Contacts of the helix formed by residues 373 - 383 (chain C) in PDB entry 5I94
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 373 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C GLN* 4.9 0.7 - - - +
282C CYS* 3.7 15.9 - - - -
372C PHE* 1.3 74.7 - - - +
374C ASN* 1.3 61.7 + - - +
375C ALA* 3.8 6.9 + - - +
376C THR* 3.0 23.4 + - - -
377C PHE* 3.2 15.6 + - - +
418C SER* 3.0 26.0 + - - -
420C GLU* 3.3 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 374 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C PHE* 3.5 23.8 + - + -
373C SER* 1.3 71.1 - - - +
375C ALA* 1.3 62.1 + - - +
377C PHE* 3.1 10.7 + - - +
378C GLN* 2.9 57.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 375 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C GLN* 3.3 31.3 + - + +
254C LYS* 5.4 2.0 - - - +
373C SER* 3.2 6.2 - - - +
374C ASN* 1.3 83.3 - - - +
376C THR* 1.3 63.3 + - - +
378C GLN* 3.3 4.7 + - - +
379C SER* 3.0 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 376 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ILE* 5.3 3.4 - - + -
251C GLN* 3.6 24.0 - - + +
252C LEU* 5.5 3.7 - - + +
282C CYS* 3.4 22.0 - - - -
284C GLN* 3.7 27.1 - - - +
373C SER* 3.0 20.9 + - - -
375C ALA* 1.3 78.0 - - - +
377C PHE* 1.3 55.9 + - - +
379C SER* 3.7 3.2 - - - -
380C GLU* 2.8 41.7 + - - +
417C CYS 5.3 0.2 - - - -
418C SER* 3.7 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C PHE* 3.6 27.4 - + + -
373C SER 3.2 6.0 + - - +
374C ASN* 3.1 24.0 + - - +
375C ALA 3.1 0.6 - - - -
376C THR* 1.3 77.9 - - - +
378C GLN* 1.3 70.2 + - - +
380C GLU* 3.5 2.0 + - - +
381C ARG* 3.3 56.3 + - - +
411C ASP* 3.6 17.3 - - - -
414C PHE* 3.7 13.9 - - + -
415C GLN* 3.5 49.6 - - + -
418C SER* 3.2 9.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 378 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C ASN* 2.9 49.5 + - - +
375C ALA* 3.8 4.7 - - - +
377C PHE* 1.3 86.6 - - - +
379C SER* 1.3 64.5 + - - +
381C ARG* 3.1 27.9 + - - +
382C GLU* 3.0 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 379 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ILE* 3.3 24.0 - - - -
250C PRO* 4.0 8.1 - - - +
251C GLN* 2.5 32.6 + - - -
375C ALA 3.0 11.9 + - - -
376C THR 3.7 2.2 - - - -
378C GLN* 1.3 77.6 - - - +
380C GLU* 1.3 63.9 + - - +
381C ARG 3.0 1.2 + - - -
382C GLU* 3.0 16.4 + - - +
383C SER* 3.1 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 380 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C TYR* 2.9 26.7 + - - -
249C ILE* 3.3 15.2 - - - +
252C LEU* 5.5 0.5 - - - +
284C GLN* 3.5 32.5 + - - +
376C THR* 2.8 26.1 + - - +
377C PHE* 3.9 5.8 - - - +
379C SER* 1.3 72.9 - - - +
381C ARG* 1.3 56.1 + - - +
383C SER* 4.1 0.9 - - - -
384C GLY* 3.4 17.9 + - - -
387C ASN* 5.4 4.2 + - - +
414C PHE* 3.5 37.2 - - + +
417C CYS* 5.1 10.0 - - + +
418C SER* 4.7 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 381 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C PHE* 3.3 45.4 + - - +
378C GLN* 3.1 40.1 + - - +
379C SER 3.0 0.6 - - - -
380C GLU* 1.3 75.4 - - - +
382C GLU* 1.3 65.4 + - + +
383C SER 3.2 1.8 - - - -
384C GLY 4.2 3.1 + - - -
388C PHE* 4.3 15.5 - - + -
411C ASP* 2.9 31.6 + - - +
414C PHE* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 382 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B LYS* 5.4 3.3 + - - -
378C GLN* 3.0 18.9 + - + +
379C SER* 3.0 8.3 + - - +
381C ARG* 1.3 79.1 - - + +
383C SER* 1.3 59.3 + - - +
384C GLY 3.7 0.2 - - - -
385C ASP* 5.1 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 383 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B GLU* 5.6 1.9 - - - +
248C TYR* 4.0 27.0 + - - -
249C ILE* 4.0 12.2 - - - +
379C SER 3.1 15.3 + - - -
380C GLU 4.2 0.9 - - - -
382C GLU* 1.3 80.8 - - - +
384C GLY* 1.3 58.1 + - - +
385C ASP* 3.1 16.4 + - - +
----------------------------------------------------------
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