Contacts of the strand formed by residues 258 - 263 (chain C) in PDB entry 6S6A
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 LYS 258 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C ILE* 4.6 0.7 - - - -
256C ILE* 3.5 6.8 - - - +
257C GLU* 1.3 81.2 - - + +
259C ALA* 1.3 60.2 + - - +
260C PHE* 3.7 24.7 - - + -
272C THR* 3.1 22.2 + - - +
273C ASP* 2.9 26.9 + - - +
275C SER* 2.8 43.0 + - - +
276C PRO 3.9 7.6 - - - -
277C VAL* 3.4 22.6 - - - +
278C ASP 5.5 0.2 - - - +
281C SER* 5.4 3.1 - - - -
338C VAL 4.2 0.6 - - - +
340C ILE* 2.9 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C LEU* 3.8 21.1 - - + +
250C PHE* 5.0 0.4 - - + -
251C ILE* 3.5 25.8 - - + -
258C LYS* 1.3 71.7 - - - +
260C PHE* 1.3 58.9 - - - +
272C THR* 2.9 32.9 + - - -
273C ASP* 3.0 12.0 + - - +
337C LEU* 4.1 9.2 - - + -
338C VAL 3.4 6.5 - - - +
339C CYS* 4.2 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C LYS* 3.7 27.6 - - + -
259C ALA* 1.3 74.2 - - - +
261C LEU* 1.3 58.6 + - - +
262C PHE* 3.5 23.5 + + + -
269C TYR* 3.9 27.8 - + + -
271C ALA 3.6 3.6 - - - +
272C THR* 3.9 13.7 - - - -
277C VAL* 3.9 30.1 - - + -
281C SER* 4.6 2.9 - - - -
282C TYR* 4.0 31.6 - + + -
285C CYS* 4.1 28.0 - - - -
336C ALA 3.6 1.0 - - - +
337C LEU* 3.6 7.8 - - - +
338C VAL 2.9 37.0 + - - +
340C ILE* 4.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C LEU* 4.1 27.6 - - + -
247C LEU* 4.5 7.0 - - + +
259C ALA 4.3 0.4 + - - -
260C PHE* 1.3 70.1 - - - +
262C PHE* 1.3 61.3 + - - +
269C TYR* 3.3 4.4 - - - -
270C ILE* 2.9 56.2 + - + +
271C ALA* 2.9 23.2 + - + +
331C VAL* 4.3 22.9 - - + -
335C LEU* 4.5 16.8 - - + -
336C ALA 3.8 2.9 - - - +
337C LEU* 4.5 4.0 - - + -
359C PHE* 4.1 23.1 - - + -
363C ILE* 4.5 7.6 - - + -
367C PHE* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C PHE* 3.5 27.6 - - + -
261C LEU* 1.3 72.1 - - - +
263C ASP* 1.3 57.0 + - - +
264C VAL* 3.7 0.8 + - - +
267C LYS* 3.3 26.2 - - - -
268C ILE 3.4 13.7 - - - -
269C TYR* 4.5 1.6 - - + -
270C ILE* 5.3 0.2 - - - -
282C TYR* 3.6 25.1 - + - -
285C CYS* 3.8 30.3 - - + -
286C CYS* 3.8 8.1 - - - -
289C ILE* 3.4 35.4 - - + -
334C PHE 3.5 0.3 - - - +
335C LEU* 2.9 19.2 - - - -
336C ALA* 2.9 43.0 + - + +
338C VAL* 3.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C SER 4.5 0.9 - - - +
108C SER* 2.6 32.3 + - - -
109C PHE* 2.9 33.0 + - + +
110C VAL* 4.9 2.1 - - + +
261C LEU 4.4 0.4 + - - -
262C PHE* 1.3 69.2 - - - +
264C VAL* 1.3 60.9 + - - +
265C VAL* 4.3 2.6 + - - +
266C SER* 2.5 31.5 + - - +
267C LYS* 2.9 30.0 + - - -
268C ILE* 2.9 15.5 + - + +
270C ILE* 4.8 6.1 - - + +
334C PHE* 3.5 14.9 - - - +
335C LEU* 3.8 4.3 - - + +
----------------------------------------------------------
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