -
515B PHE* 3.9 13.0 - - + -
543B PHE* 4.1 7.9 - - + -
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Residues in contact with LEU 431 (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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427B ARG 3.0 16.2 + - - +
428B SER* 3.5 11.7 - - - +
430B LEU* 1.3 72.2 - - + +
432B ASP* 1.3 70.3 + - - +
433B LEU 3.2 0.2 + - - -
434B LEU* 3.2 3.9 + - + +
435B ASN* 2.9 33.2 + - - +
459B PHE* 3.5 36.1 - - + -
460B LEU* 3.8 20.2 - - + -
463B GLU* 3.7 27.8 - - + +
465B TYR* 4.1 17.5 - - + -
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Residues in contact with ASP 432 (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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428B SER* 3.0 23.6 + - - +
429B PHE* 3.7 10.9 - - + +
431B LEU* 1.3 80.8 - - - +
433B LEU* 1.3 57.2 + - - +
435B ASN* 3.3 11.3 + - - +
436B ALA* 2.8 33.4 + - + +
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Residues in contact with LEU 433 (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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429B PHE* 2.7 26.5 + - + +
430B LEU* 3.0 4.7 + - + +
432B ASP* 1.3 78.4 - - - +
434B LEU* 1.3 56.0 - - - +
436B ALA* 4.6 6.1 - - + -
437B THR* 2.8 53.6 + - - +
511B HIS* 4.1 9.4 - - + -
513B ILE* 4.0 22.7 - - + -
539B LEU* 6.2 0.2 - - + -
541B THR* 3.8 34.8 - - + +
543B PHE* 3.9 18.4 - - + -
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Residues in contact with LEU 434 (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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430B LEU* 2.7 36.3 + - + +
431B LEU* 3.7 2.2 - - + +
433B LEU* 1.3 71.9 - - - +
435B ASN* 1.3 61.6 + - - +
437B THR* 4.8 2.2 - - - -
438B GLY* 3.3 20.4 + - - -
443B THR* 4.2 16.2 - - + +
445B VAL* 5.4 0.4 - - + -
460B LEU* 3.6 31.6 - - + -
465B TYR* 3.6 26.1 + - + +
493B ILE* 3.8 28.0 - - + -
511B HIS* 5.8 1.1 - - - +
513B ILE* 4.1 20.6 - - + -
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Residues in contact with ASN 435 (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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431B LEU* 2.9 17.6 + - - +
432B ASP* 3.5 12.7 - - - +
434B LEU* 1.3 77.3 - - - +
436B ALA* 1.3 61.4 + - + +
437B THR 3.4 0.2 - - - -
438B GLY* 3.5 10.2 + - - -
465B TYR* 2.4 31.9 + - - -
553C LYS* 5.3 4.7 + - - -
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Residues in contact with ALA 436 (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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432B ASP* 2.8 18.4 + - + +
433B LEU* 4.1 7.6 - - + +
435B ASN* 1.3 77.1 - - + +
437B THR* 1.3 63.7 + - - +
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Residues in contact with THR 437 (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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433B LEU* 2.8 26.7 + - - +
434B LEU* 4.8 2.5 - - - -
436B ALA* 1.3 77.8 - - - +
438B GLY* 1.3 65.3 + - - +
510B LYS* 5.7 10.1 - - + -
511B HIS* 3.6 35.8 - - + +
539B LEU* 4.0 17.4 - - + +
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Residues in contact with GLY 438 (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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434B LEU 3.3 19.3 + - - -
435B ASN* 3.5 7.8 + - - -
436B ALA 3.3 3.2 - - - -
437B THR* 1.3 84.0 - - - +
441B SER* 4.0 25.4 + - - -
510B LYS* 5.8 2.3 - - - -
553C LYS* 4.7 16.2 + - - -
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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