Contacts of the strand formed by residues 238 - 241 (chain E) in PDB entry 3SRF
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 MET 238 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E VAL* 3.8 19.5 - - + -
108E ALA* 3.6 31.2 - - + -
109E VAL 3.6 1.5 + - - +
110E ALA* 3.7 17.2 - - + -
111E LEU 3.2 19.8 + - - -
236E VAL* 3.6 5.9 - - - +
237E ASP* 1.3 91.2 - - + +
239E VAL* 1.3 68.7 + - - +
240E PHE* 3.9 14.6 - - + -
264E ILE* 3.9 2.7 - - - -
265E LYS* 3.3 22.7 - - + +
267E ILE* 4.5 4.7 - - + -
460E ARG 4.5 5.2 - - - +
461E GLN* 4.6 4.0 - - + -
464E LEU* 3.7 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 239 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E LEU* 3.2 22.9 - - + +
113E THR* 4.2 6.7 - - + -
228E LEU* 3.7 34.8 - - + +
231E GLY* 6.3 0.2 - - - -
236E VAL* 4.4 6.3 - - + -
238E MET* 1.3 80.0 - - - +
240E PHE* 1.3 65.8 + - - +
241E ALA* 3.8 17.3 - - + +
253E VAL* 4.6 5.6 - - + -
257E LEU* 4.9 6.3 - - + -
264E ILE* 4.2 13.2 - - + -
265E LYS 2.8 13.0 + - - +
266E ILE* 3.8 6.9 - - + -
267E ILE* 2.8 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 240 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E ILE* 4.3 15.9 - - + -
72E ARG* 4.0 27.4 - - + -
110E ALA* 3.5 29.8 - - + -
111E LEU 2.8 8.9 + - - -
112E ASP* 3.1 34.5 - - + +
113E THR 3.1 21.5 + - - -
238E MET* 3.9 18.2 - - + -
239E VAL* 1.3 72.6 - - - +
241E ALA* 1.3 63.1 + - - +
267E ILE* 3.4 39.0 - - + -
269E LYS* 3.6 11.8 - - + +
290E MET* 4.4 8.3 - - - -
324E ILE* 3.7 21.3 - - + -
359E MET* 4.8 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E THR* 3.4 9.6 - - + +
239E VAL* 3.7 13.0 + - + -
240E PHE* 1.3 71.6 - - - +
242E SER* 1.3 61.2 + - - +
244E ILE* 3.6 25.2 - - + +
253E VAL* 4.2 20.9 - - + -
266E ILE* 4.7 6.3 - - + -
267E ILE 3.0 12.3 + - - +
268E SER* 5.1 0.2 - - - -
269E LYS* 3.0 27.7 + - - +
----------------------------------------------------------
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