Contacts of the strand formed by residues 237 - 243 (chain C) in PDB entry 6RKU
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 ARG 237 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C GLU* 3.5 12.2 - - - +
232C ALA* 3.4 17.8 + - - +
235C THR* 3.4 11.9 + - - +
236C GLY* 1.3 85.9 - - - +
238C GLY* 1.3 59.3 + - - +
332C ILE 3.8 5.4 - - - +
333C ASN* 3.2 38.0 + - - +
344C ILE* 5.9 4.3 - - + -
24H G 5.2 10.3 + - - -
25H C 4.2 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C GLY* 4.2 13.2 - - - -
231C GLU* 5.1 7.9 - - - -
232C ALA* 4.3 3.7 - - - +
237C ARG* 1.3 78.4 - - - +
239C LYS* 1.3 67.1 + - - +
331C GLY* 4.1 1.0 - - - -
332C ILE* 3.3 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C GLY* 3.2 27.2 - - - -
238C GLY* 1.3 80.0 - - - +
240C VAL* 1.3 62.5 + - - +
241C TYR* 4.9 20.4 + - + -
329C SER* 4.4 16.3 - - - -
330C PHE 3.6 11.4 - - - +
331C GLY* 5.1 3.8 - - - -
332C ILE* 5.4 0.7 - - - -
25H C 4.0 21.6 + - - +
26H T 2.7 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C PRO* 6.1 0.2 - - + -
215C PRO* 6.2 2.2 - - + -
217C PHE* 5.9 2.7 - - + -
223C ILE* 3.7 30.7 - - + -
225C GLY* 4.6 7.4 - - - +
229C ILE* 4.0 23.6 - - + +
239C LYS* 1.3 77.8 - - - +
241C TYR* 1.3 73.1 + - - +
242C ILE* 4.9 9.6 - - + -
328C VAL 4.2 0.2 - - - +
329C SER* 3.4 5.4 - - - -
330C PHE* 3.1 48.9 + - + +
332C ILE* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C ILE 4.7 0.2 - - - -
223C ILE* 3.8 15.8 - - - +
224C ASN* 4.6 18.2 - - + +
225C GLY* 5.3 12.0 - - - +
239C LYS* 4.9 18.5 + - + -
240C VAL* 1.3 90.1 - - - +
242C ILE* 1.3 71.1 + - - +
243C ARG 4.3 0.2 - - - -
327C GLN* 4.0 30.7 - - + +
328C VAL 3.9 1.6 - - - -
329C SER* 4.6 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C PHE* 3.8 35.9 - - + -
221C ALA* 3.8 21.5 - - + -
222C ILE 3.7 0.9 - - - -
223C ILE* 3.9 13.2 - - + -
240C VAL* 4.9 10.8 - - + +
241C TYR* 1.3 85.9 - - - +
243C ARG* 1.3 63.5 + - - +
265C PRO* 3.7 28.6 - - + +
266C TYR* 4.5 8.3 - - + +
326C LEU 3.5 1.6 - - - +
327C GLN* 3.2 27.5 - - - +
328C VAL* 3.0 22.3 + - + +
330C PHE* 5.1 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ALA* 3.8 3.3 - - - +
222C ILE* 2.8 49.9 + - + +
224C ASN* 3.0 32.0 + - - +
242C ILE* 1.3 78.7 - - - +
244C ALA* 1.3 74.1 + - - +
265C PRO* 4.9 0.2 - - - -
321C TYR* 3.1 52.2 - - + +
326C LEU 3.8 3.8 - - - +
327C GLN* 3.1 39.7 + - + +
----------------------------------------------------------
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