Contacts of the strand formed by residues 350 - 354 (chain C) in PDB entry 3OEH
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 GLY 350 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C GLU* 3.5 8.8 - - - +
168C LEU 3.1 19.4 + - - -
348C THR* 3.3 10.4 + - - -
349C ASP* 1.3 77.1 - - - +
351C GLN* 1.3 80.6 + - - +
373C VAL* 3.4 20.4 - - - -
375C ARG* 3.9 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C GLU* 3.5 8.2 - - - +
168C LEU* 3.1 37.7 - - + +
170C ILE* 3.9 13.9 - - + -
345C ILE* 3.5 34.6 + - + +
348C THR* 4.0 1.5 + - - +
350C GLY* 1.3 95.4 - - - +
352C ILE* 1.3 59.5 + - - +
353C PHE* 3.6 20.4 - - + -
371C LEU 4.0 6.6 - - - +
372C SER* 3.1 8.8 - - - -
373C VAL* 3.1 32.6 + - - +
375C ARG* 3.9 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C VAL* 4.0 15.7 - - + -
159C VAL* 3.5 30.7 - - + -
161C ILE* 4.0 17.0 - - + -
167C GLU* 3.7 17.3 - - + +
168C LEU 2.7 10.1 + - - +
169C ILE* 3.7 14.0 - - + +
170C ILE* 2.9 30.2 + - - +
180C VAL* 4.5 14.6 - - + -
351C GLN* 1.3 71.4 - - - +
353C PHE* 1.3 60.5 + - - +
354C LEU* 3.9 13.8 + - + -
367C ILE* 3.7 33.0 - - + -
372C SER* 3.5 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 353 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C ILE* 3.5 25.1 - - + -
171C GLY* 6.0 0.7 - - - -
336C VAL* 3.4 39.7 - - + -
345C ILE* 4.4 15.7 - - + -
351C GLN* 3.6 26.0 - - + -
352C ILE* 1.3 72.5 - - - +
354C LEU* 1.3 62.0 + - - +
355C GLU* 5.1 4.7 - - + +
366C ALA 3.4 1.2 - - - +
367C ILE* 3.4 4.2 - - - -
368C ASN* 2.9 43.1 + - + +
371C LEU* 3.5 46.7 - - + -
372C SER* 2.9 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ILE* 4.2 4.0 - - + -
170C ILE 2.9 15.5 + - - +
171C GLY* 3.7 16.3 - - - -
172C ASP* 4.3 1.7 + - - +
175C THR* 3.8 26.0 - - - +
176C GLY 3.5 11.2 - - - +
177C LYS* 3.5 39.9 - - + +
180C VAL* 4.1 9.6 - - + -
352C ILE* 4.0 11.7 - - + +
353C PHE* 1.3 76.5 - - - +
355C GLU* 1.3 67.3 + - - +
365C PRO* 4.5 4.7 - - + -
366C ALA 3.1 31.2 - - - +
367C ILE* 3.7 20.4 - - + -
----------------------------------------------------------
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