Contacts of the helix formed by residues 374 - 390 (chain B) in PDB entry 1JPW
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 SER 374 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B GLU* 3.1 37.9 + - - -
372B ASP* 3.2 12.3 - - - +
373B PRO* 1.3 81.5 - - - +
375B GLN* 1.3 63.0 + - - +
376B ARG* 3.3 16.3 + - - +
377B LEU* 3.4 20.3 + - - +
378B VAL* 3.2 13.9 + - - +
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Residues in contact with GLN 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ASP 4.1 5.7 + - - -
373B PRO 3.4 12.4 + - - +
374B SER* 1.3 82.1 + - - +
376B ARG* 1.3 67.0 + - - +
377B LEU 3.0 2.0 - - - -
378B VAL* 3.1 14.8 + - - +
379B GLN* 2.9 26.5 + - - +
413B ASP* 4.3 17.2 - - - +
416B VAL* 4.4 13.7 - - - +
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Residues in contact with ARG 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLU* 2.6 37.5 + - - +
335B LYS* 4.2 5.9 - - - +
338B TRP* 3.3 57.6 - - + +
374B SER* 3.3 8.7 + - - +
375B GLN* 1.3 79.2 - - - +
377B LEU* 1.3 64.7 + - - +
379B GLN* 3.7 5.9 + - - +
380B ASN* 3.0 32.0 + - - +
40E ASP* 3.6 29.9 + - - +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B MET* 4.8 1.3 - - + -
334B GLU* 4.4 11.2 - - + +
337B LEU* 3.6 52.9 - - + +
338B TRP* 3.8 9.9 - - - +
341B SER* 4.0 5.8 - - - +
369B HIS* 4.2 13.7 - - + +
372B ASP* 4.0 25.1 - - + +
374B SER* 3.4 25.5 + - - +
376B ARG* 1.3 81.7 - - - +
378B VAL* 1.3 66.7 + - - +
380B ASN* 3.2 4.8 + - - +
381B CYS* 3.0 33.4 + - - -
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Residues in contact with VAL 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B HIS 3.4 18.8 - - - +
370B LEU* 3.3 32.3 - - + +
371B THR 4.7 0.2 - - - -
372B ASP* 3.6 12.8 - - + +
374B SER 3.2 17.9 + - - +
375B GLN* 3.1 23.2 + - - +
377B LEU* 1.3 79.2 - - - +
379B GLN* 1.3 56.9 + - - +
381B CYS* 3.3 5.8 + - - +
382B LEU* 2.9 45.5 + - + +
408B LEU* 5.1 3.8 - - + -
416B VAL* 4.9 6.3 - - + -
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Residues in contact with GLN 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B GLN 2.9 19.4 + - - +
376B ARG* 3.9 7.2 - - - +
378B VAL* 1.3 75.5 - - - +
380B ASN* 1.3 51.6 + - - +
382B LEU* 2.8 21.6 + - - +
383B TRP* 2.7 72.3 + - + +
413B ASP* 4.8 3.8 + - - -
415B ASN* 3.6 33.8 - - - +
416B VAL* 4.4 9.3 - - + +
419B CYS* 3.8 13.3 - - - -
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Residues in contact with ASN 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B TRP* 3.5 21.0 + - - -
341B SER* 3.6 25.4 - - - +
342B ARG* 4.0 9.2 - - - +
345B LYS* 3.3 36.8 - - + +
376B ARG* 3.0 21.0 + - - +
377B LEU 3.7 1.8 - - - +
379B GLN* 1.3 78.1 - - - +
381B CYS* 1.3 64.0 + - - +
383B TRP* 3.7 17.5 - - - +
384B THR* 2.9 29.7 + - - -
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Residues in contact with CYS 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B MET* 4.2 16.2 - - - -
341B SER* 4.8 1.8 - - - -
366B LEU* 3.4 50.0 - - - +
369B HIS* 4.2 17.3 - - - -
370B LEU* 4.2 8.1 - - + -
377B LEU* 3.0 22.9 + - - +
378B VAL* 3.5 9.0 - - - +
380B ASN* 1.3 76.1 - - - +
382B LEU* 1.3 57.0 + - - +
384B THR* 3.8 1.0 - - - -
385B LEU* 2.9 37.0 + - - +
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LEU* 3.4 24.5 - - + -
378B VAL* 2.9 27.3 + - + +
379B GLN* 2.8 26.3 + - - +
381B CYS* 1.3 75.1 - - - +
383B TRP* 1.3 59.7 + - - +
385B LEU* 3.2 4.9 + - + +
386B ARG* 2.9 28.6 + - - +
405B LEU* 4.4 10.1 - - + -
408B LEU* 4.4 5.6 - - + -
416B VAL* 3.8 42.0 - - + +
419B CYS* 4.1 11.2 - - + +
420B ALA* 4.8 3.6 - - - +
423B ILE* 3.6 22.4 - - + +
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Residues in contact with TRP 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LYS* 4.4 16.4 - - + -
379B GLN* 2.7 50.5 + - + +
380B ASN* 3.7 28.9 - - - +
382B LEU* 1.3 72.2 - - - +
384B THR* 1.3 62.1 + - - +
386B ARG* 3.2 21.8 + - - +
387B ASN* 3.0 32.8 + - - +
415B ASN* 6.1 3.3 - - + +
419B CYS* 3.5 27.1 - - - -
23E ASP* 3.8 31.6 + - + +
25E GLY* 6.0 2.0 - - - -
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Residues in contact with THR 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B SER 3.9 3.1 + - - -
344B LEU* 4.0 16.2 - - + +
345B LYS* 2.9 26.3 + - - +
348B SER* 3.9 24.0 - - - +
357B ILE* 5.5 0.7 - - + -
366B LEU* 3.3 25.7 - - + +
380B ASN 2.9 20.1 + - - -
381B CYS* 3.8 3.6 - - - -
383B TRP* 1.3 74.3 - - - +
385B LEU* 1.3 65.3 + - - +
387B ASN* 3.0 12.8 + - - +
388B LEU* 3.1 19.0 + - + +
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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
----------------------------------------------------------
363B MET* 3.5 56.4 - - - +
366B LEU* 3.8 14.1 - - + -
367B GLY 4.2 7.0 - - - +
370B LEU* 4.0 23.6 - - + -
381B CYS 2.9 24.7 + - - +
382B LEU* 3.2 5.4 + - + +
384B THR* 1.3 75.8 - - - +
386B ARG* 1.3 58.1 + - - +
388B LEU 4.0 0.4 - - - -
389B SER* 3.0 28.1 + - - -
401B LEU* 3.7 30.5 - - + -
405B LEU* 4.6 0.4 - - + -
423B ILE* 3.7 20.7 - - + +
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Residues in contact with ARG 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B LEU 2.9 12.6 + - - +
383B TRP* 3.4 26.4 - - - +
384B THR 3.0 0.4 - - - -
385B LEU* 1.3 75.3 - - - +
387B ASN* 1.3 63.5 + - - +
389B SER* 2.5 24.3 + - - +
390B ASP* 5.6 0.3 - - - -
418B THR* 5.2 12.2 + - - +
419B CYS* 3.6 46.0 - - - +
422B GLY* 4.7 3.8 - - - -
423B ILE* 3.8 13.9 - - + +
459B ASP* 5.2 3.4 + - - -
21E PHE* 3.1 63.9 + - + +
23E ASP* 4.5 11.6 + - + +
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Residues in contact with ASN 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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345B LYS* 4.2 1.8 + - - +
348B SER* 3.5 34.3 + - - +
349B VAL* 4.1 3.5 - - + +
354B LYS* 3.0 30.2 + - - -
383B TRP* 3.0 24.9 + - - +
384B THR* 3.0 3.7 + - - +
386B ARG* 1.3 77.8 - - - +
388B LEU* 1.3 59.2 + - - +
390B ASP* 3.4 3.3 - - - +
21E PHE* 2.9 26.4 + - - +
22E LYS* 2.9 3.2 - - - -
23E ASP* 2.6 51.4 + - - +
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Residues in contact with LEU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B SER* 3.6 22.9 - - - -
354B LYS* 3.7 38.6 - - + +
357B ILE* 3.6 29.6 - - + -
358B VAL* 3.9 13.1 - - + +
363B MET* 4.0 22.9 - - + +
366B LEU* 4.0 19.5 - - + -
384B THR* 3.1 21.8 + - + +
387B ASN* 1.3 77.9 - - - +
389B SER* 1.3 53.8 + - - +
390B ASP 3.3 0.2 - - - -
391B ALA* 2.8 35.5 + - - +
392B ALA* 3.5 4.6 + - - +
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Residues in contact with SER 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B MET* 4.3 10.1 - - - -
385B LEU 3.0 16.7 + - - -
386B ARG* 2.5 27.0 + - - +
388B LEU* 1.3 74.3 - - - +
390B ASP* 1.3 58.1 + - - -
391B ALA 2.9 5.7 + - - -
392B ALA* 3.0 14.4 + - - +
393B THR* 3.9 8.5 + - - +
423B ILE* 4.4 17.4 - - - -
426B ASN* 2.9 38.1 + - - +
427B LEU* 4.2 5.6 - - - +
21E PHE* 4.2 0.3 - - - -
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Residues in contact with ASP 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B LYS* 2.8 35.0 + - - +
386B ARG 5.6 0.2 - - - -
387B ASN 3.4 7.2 + - - +
388B LEU 3.5 1.0 - - - +
389B SER* 1.3 76.7 + - - +
391B ALA* 1.3 64.7 + - - +
392B ALA 3.5 0.2 - - - -
393B THR* 3.9 7.3 + - - +
426B ASN* 4.0 1.5 - - - +
18E LEU* 3.5 42.2 - - + +
19E ILE 4.0 17.7 - - - +
20E SER* 4.2 20.6 + - - +
21E PHE* 4.7 2.1 + - - -
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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
------------------------------------------------------------
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