Contacts of the helix formed by residues 381 - 392 (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 ILE 381 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340B LEU* 3.5 46.7 - - + +
343B LEU* 4.9 0.2 - - + -
344B LEU* 3.9 29.4 - - + +
347B LEU* 4.5 2.2 - - + -
362B ILE* 4.0 20.4 - - + -
376B VAL* 3.4 29.0 + - + +
379B ALA* 4.0 14.4 - - + +
380B ASN* 1.3 77.6 - - - +
382B PHE* 1.3 66.8 + - - +
383B PRO 3.4 0.2 - - - -
384B ALA* 3.1 16.3 + - - +
385B LEU* 3.2 29.3 + - + -
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Residues in contact with PHE 382 (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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366B THR* 4.0 8.1 - - + -
373B ILE* 4.3 4.0 - - + -
376B VAL* 3.5 27.4 - - + -
377B ILE* 3.6 40.8 + - + -
381B ILE* 1.3 73.8 - - - +
383B PRO* 1.4 71.7 - - + +
385B LEU* 3.1 15.9 + - + +
386B ILE* 3.0 27.4 + - - +
403B ALA 4.4 4.5 - - - -
404B ILE* 3.5 23.1 - - + -
407B ALA* 3.7 28.3 - - + -
418B TYR* 4.5 3.8 - + + +
419B LEU* 3.1 33.9 - - + -
422B LEU* 3.8 12.3 - - + -
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Residues in contact with PRO 383 (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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257A ASN* 6.1 0.9 - - - +
261A TRP* 4.0 34.7 - - + +
380B ASN* 3.7 18.6 - - + +
381B ILE 3.5 3.8 - - - -
382B PHE* 1.4 92.5 - - + +
384B ALA* 1.3 59.5 + - - +
386B ILE* 3.6 5.4 + - + +
387B SER* 3.1 22.9 + - - -
418B TYR* 4.1 10.1 - - - +
422B LEU* 3.8 26.4 - - + -
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Residues in contact with ALA 384 (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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344B LEU* 4.0 16.6 - - + -
347B LEU* 3.7 26.0 - - + -
380B ASN 4.7 1.2 + - - +
381B ILE 3.1 11.1 + - - +
383B PRO* 1.3 77.5 - - - +
385B LEU* 1.3 58.9 + - - +
387B SER* 3.4 7.6 + - - -
388B ILE* 3.0 32.6 + - + +
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Residues in contact with LEU 385 (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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347B LEU* 4.1 14.1 - - + -
359B CYS* 3.9 28.7 - - + -
362B ILE* 4.0 13.2 - - + -
381B ILE* 3.2 27.5 + - + +
382B PHE* 3.1 27.4 + - + +
384B ALA* 1.3 77.2 - - - +
386B ILE* 1.3 58.0 + - - +
388B ILE* 3.4 5.5 + - - +
389B LEU* 2.8 30.4 + - - +
400B ALA* 3.8 11.4 - - + +
403B ALA* 3.7 28.3 - - + -
404B ILE* 4.1 12.8 - - + -
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Residues in contact with ILE 386 (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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257A ASN* 4.9 5.2 - - + +
382B PHE 3.0 15.9 + - - +
383B PRO* 4.0 4.9 - - + +
385B LEU* 1.3 72.4 - - - +
387B SER* 1.3 67.6 + - - +
389B LEU* 3.5 9.1 + - + +
390B GLN* 3.0 33.7 + - - +
404B ILE* 4.2 16.6 - - + -
419B LEU* 4.0 4.5 - - + +
422B LEU* 3.7 36.6 - - + +
423B GLY* 3.9 16.8 - - - +
424B CYS* 3.7 32.5 - - + +
427B PRO* 4.3 9.7 - - + +
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Residues in contact with SER 387 (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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257A ASN* 5.0 8.7 + - - +
383B PRO 3.1 14.8 + - - -
384B ALA* 3.4 12.6 - - - -
386B ILE* 1.3 76.2 - - - +
388B ILE* 1.3 64.2 + - - +
390B GLN* 3.2 12.6 + - - +
391B THR* 3.0 37.6 + - - +
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Residues in contact with ILE 388 (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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347B LEU* 3.8 25.4 - - + +
355B LYS* 4.1 23.3 - - + +
359B CYS* 3.5 23.1 - - - -
384B ALA* 3.0 20.4 + - + +
385B LEU* 3.6 8.3 - - - +
387B SER* 1.3 75.4 + - - +
389B LEU* 1.3 61.9 + - - +
390B GLN 3.1 0.2 - - - -
391B THR* 4.1 5.4 - - - -
392B ALA* 2.9 33.1 + - + +
396B THR* 3.5 29.6 - - + +
397B ARG* 3.8 2.9 - - - +
400B ALA* 4.0 14.4 - - + -
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Residues in contact with LEU 389 (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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385B LEU 2.8 20.7 + - - +
386B ILE* 3.9 8.5 - - + +
387B SER 3.3 0.6 - - - -
388B ILE* 1.3 72.9 - - - +
390B GLN* 1.3 58.3 + - - +
397B ARG* 3.2 50.8 + - + +
400B ALA* 4.1 6.3 - - + -
401B ALA* 3.5 22.9 - - + +
404B ILE* 4.2 23.3 - - + -
424B CYS* 5.1 1.6 - - - +
427B PRO* 3.8 30.1 - - + +
428B LEU* 4.3 19.7 - - + +
431B LEU* 3.6 13.9 - - + -
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Residues in contact with GLN 390 (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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257A ASN* 2.6 41.7 + - - +
386B ILE* 3.0 22.6 + - - +
387B SER* 3.5 10.4 - - - +
388B ILE 3.1 0.4 - - - -
389B LEU* 1.3 80.3 - - - +
391B THR* 1.3 70.3 + - + +
392B ALA 3.9 0.4 - - - -
397B ARG* 4.6 10.0 + - - +
423B GLY 5.6 0.2 + - - -
426B LYS* 5.5 4.8 - - - +
427B PRO* 4.3 24.7 - - + +
430B ASP* 5.9 2.2 - - - +
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Residues in contact with THR 391 (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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257A ASN* 5.3 3.6 - - - +
387B SER* 3.0 30.6 + - - +
388B ILE* 4.1 2.3 - - - -
390B GLN* 1.3 93.4 - - + +
392B ALA* 1.3 67.8 + - - +
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Residues in contact with ALA 392 (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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352B GLU* 4.3 5.2 - - - +
355B LYS* 5.0 8.7 - - - +
388B ILE* 2.9 39.6 + - + +
391B THR* 1.3 84.4 + - - +
393B GLU* 1.3 66.2 + - - +
394B PHE 4.0 0.3 + - - -
396B THR* 4.0 15.9 - - + -
397B ARG* 3.3 15.7 + - + +
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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