Contacts of the helix formed by residues 387 - 399 (chain C) in PDB entry 1P4K
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 ASN 387 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C ARG* 3.4 46.0 - - - +
343C GLU* 3.1 23.2 - - - +
344C ASP* 2.9 26.0 + - - +
385C ILE* 3.3 7.1 - - - +
386C LYS* 1.3 92.4 - - - +
388C PRO* 1.3 63.9 - - - +
389C ILE 3.2 3.1 - - - -
390C SER* 3.1 14.0 + - - +
391C VAL* 3.4 13.0 + - - +
418C PHE* 4.3 7.5 - - + -
421C GLU* 5.5 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C GLU* 3.3 18.2 - - + +
352C GLY* 5.3 0.9 - - - -
365C LEU* 3.5 34.5 - - + -
366C ASP 4.6 1.1 - - - +
367C ALA* 3.9 7.9 - - + -
379C VAL* 3.5 13.8 - - + +
382C MET* 3.6 27.4 - - + -
385C ILE 3.7 2.2 - - - +
386C LYS 3.1 14.1 - - - +
387C ASN* 1.3 82.9 - - - +
389C ILE* 1.3 57.4 + - - -
391C VAL* 3.1 0.6 + - + -
392C ALA* 2.8 30.8 + - - +
469C THR* 3.5 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C GLU* 4.1 7.6 - - + +
339C VAL* 3.7 22.4 - - + -
340C ARG* 3.6 20.9 - - + -
343C GLU* 3.0 33.3 + - - +
367C ALA* 3.8 4.2 - - + +
368C CYS* 3.1 35.9 - - - +
369C ILE* 3.8 13.3 - - + +
388C PRO* 1.3 77.5 - - - +
390C SER* 1.3 62.9 + - - +
392C ALA* 3.4 4.1 - - + +
393C ARG* 3.1 24.1 + - - +
467C ALA* 3.6 19.3 - - + -
468C CYS 4.0 10.3 - - - +
469C THR* 4.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C GLU* 2.6 26.6 + - - -
340C ARG* 2.9 32.9 + - - +
387C ASN 3.1 10.1 + - - -
389C ILE* 1.3 78.0 - - - +
391C VAL* 1.3 63.2 + - - +
393C ARG* 3.3 4.9 + - - +
394C ALA* 3.1 17.7 + - - +
418C PHE* 3.6 25.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C VAL* 3.8 16.6 - - + -
382C MET* 3.6 25.6 - - + -
385C ILE* 3.6 14.8 - - + -
387C ASN 3.6 14.6 - - - +
388C PRO 3.1 5.1 + - - +
390C SER* 1.3 75.0 - - - +
392C ALA* 1.3 60.2 + - - +
394C ALA* 3.0 4.0 + - - +
395C VAL* 2.8 26.3 + - - +
409C ALA 4.3 1.6 - - - +
412C PHE* 4.0 18.4 - - + -
413C ALA* 3.8 25.8 - - + -
418C PHE* 3.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C ALA 3.9 15.7 - - - +
368C CYS* 4.2 6.1 - - - -
369C ILE* 4.1 5.8 - - + -
377C GLY* 3.2 30.6 - - - +
378C SER* 4.0 6.7 - - - +
379C VAL* 4.2 8.9 - - - +
388C PRO 2.8 16.8 + - - +
389C ILE* 3.4 9.6 - - - +
390C SER 3.2 0.2 - - - -
391C VAL* 1.3 79.2 - - - +
393C ARG* 1.3 61.7 + - - +
395C VAL* 3.1 2.8 + - - +
396C MET 3.0 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C LYS* 4.4 12.1 - - - +
332C LEU* 3.6 23.0 + - - +
333C ASP* 2.7 38.8 + - - +
336C GLU* 2.7 38.8 + - - -
369C ILE* 3.9 24.8 - - + +
389C ILE 3.1 14.6 + - - +
390C SER* 3.6 11.0 - - - +
391C VAL 3.2 0.4 - - - -
392C ALA* 1.3 76.1 - - - +
394C ALA* 1.3 58.1 + - - +
396C MET* 3.3 9.2 + - + +
397C GLU* 2.7 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C SER 3.1 13.3 + - - +
391C VAL* 3.0 12.9 + - - +
393C ARG* 1.3 75.0 - - - +
395C VAL* 1.3 59.5 + - - +
397C GLU* 4.4 2.7 - - - +
398C LYS* 2.8 45.7 + - + +
412C PHE* 3.4 19.6 - - + -
416C GLN* 4.4 12.6 - - + +
418C PHE* 4.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C SER 4.0 5.8 - - - +
379C VAL* 3.9 18.4 - - + -
391C VAL 2.8 18.4 + - - +
392C ALA 3.1 7.2 + - - +
394C ALA* 1.3 76.2 - - - +
396C MET* 1.3 65.5 + - - +
399C THR* 2.8 32.0 + - - +
401C HIS 3.4 10.2 - - - +
402C VAL* 3.6 32.8 - - - +
403C MET 3.9 3.6 - - - +
404C LEU* 3.8 24.0 - - + -
412C PHE* 3.6 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C LEU* 4.0 28.3 - - + -
369C ILE* 4.1 15.7 - - + +
371C ASP* 4.6 8.5 - - + +
375C ASN* 3.4 39.7 + - + +
376C ILE* 3.3 36.6 - - - +
377C GLY* 3.7 3.8 - - - -
392C ALA 3.0 6.3 + - - +
393C ARG* 3.4 16.4 - - + +
395C VAL* 1.3 80.6 - - - +
397C GLU* 1.3 79.0 + - + +
399C THR 4.1 7.6 - - - +
401C HIS 4.7 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 397 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C LEU* 4.2 2.8 - - - +
393C ARG* 2.7 65.7 + - - +
394C ALA* 5.2 1.0 - - - -
396C MET* 1.3 89.6 - - + +
398C LYS* 1.3 86.3 + - + +
399C THR 3.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 398 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ALA* 2.8 29.1 + - + +
397C GLU* 1.3 100.9 + - + +
399C THR* 1.3 59.6 + - + +
400C PRO* 4.7 0.2 - - - +
412C PHE* 4.3 7.4 - - + -
416C GLN* 3.7 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 399 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A MET* 3.8 20.2 - - + -
395C VAL* 2.8 28.7 + - + +
396C MET 4.1 7.6 - - - +
397C GLU 3.8 0.9 - - - +
398C LYS* 1.3 83.1 - - - +
400C PRO* 1.3 70.4 - - - +
401C HIS* 3.0 23.9 + - - +
404C LEU* 5.1 1.3 - - + +
412C PHE* 3.4 36.6 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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