Contacts of the helix formed by residues 351 - 366 (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 LYS 351 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310B TYR* 3.9 42.5 + - + +
314B SER* 3.1 26.3 + - - -
349B SER* 3.2 19.6 + - - +
350B PRO* 1.3 78.3 - - - +
352B GLU* 1.3 67.3 + - - +
353B SER* 3.4 25.9 + - - +
354B ILE* 3.2 16.2 + - + +
355B LYS 3.3 9.0 + - - -
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Residues in contact with GLU 352 (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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349B SER 5.1 0.2 - - - -
350B PRO 3.4 7.2 + - - +
351B LYS* 1.3 73.7 - - - +
353B SER* 1.3 61.3 + - - +
355B LYS* 3.3 29.8 + - - +
356B LYS* 3.2 22.2 + - - +
392B ALA* 4.3 1.4 - - - +
393B GLU* 3.4 46.1 + - + +
396B THR* 2.9 29.5 + - - +
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Residues in contact with SER 353 (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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314B SER* 5.0 0.3 + - - -
351B LYS* 3.3 28.7 + - - +
352B GLU* 1.3 81.3 - - - +
354B ILE* 1.3 58.2 + - - +
356B LYS* 3.6 9.8 + - - +
357B GLU* 3.2 42.2 + - - +
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Residues in contact with ILE 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B TYR* 3.4 30.1 - - + -
313B VAL* 3.3 29.4 - - + -
314B SER* 4.0 22.4 - - - +
317B LEU* 3.6 14.3 - - + +
346B LEU* 3.9 23.8 - - + -
349B SER* 3.8 18.2 - - - +
351B LYS* 3.2 19.1 + - + +
353B SER* 1.3 77.7 + - - +
355B LYS* 1.3 60.2 + - - +
357B GLU* 3.4 2.4 + - - +
358B ALA* 2.9 28.6 + - - +
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Residues in contact with LYS 355 (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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346B LEU 3.7 10.2 + - - +
347B LEU* 3.2 28.8 - - - +
348B SER 4.9 1.3 - - - -
349B SER 3.4 20.4 - - - +
351B LYS 3.3 8.1 + - - +
352B GLU* 3.4 31.6 + - - +
354B ILE* 1.3 79.9 - - - +
356B LYS* 1.3 55.9 + - - +
358B ALA* 3.3 3.5 + - - +
359B CYS* 2.9 32.3 + - - -
388B ILE* 4.1 22.9 - - + +
392B ALA* 5.0 7.8 - - + +
396B THR* 4.2 13.9 - - + -
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Residues in contact with LYS 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B GLU 3.2 9.4 + - - +
353B SER* 3.8 9.2 - - - +
355B LYS* 1.3 81.0 - - - +
357B GLU* 1.3 56.3 + - + +
359B CYS* 3.1 4.9 + - - +
360B TRP* 2.8 33.5 + - + +
395B ARG* 3.4 50.5 + - + +
396B THR* 3.7 24.0 - - - +
399B GLU* 3.9 23.3 + - + +
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Residues in contact with GLU 357 (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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314B SER* 3.2 35.4 - - - +
317B LEU* 3.5 25.1 - - + +
318B ARG* 3.9 31.4 + - - +
353B SER* 3.2 28.9 + - - +
354B ILE* 3.8 1.7 - - - +
356B LYS* 1.3 80.4 - - + +
358B ALA* 1.3 60.9 + - - +
360B TRP* 3.6 19.9 - - + -
361B THR* 2.8 34.6 + - - -
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Residues in contact with ALA 358 (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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317B LEU* 3.7 6.4 - - + +
343B LEU* 4.1 26.1 - - + +
346B LEU* 4.1 15.5 - - + -
347B LEU* 3.7 15.0 - - + -
354B ILE 2.9 14.4 + - - +
355B LYS 3.4 9.2 - - - +
357B GLU* 1.3 76.4 - - - +
359B CYS* 1.3 61.8 + - - +
361B THR* 3.3 1.9 + - - -
362B ILE* 3.0 31.6 + - + +
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Residues in contact with CYS 359 (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* 3.6 8.0 - - - +
355B LYS 2.9 18.2 + - - -
356B LYS* 3.1 9.4 + - - +
358B ALA* 1.3 75.8 - - - +
360B TRP* 1.3 58.2 + - - +
362B ILE* 3.5 5.6 + - - +
363B SER* 3.0 28.4 + - - -
385B LEU* 3.9 12.8 - - - -
388B ILE* 3.5 40.8 - - - -
396B THR* 4.1 6.3 - - - -
399B GLU* 3.7 20.6 - - + +
400B ALA* 3.9 8.1 - - - +
403B ALA* 4.2 2.4 - - - +
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Residues in contact with TRP 360 (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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317B LEU 4.2 5.8 - - - -
318B ARG* 3.9 20.4 - - - -
321B GLY* 3.6 29.6 - - - -
322B ASN* 3.4 26.7 - - - -
356B LYS* 2.8 19.5 + - + +
357B GLU* 3.6 28.0 - - + +
359B CYS* 1.3 71.5 - - - +
361B THR* 1.3 67.8 + - - +
363B SER* 2.8 21.0 + - - -
364B ASN* 3.2 16.2 + - - +
399B GLU* 3.4 30.6 - - + +
739D ARG* 2.9 41.2 + - + -
740D ASP* 3.9 6.4 + - - -
741D SER* 3.6 23.8 - - - -
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Residues in contact with THR 361 (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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317B LEU* 3.7 9.6 + - + +
320B VAL* 4.1 12.3 - - + -
321B GLY* 3.4 29.7 - - - -
324B VAL* 3.6 16.7 - - + +
343B LEU* 3.7 31.4 - - + -
357B GLU 2.8 21.8 + - - -
358B ALA 3.6 4.5 - - - -
360B TRP* 1.3 78.5 - - - +
362B ILE* 1.3 63.8 + - - +
364B ASN* 3.2 10.7 + - - +
365B ILE* 3.3 14.9 + - + +
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Residues in contact with ILE 362 (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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340B LEU* 5.0 2.2 - - + -
343B LEU* 4.3 28.3 - - + +
347B LEU* 3.8 31.6 - - + -
358B ALA 3.0 27.9 + - - +
359B CYS* 3.8 5.4 - - - +
361B THR* 1.3 74.6 - - - +
363B SER* 1.3 57.0 + - - +
365B ILE* 3.1 10.9 + - - +
366B THR* 2.8 39.1 + - + +
376B VAL* 4.1 7.9 - - + -
381B ILE* 4.0 22.9 - - + -
385B LEU* 4.0 24.5 - - + -
403B ALA* 4.3 1.8 - - + -
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Residues in contact with SER 363 (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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359B CYS 3.0 15.2 + - - -
360B TRP 2.8 12.1 + - - -
361B THR 3.3 0.4 - - - -
362B ILE* 1.3 77.3 - - - +
364B ASN* 1.3 58.4 + - - +
366B THR* 3.3 8.1 + - - -
367B ALA 3.2 10.9 + - - -
399B GLU 3.9 2.2 - - - -
402B TRP* 3.8 3.1 - - - -
403B ALA* 3.4 27.1 - - - +
406B ASN* 2.8 26.3 + - - -
739D ARG* 2.7 31.3 + - - -
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Residues in contact with ASN 364 (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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321B GLY 3.8 4.0 + - - -
324B VAL* 3.4 21.1 - - + +
325B THR* 3.6 13.2 - - - +
360B TRP* 3.2 27.5 + - - +
361B THR 3.2 8.8 + - - +
363B SER* 1.3 83.8 + - - +
365B ILE* 1.3 60.7 + - - +
367B ALA* 3.6 6.2 - - - +
737D ARG 3.8 3.8 - - - +
738D LYS* 2.8 39.4 + - + -
739D ARG* 2.9 46.8 + - - +
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Residues in contact with ILE 365 (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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324B VAL* 4.0 25.8 - - + -
331B THR* 4.7 8.3 - - - +
334B ILE* 5.1 3.1 - - + -
335B LEU* 3.6 45.1 - - + -
339B ALA* 5.6 0.2 - - + -
340B LEU* 4.1 13.2 - - + -
343B LEU* 4.3 15.3 - - + -
361B THR* 3.3 15.2 + - + +
362B ILE* 3.1 10.4 + - - +
364B ASN* 1.3 74.2 - - - +
366B THR* 1.3 55.8 + - - +
367B ALA 3.1 4.3 - - - -
368B GLY* 2.9 23.0 + - - -
372B GLN* 4.3 12.3 - - + +
373B ILE 4.9 0.2 + - - -
376B VAL* 3.8 22.0 - - + -
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Residues in contact with THR 366 (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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362B ILE* 2.8 34.5 + - + +
363B SER* 3.3 13.7 + - - -
365B ILE* 1.3 72.5 - - - +
367B ALA* 1.3 58.1 + - - +
368B GLY 3.1 2.6 + - - +
373B ILE* 3.7 20.4 - - + +
376B VAL* 4.1 13.5 - - + -
382B PHE* 4.0 22.4 - - + -
403B ALA 2.8 28.2 + - - +
406B ASN* 3.1 22.6 - - - +
407B ALA* 3.6 10.2 + - + -
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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