Contacts of the strand formed by residues 316 - 323 (chain C) in PDB entry 1OPO
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 ILE 316 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ILE* 4.5 7.0 - - + -
286C VAL 3.2 14.6 - - - +
287C ARG* 3.7 28.5 - - + +
294C PHE* 3.5 6.5 - - - -
309C ASP 3.8 1.6 - - - +
310C TYR* 3.7 2.6 - - - -
311C GLU* 3.0 44.4 + - + +
314C ARG* 2.8 28.2 + - + +
315C PRO* 1.3 74.8 - - - +
317C ALA* 1.3 71.5 + - - +
318C VAL* 4.8 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 317 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ILE 3.7 0.3 - - - +
285C ILE* 3.3 8.1 - - - +
286C VAL* 3.0 37.4 + - + -
294C PHE* 4.1 17.7 - - + -
297C PRO* 4.1 25.1 - - + -
308C VAL* 4.8 2.0 - - + -
309C ASP 3.4 6.5 - - - +
310C TYR* 4.6 3.1 - - + -
316C ILE* 1.3 75.1 - - - +
318C VAL* 1.3 65.8 + - - +
319C CYS* 3.9 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 318 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C CYS* 4.8 11.0 - - - -
284C ILE 3.7 2.2 - - - -
285C ILE* 4.4 20.2 - - + -
307C ASP* 3.6 4.3 - - - +
309C ASP* 3.0 43.7 + - + +
316C ILE* 4.8 16.6 - - + -
317C ALA* 1.3 79.8 - - - +
319C CYS* 1.3 60.4 + - - +
320C GLU* 3.9 13.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C TRP 3.7 0.2 - - - +
283C CYS* 3.2 5.1 - - - -
284C ILE* 2.8 46.5 + - + +
286C VAL* 5.4 3.1 - - - -
297C PRO* 4.3 9.2 - - - -
307C ASP 3.5 3.6 - - - -
308C VAL* 4.2 20.6 - - + +
317C ALA* 4.2 20.0 - - - -
318C VAL* 1.3 76.4 - - - +
320C GLU* 1.3 63.0 + - - +
321C LEU* 3.7 27.2 + - + +
330C LEU* 4.5 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C TRP 3.5 6.1 - - - +
283C CYS* 4.5 16.0 - - + -
306C GLY* 3.2 3.3 - - - -
307C ASP* 3.0 52.1 + - + +
318C VAL* 4.8 12.6 - - + +
319C CYS* 1.3 73.5 - - - +
321C LEU* 1.3 62.6 + - - +
322C VAL* 5.1 1.1 - - - +
348C MET* 4.1 23.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C VAL* 5.1 5.8 - - + -
281C LYS* 3.6 2.4 - - - +
282C TRP* 2.8 44.2 + - + +
284C ILE* 4.0 27.6 - - + -
299C LEU* 4.0 26.2 - - + -
304C ILE* 4.0 20.2 - - + -
305C SER 3.5 10.8 - - - +
306C GLY* 4.2 2.9 - - - -
307C ASP 4.8 1.8 - - - +
308C VAL* 4.9 1.8 - - + -
319C CYS* 4.1 22.0 - - + +
320C GLU* 1.3 78.9 - - - +
322C VAL* 1.3 71.0 + - - +
323C THR* 4.2 1.1 - - - +
330C LEU* 4.2 17.0 - - + -
348C MET* 5.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 322 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C GLY 3.4 9.2 - - - +
281C LYS* 4.5 21.5 - - + -
303C GLY 3.4 4.7 - - - +
304C ILE* 4.6 1.1 - - - -
305C SER* 2.8 44.9 + - - +
306C GLY* 5.1 1.8 - - - -
320C GLU 5.1 2.7 - - - +
321C LEU* 1.3 82.1 - - - +
323C THR* 1.3 67.3 + - - +
324C GLN* 3.7 11.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 323 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C VAL* 3.5 15.4 - - + +
278C ALA 3.8 12.1 - - - +
279C ALA* 3.4 1.2 - - - +
280C GLY* 2.7 37.7 + - - +
282C TRP* 3.3 20.8 + - - -
303C GLY 3.4 3.8 - - - -
304C ILE* 4.7 6.9 - - - +
321C LEU* 5.2 0.7 - - - +
322C VAL* 1.3 74.7 + - - +
324C GLN* 1.3 59.1 + - - +
325C MET 2.7 31.0 - - - +
328C GLN* 3.4 24.5 - - + +
----------------------------------------------------------
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