Contacts of the helix formed by residues 380 - 394 (chain C) in PDB entry 4P0S
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 PRO 380 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378C SER 4.4 1.6 - - - +
379C LEU* 1.4 98.1 - - + +
381C GLU* 1.3 61.3 + - - +
382C SER* 3.4 7.4 - - - +
383C THR* 3.0 46.5 - - - +
384C LEU* 3.4 7.8 + - - +
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Residues in contact with GLU 381 (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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375C HIS* 4.9 21.5 + - + +
379C LEU 4.0 0.8 + - - -
380C PRO* 1.3 67.6 - - - +
382C SER* 1.3 67.5 + - - +
383C THR 3.0 2.1 + - - -
384C LEU* 3.5 4.9 + - - +
385C LEU* 3.4 27.6 + - + +
434D ASP* 4.7 10.9 - - - +
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Residues in contact with SER 382 (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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380C PRO* 4.6 5.8 - - - +
381C GLU* 1.3 80.4 - - - +
383C THR* 1.3 69.4 + - - +
385C LEU* 3.9 8.5 - - - +
386C GLN* 3.1 26.2 + - - +
441D LYS* 5.9 3.5 + - - -
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Residues in contact with THR 383 (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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344C ILE* 6.0 0.9 - - + -
379C LEU* 4.2 15.7 - - + -
380C PRO* 3.0 29.4 + - + +
382C SER* 1.3 81.8 + - - +
384C LEU* 1.3 83.4 + - + +
386C GLN* 3.0 17.1 + - - +
387C ALA* 3.0 10.5 + - + +
1U G 4.5 24.7 - - - +
2U A 4.6 19.4 + - - -
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Residues in contact with LEU 384 (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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337C LEU* 4.9 10.8 - - + +
340C LEU* 4.5 17.9 - - + -
341C CYS* 3.5 25.4 - - - -
344C ILE* 4.3 9.4 - - + -
377C LEU* 4.5 13.5 - - + -
379C LEU* 3.5 44.2 - - + +
380C PRO 3.4 6.4 + - - +
381C GLU* 3.5 6.0 + - - +
383C THR* 1.3 83.3 - - + +
385C LEU* 1.3 56.4 + - - +
387C ALA* 2.6 31.3 + - - +
388C VAL* 2.9 13.4 + - + +
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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
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381C GLU* 3.4 22.2 + - + +
382C SER* 3.9 7.9 - - - +
383C THR 3.2 0.2 - - - -
384C LEU* 1.3 77.8 - - - +
386C GLN* 1.3 59.4 + - - +
388C VAL* 4.0 5.4 - - + +
389C THR* 2.5 38.8 + - - +
401C ARG* 4.1 27.6 - - - +
434D ASP* 3.7 43.3 - - + +
435D PHE* 4.6 10.1 - - + +
438D ALA* 4.7 4.7 - - + -
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Residues in contact with GLN 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 SER 3.1 15.0 + - - +
383C THR* 3.0 15.2 + - - +
384C LEU 2.9 0.4 - - - -
385C LEU* 1.3 78.6 - - - +
387C ALA* 1.3 54.6 + - - +
389C THR* 3.2 3.5 + - - -
390C ASN* 2.9 56.6 + - - +
437D CYS 5.1 0.2 - - - -
438D ALA* 3.2 33.0 + - - +
441D LYS* 3.1 58.1 + - + +
445D GLU* 4.9 1.5 + - - +
1U G 5.2 4.5 - - - +
2U A 4.6 10.3 - - - +
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Residues in contact with ALA 387 (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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340C LEU* 5.2 4.7 - - + -
344C ILE* 4.6 18.2 - - + -
349C PHE* 5.3 8.7 - - + -
383C THR* 3.0 8.0 + - + +
384C LEU* 2.6 26.7 + - - +
386C GLN* 1.3 68.3 - - - +
388C VAL* 1.3 60.3 + - + +
389C THR 3.0 0.9 - - - -
390C ASN* 3.2 6.6 + - - +
391C THR* 2.4 35.7 + - - +
1U G 5.3 16.1 - - - -
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Residues in contact with VAL 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C LEU* 5.3 11.4 - - + -
349C PHE* 6.2 0.2 - - - -
368C VAL* 5.1 14.6 - - + -
384C LEU* 2.9 22.2 + - + +
385C LEU* 4.0 7.0 - - + +
387C ALA* 1.3 74.3 - - + +
389C THR* 1.3 65.8 + - - +
391C THR* 3.0 10.3 + - - -
392C GLN* 3.0 21.9 + - - +
399C VAL* 3.5 34.2 - - + +
401C ARG* 4.2 25.4 - - + +
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Residues in contact with THR 389 (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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385C LEU* 2.5 25.4 + - - +
386C GLN 3.4 4.3 - - - -
387C ALA 3.0 0.4 - - - -
388C VAL* 1.3 77.6 - - - +
390C ASN* 1.3 66.5 + - - +
392C GLN* 2.9 16.3 + - - +
393C VAL* 3.2 12.9 + - + +
401C ARG* 4.5 1.0 + - - -
435D PHE* 3.9 28.5 - - + -
438D ALA* 3.6 17.7 - - + +
439D PHE* 3.6 39.9 - - + +
442D ALA* 4.2 4.0 - - + -
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Residues in contact with ASN 390 (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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386C GLN* 2.9 41.4 + - - +
387C ALA* 3.9 4.6 - - - +
389C THR* 1.3 75.3 - - - +
391C THR* 1.3 58.0 + - - +
392C GLN 3.1 0.2 + - - -
394C ILE* 2.8 56.3 + - + +
395C ASP* 5.2 0.4 - - - -
442D ALA* 3.1 30.7 - - - +
445D GLU* 4.3 12.2 + - - +
449D LYS* 4.8 6.2 - - - +
1U G 4.3 22.9 + - - +
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Residues in contact with THR 391 (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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349C PHE* 3.4 25.6 - - + -
353C LYS* 4.1 15.8 + - + +
366C TYR* 4.8 7.6 - - + -
387C ALA 2.4 20.2 + - - -
388C VAL* 3.1 14.0 - - - -
390C ASN* 1.3 79.3 - - - +
392C GLN* 1.3 59.0 + - - +
395C ASP* 3.6 13.6 + - - +
396C GLY 3.5 15.6 + - - -
397C PHE* 3.6 29.4 + - + +
399C VAL* 4.9 7.2 - - + -
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Residues in contact with GLN 392 (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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388C VAL* 3.0 11.0 + - - +
389C THR 2.9 9.4 + - - +
391C THR* 1.3 78.9 - - - +
393C VAL* 1.3 63.9 + - + +
396C GLY* 3.2 24.9 - - - -
397C PHE 3.6 8.9 - - - +
399C VAL* 3.5 30.9 - - + +
401C ARG* 4.4 4.5 + - - -
360D SER* 4.4 9.9 + - - +
361D LEU 5.9 0.2 + - - -
422D GLN* 3.4 46.9 + - + +
424D GLN* 3.5 17.9 + - - +
435D PHE* 3.4 31.9 - - + -
439D PHE* 4.6 0.4 - - - -
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Residues in contact with VAL 393 (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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389C THR 3.2 11.7 + - - +
390C ASN 4.4 0.4 - - - +
392C GLN* 1.3 79.0 - - + +
394C ILE* 1.3 73.8 + - + +
396C GLY* 3.9 4.7 + - - -
311D THR* 5.0 13.5 - - + +
360D SER* 5.3 0.4 - - - +
439D PHE* 3.4 48.7 - - + -
442D ALA* 4.5 9.6 - - + -
443D VAL* 5.1 9.9 - - + -
446D ALA* 5.0 13.0 - - + -
450D LYS* 5.2 3.8 + - - -
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Residues in contact with ILE 394 (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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357C LYS* 5.2 4.0 + - - +
390C ASN* 2.8 51.8 + - + +
393C VAL* 1.3 77.9 - - + +
395C ASP* 1.3 71.9 + - - +
396C GLY* 3.1 4.7 + - - -
442D ALA* 4.5 16.8 - - + +
445D GLU* 4.8 9.0 - - + +
446D ALA* 4.6 10.3 - - - +
449D LYS* 4.5 35.7 - - + +
450D LYS* 4.0 30.2 + - + +
453D ASP* 5.6 3.1 - - - +
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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
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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