Contacts of the helix formed by residues 424 - 432 (chain B) in PDB entry 2JDQ
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 CYS 424 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B ILE* 3.7 18.5 - - + +
389B LEU* 5.1 1.2 - - + +
404B ILE* 4.2 23.3 - - + -
419B LEU* 3.2 36.7 + - + +
420B VAL* 4.0 8.4 + - - -
423B GLY* 1.3 75.1 - - - +
425B ILE* 1.3 70.3 + - - +
427B PRO* 3.6 8.1 - - + +
428B LEU* 3.4 23.6 + - - +
450B ILE* 3.8 26.9 - - - -
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Residues in contact with ILE 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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294A ASP 6.0 0.2 - - - +
420B VAL* 3.9 37.7 + - + -
423B GLY 3.3 1.8 - - - -
424B CYS* 1.3 78.1 - - - +
426B LYS* 1.3 68.9 + - - +
428B LEU* 3.2 8.4 + - - +
429B CYS* 3.0 21.4 + - - -
447B LEU* 4.3 5.8 - - + -
450B ILE* 4.2 20.6 - - + -
468B TYR* 4.2 11.9 - - + -
471B LEU* 3.8 31.0 - - + +
472B ILE* 3.9 21.5 - - + -
475B ALA* 3.9 18.8 - - + -
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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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290A GLN* 5.9 1.4 - - - +
294A ASP* 3.3 57.7 + - + +
390B GLN* 5.5 5.4 - - - +
423B GLY 4.0 0.6 + - - -
425B ILE* 1.3 76.8 - - - +
427B PRO* 1.4 67.4 - - + +
429B CYS* 2.9 20.4 + - - +
430B ASP* 2.9 42.1 + - - +
474B GLU 5.2 0.2 + - - -
475B ALA* 2.9 33.6 + - + +
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Residues in contact with PRO 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ILE* 4.3 11.9 - - + +
389B LEU* 3.8 37.5 - - + +
390B GLN* 4.3 22.4 - - + +
397B ARG* 5.2 0.7 + - - +
423B GLY 3.1 23.1 - - - +
424B CYS* 3.6 11.7 - - - +
426B LYS* 1.4 90.2 - - + +
428B LEU* 1.3 61.4 + - - +
430B ASP* 3.4 13.3 + - + +
431B LEU* 3.2 27.7 + - - +
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Residues in contact with LEU 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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389B LEU* 4.3 17.5 - - + -
401B ALA* 4.8 6.7 - - + +
404B ILE* 4.4 18.6 - - + -
405B THR* 4.2 15.9 - - - +
408B THR* 5.4 0.2 - - + -
424B CYS 3.4 16.0 + - - +
425B ILE 3.2 8.1 + - - +
427B PRO* 1.3 78.1 - - - +
429B CYS* 1.3 60.8 - - - +
431B LEU* 3.1 18.4 + - + +
432B LEU* 3.6 4.0 + - - +
443B ALA* 3.4 31.5 - - + +
446B GLY* 4.3 5.4 - - - -
447B LEU* 4.2 28.9 - - + +
450B ILE* 4.2 24.2 - - + -
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Residues in contact with CYS 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 ILE* 3.0 24.2 + - - +
426B LYS 2.9 8.3 + - - +
428B LEU* 1.3 73.1 - - - +
430B ASP* 1.3 67.0 + - - +
432B LEU* 3.1 26.2 + - - +
433B THR* 4.3 2.9 + - - +
447B LEU* 4.0 19.7 - - - -
472B ILE* 4.1 8.7 - - - -
475B ALA* 3.7 29.2 - - + +
476B TYR* 3.9 35.3 - - + -
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Residues in contact with ASP 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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390B GLN* 5.9 2.4 - - - +
397B ARG* 5.0 8.9 + - - +
426B LYS* 2.9 49.9 + - - +
427B PRO* 3.6 13.8 - - + +
428B LEU 3.3 0.2 - - - -
429B CYS* 1.3 77.6 - - - +
431B LEU* 1.3 57.5 + - - +
433B THR* 2.8 28.5 + - - +
434B VAL* 3.7 6.6 - - - +
475B ALA 4.6 0.9 - - - +
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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
----------------------------------------------------------
389B LEU* 3.6 29.2 - - + -
397B ARG* 3.4 34.5 - - - +
401B ALA* 3.7 18.6 - - + -
427B PRO 3.2 13.9 + - - +
428B LEU* 3.1 18.0 + - + +
429B CYS 3.1 1.8 - - - -
430B ASP* 1.3 73.3 - - - +
432B LEU* 1.3 59.5 + - - +
433B THR 3.1 5.6 - - - -
434B VAL* 2.9 29.7 + - + +
439B ILE* 3.6 31.0 - - + +
440B VAL* 3.5 7.9 - - - +
443B ALA* 3.8 15.3 - - + -
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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 LEU 3.8 6.1 - - - +
429B CYS* 3.1 16.3 + - + +
431B LEU* 1.3 77.5 - - - +
433B THR* 1.3 58.8 + - - +
434B VAL 3.5 0.8 - - - +
435B MET* 5.8 0.9 - - - +
440B VAL* 3.9 27.5 - - + +
443B ALA* 3.9 5.8 - - + -
444B LEU* 3.7 48.5 - - + +
447B LEU* 3.7 21.1 - - + -
472B ILE* 6.5 0.2 - - + -
476B TYR* 3.9 43.1 + - + +
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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