Contacts of the strand formed by residues 279 - 285 (chain L) in PDB entry 2B4X
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 279 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138L SER* 3.6 23.3 - - - +
140L LEU* 4.0 22.7 - - + -
221L PHE* 3.2 49.1 - - + -
274L PHE* 2.8 36.9 + - + +
277L ASP 4.5 0.2 - - - +
278L ASP* 1.3 94.9 + - - +
280L THR* 1.3 64.4 + - - +
412L ILE* 3.9 14.1 - - + -
413L ARG 3.1 11.4 - - - +
414L GLU* 4.5 11.7 - - + -
421L ILE* 5.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 280 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271L GLU* 3.1 25.6 + - - +
272L LEU 4.0 1.6 - - - -
273L PRO* 3.6 24.9 - - + -
274L PHE* 3.9 7.6 - - - -
277L ASP* 4.2 9.6 - - - +
278L ASP 4.2 0.4 + - - -
279L ILE* 1.3 80.4 - - - +
281L MET* 1.3 59.3 + - - +
282L VAL* 4.3 0.5 - - - +
411L PHE 3.6 1.2 - - - +
412L ILE* 3.5 0.5 - - - -
413L ARG* 2.8 68.7 + - - +
415L VAL* 3.8 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 281 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225L TRP* 3.9 19.7 - - + -
270L LEU 3.8 0.5 - - - +
271L GLU* 3.5 1.6 - - - -
272L LEU* 2.8 45.4 + - + +
274L PHE* 3.7 11.1 - - + -
280L THR* 1.3 73.9 - - - +
282L VAL* 1.3 63.2 + - - +
283L LEU* 4.0 19.5 + - + -
320L MET* 5.2 2.9 - - - -
323L PHE* 6.1 0.2 - - + -
373L LEU* 4.3 4.3 - - + -
375L VAL* 4.2 21.3 - - + -
380L SER* 4.0 13.0 - - - +
410L VAL* 3.5 28.7 - - + -
411L PHE 3.1 11.0 - - - +
412L ILE* 3.7 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 282 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269L VAL* 4.2 11.0 - - + -
270L LEU 3.3 4.9 - - - +
271L GLU* 4.0 18.6 - - + -
280L THR* 4.3 0.9 - - - +
281L MET* 1.3 78.4 - - - +
283L LEU* 1.3 72.5 + - - +
284L ILE* 4.1 18.2 - - + -
304L LEU* 5.1 4.3 - - + -
308L LEU* 4.1 15.9 - - + -
311L LEU* 5.2 0.2 - - + -
409L LEU 3.8 0.2 - - - +
410L VAL* 3.4 5.4 - - - -
411L PHE* 2.8 46.4 + - + +
413L ARG* 3.9 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 283 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389I VAL* 5.7 1.1 - - + -
391I ALA* 4.5 11.0 - - + -
270L LEU* 2.8 55.9 + - + +
272L LEU* 4.2 11.0 - - + -
281L MET* 4.1 16.4 - - + -
282L VAL* 1.3 76.0 - - - +
284L ILE* 1.3 72.5 + - - +
285L LEU* 3.8 13.0 - - + -
318L VAL* 5.8 0.7 - - + -
319L HIS 6.0 0.2 - - - +
320L MET* 3.1 34.8 - - + -
408L PHE* 3.6 24.5 - - + -
409L LEU 3.4 2.7 - - - +
410L VAL* 3.8 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 284 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267L THR* 4.1 19.1 - - + -
268L GLN 3.3 4.7 - - - -
269L VAL* 4.0 15.3 - - + -
282L VAL* 4.1 7.2 - - + -
283L LEU* 1.3 85.7 - - - +
285L LEU* 1.3 62.9 + - - +
292L LEU* 3.9 5.5 - - + +
295L VAL* 4.2 21.5 - - + -
304L LEU* 3.9 17.9 - - + -
307L TRP* 3.5 32.5 - - + -
408L PHE* 3.7 1.7 - - - +
409L LEU* 3.2 39.9 + - + -
411L PHE* 3.9 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 285 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389I VAL* 4.2 16.2 - - + -
390I ILE 3.7 10.8 - - - +
391I ALA* 3.3 37.0 - - + +
267L THR* 3.4 2.8 - - - +
268L GLN* 2.7 57.7 + - + +
270L LEU* 5.9 0.9 - - + -
283L LEU* 3.8 16.2 - - + -
284L ILE* 1.3 91.0 - - - +
286L PRO* 1.3 70.2 - - + +
407L PRO 5.1 0.4 - - - +
408L PHE* 3.8 18.6 - - + -
----------------------------------------------------------
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