Contacts of the helix formed by residues 325 - 332 (chain C) in PDB entry 5PAO
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 GLU 325 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TYR* 3.5 40.7 - - + +
162A CYS 4.8 0.5 + - - -
173A ARG* 2.5 48.3 + - - -
324C PRO* 1.3 75.8 - - - +
326C ARG* 1.3 65.9 + - - +
327C THR* 4.0 16.2 + - - +
328C PHE* 3.4 3.4 + - + +
329C SER* 3.0 21.5 + - - -
444C ILE* 4.5 4.0 - - - -
448C GLN* 5.1 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 326 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C PRO 3.7 1.2 + - - -
325C GLU* 1.3 71.5 - - - +
327C THR* 1.3 86.2 + - - +
329C SER* 3.2 4.6 + - - -
330C GLU* 2.9 66.3 + - + +
441C SER 3.6 19.1 - - - +
442C GLN* 5.8 2.2 - - - +
444C ILE* 4.0 21.4 - - + +
445C GLU* 3.0 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 327 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A CYS 4.2 10.8 + - - -
173A ARG* 5.4 0.2 + - - -
301A SO4 4.1 12.5 + - - +
325C GLU* 4.0 16.1 + - - +
326C ARG* 1.3 101.9 - - - +
328C PHE* 1.3 61.6 + - - +
330C GLU* 3.8 3.3 - - - -
331C ARG* 2.8 75.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 328 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASN* 3.3 31.4 - - - -
159A GLU 4.6 0.7 - - - -
160A GLN 3.3 19.3 - - - +
161A TYR* 3.6 33.9 - + + -
162A CYS 5.6 1.1 - - - +
324C PRO* 3.8 11.4 - - + -
325C GLU* 3.4 8.0 + - + +
326C ARG 3.3 0.4 - - - -
327C THR* 1.3 82.1 + - - +
329C SER* 1.3 57.9 + - - +
331C ARG* 4.9 1.3 - - - +
332C THR* 2.9 35.4 + - + +
333C LEU* 3.1 31.7 + - + -
412C TYR* 3.7 26.9 - + - -
417C TYR* 3.6 32.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 329 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C PRO* 3.8 21.0 - - - +
325C GLU 3.0 17.0 + - - -
326C ARG* 3.6 5.6 - - - -
328C PHE* 1.3 78.7 - - - +
330C GLU* 1.3 58.7 + - - +
333C LEU* 3.4 15.5 + - - +
334C ALA* 2.8 32.2 + - - +
364C ARG* 5.9 0.7 + - - -
418C LEU 4.9 0.9 + - - -
419C THR* 4.1 11.8 - - - +
441C SER* 3.7 24.5 + - - -
444C ILE* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 330 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C ARG* 2.9 58.9 + - - +
327C THR* 3.9 3.6 - - - +
329C SER* 1.3 76.8 - - - +
331C ARG* 1.3 64.0 + - + +
334C ALA* 3.6 12.5 - - - +
335C PHE* 3.4 17.3 - - - -
441C SER* 4.1 22.7 + - - +
442C GLN* 4.7 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 331 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A CYS* 3.5 30.7 - - - +
152A VAL* 3.7 44.6 - - + +
155A ASN* 5.6 0.4 - - - +
162A CYS 4.2 3.0 + - - -
164A ASP* 4.0 3.7 + - - -
301A SO4 3.0 40.4 + - - -
327C THR* 2.8 51.9 + - - +
328C PHE* 4.5 1.1 - - - +
330C GLU* 1.3 76.6 - - + +
332C THR* 1.3 65.9 + - - +
335C PHE* 3.3 19.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 332 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A CYS 4.7 0.3 + - - -
152A VAL 5.6 0.3 + - - -
155A ASN* 2.9 32.8 + - + +
328C PHE* 2.9 23.3 + - + -
330C GLU 3.5 0.4 - - - -
331C ARG* 1.3 84.6 + - - +
333C LEU* 1.3 66.8 + - - +
334C ALA 3.2 1.3 - - - -
335C PHE* 3.1 15.9 + - - +
336C VAL* 3.7 9.2 + - - +
412C TYR* 3.5 44.9 - - + +
----------------------------------------------------------
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