Contacts of the helix formed by residues 396 - 412 (chain C) in PDB entry 4U1D
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 ASP 396 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ASN 3.6 6.3 + - - +
395C PHE* 1.3 75.1 - - - +
397C VAL* 1.3 66.4 + - - +
398C ASP* 3.5 20.5 + - - +
399C THR* 3.0 44.1 + - - +
400C VAL* 3.0 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 397 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C PHE* 3.6 8.9 - - + +
396C ASP* 1.3 75.5 + - - +
398C ASP* 1.3 64.4 + - - +
399C THR 3.0 5.1 + - - -
400C VAL* 3.2 25.6 + - + +
401C LYS* 4.7 7.4 + - - +
432C VAL* 3.8 23.8 - - + +
435C ALA* 3.4 34.8 - - + +
436C ALA* 5.4 1.3 - - - +
439C LYS* 5.8 7.2 - - + -
451C LEU* 3.5 35.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 398 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C ASP* 3.1 18.9 - - - +
397C VAL* 1.3 81.2 - - - +
399C THR* 1.3 63.3 + - + +
439C LYS* 3.4 36.2 + - - +
451C LEU* 5.1 5.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
396C ASP* 3.0 36.3 + - - +
397C VAL 3.0 0.2 - - - -
398C ASP* 1.3 85.8 - - + +
400C VAL* 1.3 63.0 + - - +
401C LYS 3.4 2.7 - - - -
402C GLN* 3.1 13.4 + - - +
403C GLN* 3.0 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 400 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C ILE* 4.1 15.5 - - + +
391C ILE* 6.2 0.4 - - + -
395C PHE* 3.5 37.0 - - + -
396C ASP 3.0 21.2 + - - +
397C VAL* 3.2 31.6 + - + +
399C THR* 1.3 75.6 - - - +
401C LYS* 1.3 73.0 + - + +
403C GLN* 3.7 6.2 - - + +
404C LEU* 2.9 39.7 + - + +
428C ILE* 5.8 1.8 - - + -
432C VAL* 4.7 8.5 - - + -
451C LEU 5.8 1.6 - - - +
454C LEU* 5.5 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 401 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C VAL 5.2 5.2 - - - +
399C THR 3.4 0.8 - - - -
400C VAL* 1.3 84.3 - - + +
402C GLN* 1.3 58.9 + - - +
404C LEU* 5.2 0.7 - - - -
405C GLU* 2.9 33.8 + - - +
450C LYS* 2.6 28.6 + - - -
451C LEU* 3.3 24.5 + - - +
453C THR* 2.5 42.2 + - - +
454C LEU* 5.2 4.9 - - + +
455C PRO* 3.8 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 402 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C THR* 3.1 15.3 + - - +
400C VAL 3.1 0.4 - - - -
401C LYS* 1.3 77.1 - - - +
403C GLN* 1.3 70.4 + - - +
405C GLU* 2.9 31.2 + - - +
406C ASN* 2.9 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 403 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C GLU* 5.3 4.7 + - - +
390C ILE* 3.2 48.3 - - + +
399C THR* 3.0 40.4 + - - +
400C VAL* 3.7 6.1 - - + +
402C GLN* 1.3 77.8 - - - +
404C LEU* 1.3 59.2 + - - +
406C ASN* 3.2 6.4 + - - +
407C LEU* 2.9 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 404 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C LEU* 4.0 27.4 - - + -
390C ILE* 4.4 15.5 - - + -
391C ILE* 4.6 3.1 - - + -
400C VAL* 2.9 24.5 + - + +
403C GLN* 1.3 75.4 - - - +
405C GLU* 1.3 61.6 + - - +
407C LEU* 4.4 6.7 - - + +
408C LEU* 2.9 44.9 + - + +
428C ILE* 4.0 29.6 - - + -
454C LEU* 4.0 23.8 - - + -
455C PRO* 3.9 15.3 - - + -
458C LEU* 4.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 405 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C LYS* 2.9 21.8 + - - +
402C GLN* 2.9 27.2 + - - +
404C LEU* 1.3 77.8 - - - +
406C ASN* 1.3 61.8 + - - +
408C LEU* 4.1 5.9 + - - +
409C VAL* 4.2 11.6 + - - +
455C PRO* 4.0 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 406 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C GLN* 2.9 48.5 + - - +
403C GLN* 3.7 7.6 - - - +
405C GLU* 1.3 78.8 - - - +
407C LEU* 1.3 57.5 + - + +
408C LEU 3.6 0.2 - - - -
409C VAL* 3.4 20.5 - - - +
410C LYS* 3.7 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C GLU* 3.6 35.4 - - + +
386C GLU* 3.6 30.5 - - + +
387C LEU* 3.6 47.3 - - + +
390C ILE* 4.9 4.5 - - + -
403C GLN 2.9 16.9 + - - +
404C LEU* 4.1 8.3 - - + +
406C ASN* 1.3 78.2 - - - +
408C LEU* 1.3 58.2 + - + +
409C VAL 3.3 2.7 - - - -
410C LYS* 3.3 12.4 + - - +
411C LEU* 2.9 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 408 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C LEU* 6.0 1.6 - - + -
404C LEU* 2.9 30.1 + - + +
405C GLU* 4.7 2.9 - - - +
407C LEU* 1.3 75.5 - - + +
409C VAL* 1.3 57.5 + - - +
410C LYS 3.2 1.6 - - - -
411C LEU* 3.6 11.7 - - + -
412C SER* 2.6 39.0 + - - +
417C PHE* 3.5 36.1 - - + -
424C LEU* 5.8 1.3 - - + -
455C PRO* 3.9 20.4 - - + +
456C ALA 3.3 26.9 - - - +
457C PRO* 3.7 10.5 - - + -
458C LEU* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 409 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C GLU 4.2 8.9 + - - +
406C ASN* 3.4 24.5 - - - +
408C LEU* 1.3 79.5 - - - +
410C LYS* 1.3 71.8 + - + +
412C SER* 4.0 7.2 + - - -
413C SER* 4.2 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 410 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C GLU* 4.0 25.2 - - + +
386C GLU* 3.7 21.0 + - - -
406C ASN 3.7 18.7 + - - -
407C LEU* 3.3 16.8 + - - +
408C LEU 3.2 0.2 - - - -
409C VAL* 1.3 86.2 - - + +
411C LEU* 1.3 59.8 + - - +
413C SER* 2.5 26.0 + - - -
414C LYS* 4.0 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 411 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C GLU* 3.9 17.9 - - + +
384C LEU* 3.5 33.7 - - + -
387C LEU* 4.4 20.2 - - + -
407C LEU* 2.9 34.3 + - + +
408C LEU* 3.4 16.3 + - + -
410C LYS* 1.3 76.7 - - - +
412C SER* 1.3 64.5 + - - +
414C LYS* 3.1 33.2 + - + +
416C TYR* 4.1 0.4 - - - +
417C PHE* 3.4 38.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 412 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C LEU* 2.6 24.1 + - - +
409C VAL* 4.3 5.3 - - - -
410C LYS 3.4 0.4 - - - -
411C LEU* 1.3 76.2 - - - +
413C SER* 1.3 62.0 + - - +
414C LYS 3.3 7.6 + - - +
417C PHE* 4.1 13.9 - - - -
418C SER* 5.6 2.1 + - - -
457C PRO* 4.4 19.1 - - - +
----------------------------------------------------------
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