Contacts of the strand formed by residues 303 - 307 (chain C) in PDB entry 1L6O
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 MSE 303 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C GLN* 5.5 0.2 - - - -
279C GLY 4.3 11.7 - - - +
280C GLY* 5.1 2.5 - - - -
281C ILE 3.2 13.7 - - - +
282C TYR* 3.5 37.0 - - + -
301C GLY 3.7 0.2 + - - -
302C ASP* 1.3 69.4 - - - +
304C LEU* 1.4 69.2 + - - +
305C LEU* 3.3 27.1 + - + -
338C VAL* 2.6 28.9 - - - +
339C ALA* 2.7 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C ILE* 5.2 1.8 - - + -
269C ILE* 3.9 22.4 - - + -
281C ILE* 2.8 47.9 + - + +
282C TYR* 4.4 0.2 - - - +
283C ILE* 4.2 18.4 - - + -
302C ASP 4.3 0.2 + - - -
303C MSE 1.4 82.0 - - - +
305C LEU* 1.3 63.1 + - - +
306C GLN 4.5 2.5 - - - +
312C PHE* 3.8 25.4 - - + +
324C LEU* 3.9 14.8 - - + -
336C LEU* 4.1 33.9 - - + -
337C THR 4.0 11.9 - - - +
338C VAL* 4.3 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C ILE* 3.7 32.5 - - + -
303C MSE 3.5 33.2 - - + +
304C LEU* 1.3 74.5 - - - +
306C GLN* 1.3 59.7 + - + +
311C ASN* 3.9 8.2 + - - +
312C PHE* 2.7 34.7 + - - +
313C GLU* 4.1 23.9 + - + +
337C THR* 3.1 24.3 + - + +
338C VAL 4.0 3.4 - - - -
339C ALA* 3.9 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C LEU* 4.5 1.6 - - - +
305C LEU* 1.3 83.3 - - + +
307C VAL* 1.4 65.5 + - - +
308C ASN 4.6 0.2 - - - +
309C ASP* 3.4 37.9 + - - +
310C ILE 3.4 14.1 - - - +
311C ASN* 3.0 27.2 - - - +
312C PHE* 3.8 3.0 - - - -
335C VAL 4.0 0.2 - - - +
336C LEU* 3.8 1.9 - - - +
337C THR* 3.0 48.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C LEU* 4.8 1.1 - - + -
306C GLN* 1.4 71.0 - - - +
308C ASN* 1.3 75.8 + - + +
309C ASP 3.3 2.5 - - - -
310C ILE* 2.8 29.5 + - - +
312C PHE* 2.7 36.8 - - + -
324C LEU* 3.6 24.0 - - + -
327C ILE* 4.0 26.2 - - + +
328C VAL* 6.3 0.4 - - + -
334C ILE* 4.4 5.2 - - + -
335C VAL 3.4 10.8 - - - +
336C LEU* 4.1 14.6 - - + -
----------------------------------------------------------
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