Contacts of the helix formed by residues 374 - 390 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334C GLU* 3.1 42.0 + - - -
372C ASP* 3.1 15.7 - - - +
373C PRO* 1.3 78.7 - - - +
375C GLN* 1.3 60.3 + - - +
376C ARG* 3.3 16.3 + - - +
377C LEU* 3.3 18.0 + - - +
378C VAL* 3.2 15.8 + - - +
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Residues in contact with GLN 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C ASP 4.2 2.8 + - - -
373C PRO 3.4 10.8 + - - +
374C SER* 1.3 81.9 + - - +
376C ARG* 1.3 68.7 + - - +
377C LEU 3.0 1.6 - - - -
378C VAL* 3.1 16.8 + - - +
379C GLN* 2.9 25.9 + - - +
411C SER* 5.5 1.2 + - - -
413C ASP* 4.3 19.7 - - - +
416C VAL* 4.4 13.2 - - - +
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Residues in contact with ARG 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C GLU* 2.5 36.7 + - - -
335C LYS* 4.2 4.2 - - - +
338C TRP* 3.4 57.6 - - + +
374C SER* 3.3 8.7 + - - +
375C GLN* 1.3 78.2 - - - +
377C LEU* 1.3 64.5 + - - +
379C GLN* 3.9 5.2 - - - +
380C ASN* 2.9 31.7 + - - +
40F ASP* 3.4 30.9 + - - +
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Residues in contact with LEU 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C MET* 4.8 2.0 - - + -
334C GLU* 4.3 11.2 - - + +
337C LEU* 3.5 51.4 - - + +
338C TRP* 3.8 10.8 - - - +
341C SER* 4.0 5.4 - - - +
369C HIS* 4.1 9.2 - - + +
372C ASP* 4.0 28.0 - - + +
374C SER* 3.3 23.5 + - - +
375C GLN 3.0 0.4 - - - -
376C ARG* 1.3 80.1 - - - +
378C VAL* 1.3 67.8 + - - +
380C ASN* 3.1 5.4 + - - +
381C CYS* 2.9 39.4 + - - -
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Residues in contact with VAL 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C HIS 3.4 23.6 - - - +
370C LEU* 3.4 25.8 - - + +
372C ASP* 3.6 12.6 - - + +
374C SER 3.2 18.2 - - - +
375C GLN* 3.1 24.0 + - - +
377C LEU* 1.3 78.8 - - - +
379C GLN* 1.3 63.3 + - - +
381C CYS* 3.2 6.1 + - - +
382C LEU* 2.9 40.4 + - + +
408C LEU* 5.1 4.0 - - + -
416C VAL* 4.9 6.3 - - + -
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Residues in contact with GLN 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C GLN 2.9 15.9 + - - +
376C ARG* 3.9 6.7 - - - +
378C VAL* 1.3 78.8 - - - +
380C ASN* 1.3 52.4 + - - +
382C LEU* 2.9 22.0 + - - +
383C TRP* 2.8 74.3 + - + +
413C ASP* 4.9 3.0 + - - -
415C ASN* 3.6 33.2 - - - +
416C VAL* 4.4 9.6 - - + +
419C CYS* 3.7 13.1 - - - -
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Residues in contact with ASN 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C TRP* 3.5 20.4 + - - -
341C SER* 3.6 25.1 - - - +
342C ARG* 4.1 8.4 - - - +
345C LYS* 3.3 38.2 - - + +
376C ARG* 2.9 16.4 + - - +
377C LEU 3.1 7.7 + - - +
379C GLN* 1.3 77.3 - - - +
381C CYS* 1.3 64.5 + - - +
383C TRP* 3.3 18.2 + - - +
384C THR* 2.9 31.0 + - - -
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Residues in contact with CYS 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C MET* 4.2 15.7 - - - -
341C SER* 4.6 2.5 - - - -
366C LEU* 3.5 50.2 - - + +
369C HIS* 4.3 12.3 - - - +
370C LEU* 4.2 7.6 - - + -
377C LEU* 2.9 28.1 + - - +
378C VAL* 3.5 8.7 - - - +
380C ASN* 1.3 75.5 - - - +
382C LEU* 1.3 57.5 - - - +
384C THR* 3.8 1.2 - - - -
385C LEU* 2.9 37.3 + - - +
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Residues in contact with LEU 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C LEU* 3.4 24.7 - - + -
378C VAL* 2.9 23.1 + - + +
379C GLN* 2.9 24.0 + - - +
381C CYS* 1.3 75.1 - - - +
383C TRP* 1.3 66.6 + - - +
385C LEU* 3.2 4.7 + - + +
386C ARG* 2.9 23.9 + - - +
405C LEU* 4.3 11.4 - - + -
408C LEU* 4.4 5.8 - - + -
416C VAL* 3.7 43.7 - - + +
419C CYS* 4.0 11.8 - - + +
420C ALA* 4.9 3.1 - - - +
423C ILE* 3.6 21.2 - - + +
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Residues in contact with TRP 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C LYS* 4.4 16.2 - - + -
379C GLN* 2.8 49.6 + - + +
380C ASN* 3.7 29.2 - - - +
382C LEU* 1.3 73.1 - - - +
384C THR* 1.3 62.9 + - - +
386C ARG* 3.3 21.1 + - - +
387C ASN* 2.9 31.3 + - - +
415C ASN* 5.9 4.8 - - + +
419C CYS* 3.6 26.8 - - - -
23F ASP* 3.7 36.3 + - + +
25F GLY* 6.0 1.8 - - - -
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Residues in contact with THR 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C SER* 3.9 3.6 + - - -
344C LEU* 4.1 16.2 - - + +
345C LYS* 2.9 27.1 + - - +
348C SER* 4.0 23.8 - - - +
357C ILE* 5.5 0.4 - - + -
366C LEU* 3.3 25.4 - - + -
380C ASN 2.9 19.9 + - - -
381C CYS* 3.8 4.3 - - - -
383C TRP* 1.3 73.1 - - - +
385C LEU* 1.3 64.8 + - - +
386C ARG 3.0 3.0 + - - -
387C ASN* 3.0 12.9 + - - +
388C LEU* 3.0 18.9 + - + +
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Residues in contact with LEU 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C MET* 3.6 59.7 - - + +
366C LEU* 3.8 13.2 - - + -
367C GLY 4.2 7.4 - - - +
370C LEU* 4.0 22.7 - - + -
381C CYS 2.9 24.6 + - - +
382C LEU* 3.6 4.5 - - + +
384C THR* 1.3 77.0 - - - +
386C ARG* 1.3 56.4 + - - +
388C LEU* 3.7 1.7 + - - +
389C SER* 3.0 27.4 + - - -
401C LEU* 3.8 26.9 - - + -
405C LEU* 4.7 0.7 - - + -
423C ILE* 3.7 19.2 - - + +
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Residues in contact with ARG 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C LEU 2.9 12.4 + - - +
383C TRP* 3.4 26.6 - - - +
384C THR 3.0 0.2 - - - -
385C LEU* 1.3 76.1 - - - +
387C ASN* 1.3 64.1 + - - +
389C SER* 2.5 24.2 + - - +
390C ASP* 4.5 0.9 + - - -
418C THR* 5.0 14.1 + - - +
419C CYS* 3.6 44.9 - - + +
422C GLY* 4.7 4.0 - - - -
423C ILE* 3.8 14.1 - - + +
459C ASP* 5.1 3.8 + - - -
21F PHE* 3.1 64.4 + - + +
23F ASP* 4.6 11.2 + - + +
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Residues in contact with ASN 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C LYS* 4.2 1.8 + - - +
348C SER* 3.5 34.5 + - - +
349C VAL* 4.1 5.8 - - + +
354C LYS* 3.0 31.6 + - - -
383C TRP 2.9 21.7 + - - -
384C THR* 3.0 3.3 + - - +
386C ARG* 1.3 75.7 - - - +
388C LEU* 1.3 60.4 + - - +
390C ASP* 3.3 3.3 - - - +
21F PHE* 2.8 27.8 - - - +
22F LYS* 3.0 3.2 - - - -
23F ASP* 2.8 48.1 + - - +
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Residues in contact with LEU 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C SER* 3.6 22.4 - - - -
354C LYS* 3.6 38.8 - - + +
357C ILE* 3.7 28.7 - - + -
358C VAL* 4.0 9.8 - - + +
363C MET* 3.9 26.7 - - + +
366C LEU* 4.0 20.6 - - + -
384C THR* 3.0 21.2 + - + +
387C ASN* 1.3 78.6 - - - +
389C SER* 1.3 53.3 + - - +
390C ASP* 3.5 0.7 - - - +
391C ALA* 2.7 35.3 + - - +
392C ALA* 3.5 4.0 + - - +
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Residues in contact with SER 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C MET* 4.3 10.7 - - - +
385C LEU 3.0 16.9 + - - -
386C ARG* 2.5 26.8 + - - +
388C LEU* 1.3 75.6 - - - +
390C ASP* 1.3 56.7 + - - -
391C ALA 2.9 5.4 + - - -
392C ALA* 3.0 13.3 + - - +
393C THR* 3.9 9.2 + - - +
423C ILE* 4.4 17.3 - - - -
426C ASN* 2.8 38.0 + - - +
427C LEU* 4.3 6.3 - - - +
21F PHE* 4.3 0.3 - - - -
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Residues in contact with ASP 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C LYS* 2.8 35.7 + - - +
386C ARG 5.6 0.2 - - - -
387C ASN 3.3 7.2 - - - +
388C LEU 3.5 0.7 - - - +
389C SER* 1.3 77.1 + - - +
391C ALA* 1.3 65.6 + - - +
392C ALA 3.5 0.2 - - - -
393C THR* 4.0 8.2 + - - +
426C ASN* 4.0 2.4 - - - +
18F LEU* 3.6 42.7 - - + +
19F ILE 4.2 17.0 - - - +
20F SER* 4.4 16.2 + - - -
21F PHE* 5.1 1.7 + - - -
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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