Contacts of the helix formed by residues 393 - 411 (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 GLU 393 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B GLU* 3.4 39.9 + - + +
392B ALA* 1.3 74.7 - - - +
394B PHE* 1.3 68.0 + - - +
395B ARG* 4.7 9.2 - - + +
396B THR* 3.0 20.0 + - - +
397B ARG* 3.0 9.6 + - - -
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Residues in contact with PHE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ALA 4.0 0.4 + - - -
393B GLU* 1.3 74.5 - - - +
395B ARG* 1.3 67.6 + - + +
396B THR 3.3 0.2 - - - -
397B ARG* 3.4 27.9 + - - +
398B LYS* 3.0 33.0 + - + +
434B VAL* 4.4 11.4 - - + -
436B ASP* 3.8 35.0 - - + -
439B ILE* 3.3 35.7 - - + -
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Residues in contact with ARG 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B LYS* 3.4 32.9 + - + +
393B GLU* 3.1 10.0 + - - +
394B PHE* 1.3 84.2 - - + +
396B THR* 1.3 64.9 + - - +
398B LYS* 3.6 10.2 + - - +
399B GLU* 3.5 21.3 + - - +
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Residues in contact with THR 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B GLU* 2.9 30.0 + - - +
355B LYS* 4.2 7.6 - - + -
356B LYS* 3.7 38.3 - - - +
359B CYS* 4.1 6.4 - - - -
388B ILE* 3.5 23.1 - - + -
392B ALA* 4.0 6.7 - - + -
393B GLU* 3.0 11.9 + - - +
395B ARG* 1.3 76.8 - - - +
397B ARG* 1.3 65.0 + - - +
399B GLU* 3.2 5.4 + - - +
400B ALA* 3.2 19.4 + - - +
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Residues in contact with ARG 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ILE 3.8 14.1 - - - +
389B LEU* 3.2 38.2 + - + +
390B GLN* 4.5 8.1 + - - +
392B ALA* 3.3 27.5 + - - +
393B GLU 3.0 8.0 + - - +
394B PHE* 3.5 29.0 - - + +
396B THR* 1.3 76.5 - - - +
398B LYS* 1.3 62.0 + - - +
399B GLU 3.2 0.2 + - - -
400B ALA* 3.3 6.0 + - - -
401B ALA* 3.0 20.5 + - - +
427B PRO* 5.2 0.6 + - - +
430B ASP* 5.0 11.5 - - - +
431B LEU* 3.4 24.7 - - + +
434B VAL* 3.7 25.3 - - - +
439B ILE* 4.6 3.4 - - + -
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Residues in contact with LYS 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B PHE* 3.0 23.2 + - + +
395B ARG* 3.9 9.0 - - - +
396B THR 3.3 0.4 - - - -
397B ARG* 1.3 75.5 - - - +
399B GLU* 1.3 73.9 + - - +
401B ALA* 3.4 3.6 + - - +
402B TRP* 3.2 47.3 + - + +
436B ASP* 4.2 13.9 - - - +
438B LYS* 4.0 35.2 - - - +
439B ILE* 3.7 28.5 - - + +
442B VAL* 5.2 0.2 - - - +
739D ARG* 4.6 4.4 - - - +
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Residues in contact with GLU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B LYS* 3.9 29.3 + - + +
359B CYS* 3.7 19.7 - - + +
360B TRP* 3.4 19.2 - - - +
363B SER* 3.9 5.5 - - - -
395B ARG 3.5 15.6 - - - +
396B THR 3.2 7.4 + - - +
397B ARG 3.2 0.6 - - - -
398B LYS* 1.3 87.6 + - - +
400B ALA* 1.3 63.2 + - - +
401B ALA 3.2 0.4 - - - -
402B TRP* 3.4 5.6 + - - +
403B ALA* 3.1 20.4 + - - +
739D ARG* 2.9 41.8 + - - -
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Residues in contact with ALA 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B CYS* 3.9 11.7 - - - +
385B LEU* 3.8 27.5 - - + +
388B ILE* 4.0 15.9 - - + -
389B LEU* 4.1 8.5 - - + -
396B THR 3.2 8.9 + - - +
397B ARG 3.6 7.6 - - - +
399B GLU* 1.3 75.8 - - - +
401B ALA* 1.3 65.6 + - - +
403B ALA* 3.2 8.7 + - - +
404B ILE* 3.1 27.8 + - - +
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Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B LEU* 3.5 21.0 - - + +
397B ARG 3.0 12.8 + - - +
398B LYS* 3.4 14.1 - - - +
399B GLU 3.2 0.2 - - - -
400B ALA* 1.3 72.8 - - - +
402B TRP* 1.3 65.8 + - - +
404B ILE* 3.4 3.3 + - - +
405B THR* 3.0 29.3 + - - -
428B LEU* 4.8 3.4 - - + +
431B LEU* 3.7 17.9 - - + -
439B ILE* 4.5 4.7 - - + -
442B VAL* 3.8 13.5 - - + -
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Residues in contact with TRP 402 (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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363B SER* 3.8 4.0 - - - -
398B LYS* 3.2 46.1 + - + +
399B GLU 3.5 4.7 - - - +
400B ALA 3.3 0.2 - - - -
401B ALA* 1.3 78.2 - - - +
403B ALA* 1.3 63.6 + - - +
405B THR* 5.6 1.3 - - + -
406B ASN* 3.1 58.6 + - - +
438B LYS* 6.5 0.7 - - + -
442B VAL* 3.4 31.0 - - + +
695D LEU* 3.7 28.9 - - + -
735D MET* 4.0 27.1 - - + -
736D LYS 4.7 1.3 - - - -
737D ARG* 4.2 21.5 - - + -
739D ARG* 3.5 57.0 - - - +
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Residues in contact with ALA 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B CYS 4.2 4.5 - - - +
362B ILE* 4.3 3.8 - - + -
363B SER* 3.4 28.9 - - - +
366B THR* 2.8 24.0 + - - +
382B PHE* 4.4 1.2 - - - -
385B LEU* 3.7 24.9 - - + -
399B GLU 3.1 9.8 + - - +
400B ALA* 3.2 10.7 + - - +
402B TRP* 1.3 77.6 - - - +
404B ILE* 1.3 63.2 + - - +
407B ALA* 3.3 10.4 + - - +
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Residues in contact with ILE 404 (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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382B PHE* 3.5 30.3 - - + -
385B LEU* 4.1 17.5 - - + -
386B ILE* 4.2 16.8 - - + -
389B LEU* 4.2 19.1 - - + -
400B ALA 3.1 15.5 + - - +
401B ALA 4.0 3.4 - - - +
403B ALA* 1.3 73.3 - - - +
405B THR* 1.3 60.0 + - - +
407B ALA* 3.3 7.2 + - - +
408B THR* 3.0 43.4 + - + +
419B LEU* 4.3 7.0 - - + -
424B CYS* 4.2 20.4 - - + -
428B LEU* 4.4 17.0 - - + -
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Residues in contact with THR 405 (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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401B ALA 3.0 17.7 + - - -
402B TRP* 4.1 4.5 - - + -
404B ILE* 1.3 77.5 - - - +
406B ASN* 1.3 59.1 + - - +
408B THR* 2.7 23.7 + - - -
409B SER* 3.0 13.9 + - - -
428B LEU* 4.2 8.7 - - - +
442B VAL* 2.8 39.1 + - + +
445B ASN* 3.2 25.8 - - + +
446B GLY* 3.7 13.4 - - - +
695D LEU* 5.7 0.7 - - + -
737D ARG* 3.9 7.2 - - - +
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Residues in contact with ASN 406 (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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363B SER* 2.8 24.4 + - - -
366B THR* 3.1 27.7 - - - +
367B ALA* 3.6 20.1 - - - +
402B TRP* 3.1 38.1 + - - +
405B THR* 1.3 73.5 - - - +
407B ALA* 1.3 65.5 + - - +
409B SER* 3.3 3.5 + - - -
410B GLY* 3.1 18.4 + - - -
737D ARG* 3.1 43.2 + - - +
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Residues in contact with ALA 407 (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* 3.6 12.2 + - - -
373B ILE* 3.7 14.8 - - + +
382B PHE* 3.7 28.5 - - + -
403B ALA 3.3 12.0 + - - +
404B ILE 3.3 9.4 + - - +
405B THR 3.3 0.2 - - - -
406B ASN* 1.3 78.8 - - - +
408B THR* 1.3 56.9 + - - +
411B GLY* 2.8 32.2 + - - -
416B ILE* 3.9 3.2 - - - +
419B LEU* 4.0 10.1 - - + -
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Residues in contact with THR 408 (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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404B ILE* 3.0 26.2 + - + +
405B THR* 2.7 22.7 + - - -
407B ALA* 1.3 76.7 - - - +
409B SER* 1.3 60.6 + - - +
411B GLY 4.0 1.8 + - - -
416B ILE* 3.6 24.4 - - + +
419B LEU* 4.4 11.4 - - + -
424B CYS* 5.4 0.7 - - - -
428B LEU* 5.4 0.2 - - + -
446B GLY* 3.6 10.2 - - - +
449B ASN* 3.3 30.4 + - - +
450B ILE* 4.0 24.0 - - + -
452B ARG* 4.0 7.3 + - - -
453B LEU* 4.4 1.6 - - - +
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Residues in contact with SER 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B THR 3.0 12.5 + - - -
406B ASN 3.5 6.1 + - - -
407B ALA 3.2 0.2 - - - -
408B THR* 1.3 79.7 + - - +
410B GLY* 1.3 60.0 + - - +
411B GLY 3.4 0.4 - - - +
449B ASN* 3.2 23.1 - - - +
452B ARG* 4.3 10.0 + - - -
692D ARG* 3.7 17.5 + - - +
737D ARG* 3.3 35.5 + - - -
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Residues in contact with GLY 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B GLY 4.8 1.1 - - - -
370B ARG* 3.1 19.9 + - - +
373B ILE* 3.3 11.6 - - - +
406B ASN 3.1 12.2 + - - -
409B SER* 1.3 77.5 + - - +
411B GLY* 1.3 58.5 + - - +
692D ARG* 2.7 46.5 + - - -
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Residues in contact with GLY 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ARG* 3.7 8.3 + - - -
373B ILE* 3.8 2.9 - - - -
407B ALA 2.8 19.1 + - - -
408B THR 4.0 2.5 + - - +
409B SER 3.4 2.2 - - - +
410B GLY* 1.3 80.7 - - - +
412B SER* 1.3 64.9 + - - -
415B GLN* 3.4 13.2 - - - -
416B ILE* 3.8 8.9 - - - +
452B ARG* 5.0 4.7 + - - -
453B LEU* 3.8 14.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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