Contacts of the helix formed by residues 421 - 433 (chain B) in PDB entry 2JED
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 421 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416B VAL* 2.9 24.2 + - + +
419B ASP* 3.4 26.3 - - + +
420B ASP* 1.3 76.7 - - - +
422B VAL* 1.3 58.5 + - - +
423B GLU 3.4 2.2 - - - -
424B CYS* 3.8 24.3 - - - -
425B THR* 2.7 36.7 + - - +
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Residues in contact with VAL 422 (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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416B VAL* 3.8 19.1 - - + -
417B LEU* 4.1 19.7 - - + -
420B ASP* 3.6 5.0 + - - +
421B ASP* 1.3 78.7 - - - +
423B GLU* 1.3 65.2 + - + +
425B THR* 3.5 1.7 + - - -
426B MET* 3.2 31.7 + - + +
690B MET* 3.8 55.4 - - + +
691B PHE* 4.0 6.1 - - + -
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Residues in contact with GLU 423 (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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420B ASP 5.3 0.4 + - - -
421B ASP* 3.4 0.4 - - - +
422B VAL* 1.3 81.3 - - - +
424B CYS* 1.3 59.0 + - - +
426B MET* 3.3 6.9 + - - +
427B VAL* 2.9 41.8 + - + +
430B ARG* 3.2 27.7 + - - -
528B GLU* 4.9 0.2 - - - +
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Residues in contact with CYS 424 (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 ASP* 3.7 36.7 - - - +
423B GLU* 1.3 77.6 - - - +
425B THR* 1.3 61.2 + - - +
427B VAL* 3.8 10.9 - - + +
428B GLU* 3.0 27.5 + - - +
524B GLY* 3.8 25.4 - - - +
526B CYS 6.0 1.1 - - - +
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Residues in contact with THR 425 (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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411B LEU* 3.9 20.9 - - + +
416B VAL* 3.8 12.6 - - - +
421B ASP* 2.7 25.1 + - - +
422B VAL 3.6 5.8 - - - -
423B GLU 3.3 0.2 - - - -
424B CYS* 1.3 76.3 - - - +
426B MET* 1.3 66.0 + - + +
428B GLU* 3.5 9.7 + - - +
429B LYS* 3.1 25.5 + - - +
454B LEU* 3.8 28.7 - - + -
456B PHE* 4.1 11.5 - - + -
694B PHE* 4.4 5.2 - - + -
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Residues in contact with MET 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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422B VAL* 3.2 24.1 + - + +
423B GLU* 3.3 13.2 + - - +
425B THR* 1.3 82.1 - - + +
427B VAL* 1.3 57.4 - - - +
429B LYS* 3.3 9.3 + - + +
430B ARG* 2.9 55.4 + - + +
690B MET 4.2 9.2 - - - +
691B PHE* 3.3 38.1 - - + -
692B ARG 4.5 9.9 - - - +
693B ASN* 5.7 1.3 - - + +
694B PHE* 4.1 33.7 - - + -
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Residues in contact with VAL 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B GLU* 2.9 42.9 + - + +
424B CYS* 3.8 10.8 - - + +
425B THR 3.4 0.2 - - - -
426B MET* 1.3 75.2 - - - +
428B GLU* 1.3 58.2 + - - +
430B ARG* 3.1 15.9 + - - +
431B VAL* 2.8 34.4 + - + +
523B PHE 4.7 1.6 - - - +
524B GLY 5.9 0.7 - - - +
526B CYS* 3.3 42.6 - - + +
528B GLU* 3.8 17.0 - - + +
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Residues in contact with GLU 428 (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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409B LYS* 3.0 36.8 + - - +
411B LEU* 5.4 0.9 - - - +
424B CYS 3.0 19.3 + - - +
425B THR* 3.7 8.7 - - - +
426B MET 3.3 0.2 - - - -
427B VAL* 1.3 76.6 - - - +
429B LYS* 1.3 56.9 - - - +
431B VAL* 3.9 2.7 - - - +
432B LEU* 2.9 52.2 + - + +
456B PHE* 4.3 6.8 - - + -
522B ASP* 4.3 2.0 - - - +
523B PHE* 3.8 30.1 + - + +
524B GLY* 4.0 15.8 + - - -
1712B LG8 3.5 20.1 - - - -
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Residues in contact with LYS 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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425B THR 3.1 17.6 + - - +
426B MET* 3.6 11.7 - - + +
427B VAL 3.2 0.2 - - - -
428B GLU* 1.3 76.3 - - - +
430B ARG* 1.3 73.3 + - + +
432B LEU* 3.6 2.9 + - - -
433B SER* 2.9 37.2 + - - -
444B MET* 3.7 3.8 - - + +
447B THR* 4.1 12.3 - - + +
456B PHE* 4.2 9.1 - - + -
693B ASN* 3.3 19.9 + - - +
694B PHE* 3.3 47.6 - - + +
695B SEP 4.2 3.0 + - - -
696B PHE* 3.8 22.1 - - - +
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Residues in contact with ARG 430 (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* 3.2 28.7 + - - -
426B MET* 2.9 41.9 + - + +
427B VAL* 3.6 8.0 - - - +
429B LYS* 1.3 90.4 - - + +
431B VAL* 1.3 62.5 + - - +
433B SER* 2.7 23.9 + - - +
434B LEU* 3.8 9.5 + - - +
528B GLU* 2.9 45.2 + - - +
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Residues in contact with VAL 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 VAL* 2.8 28.7 + - + +
428B GLU 3.9 2.7 - - - +
430B ARG* 1.3 71.1 - - - +
432B LEU* 1.3 64.3 + - - +
434B LEU* 3.0 32.8 + - + +
435B ALA* 3.5 3.9 + - + +
441B LEU* 6.0 0.4 - - + -
495B LEU* 4.4 8.1 - - + -
500B ILE* 4.2 29.6 - - + -
523B PHE* 3.7 35.2 - - + -
526B CYS* 3.9 27.1 - - + -
528B GLU* 4.4 7.9 - - + +
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Residues in contact with LEU 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 GLU* 2.9 39.0 + - + +
429B LYS 3.8 0.4 - - - +
431B VAL* 1.3 73.6 - - - +
433B SER* 1.3 56.9 + - - +
434B LEU 2.9 5.5 + - - -
435B ALA* 3.0 19.3 + - + +
436B TRP* 4.5 1.2 + - - -
442B THR* 3.8 9.4 - - + +
444B MET* 3.6 28.4 + - + +
456B PHE* 3.7 28.3 - - + -
458B MET* 3.6 37.7 - - + -
523B PHE* 3.5 33.7 - - + -
1712B LG8 5.3 3.6 - - + -
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Residues in contact with SER 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 LYS* 2.9 24.2 + - - -
430B ARG* 2.7 22.5 + - - -
431B VAL 3.2 0.4 - - - -
432B LEU* 1.3 73.5 - - - +
434B LEU* 1.3 57.3 + - - +
435B ALA 3.6 0.2 - - - -
436B TRP* 3.4 14.2 + - - -
444B MET* 3.5 7.4 - - - +
696B PHE* 3.3 50.9 - - - -
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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