Contacts of the helix formed by residues 242 - 255 (chain B) in PDB entry 1RJF
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 242 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ASN* 3.6 27.6 + - - +
241B ASP* 1.3 73.0 + - - +
243B PHE* 1.3 58.0 + - - +
244B GLY 3.4 2.2 - - - -
245B ALA* 3.9 17.5 - - + +
246B ILE* 3.1 54.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B PRO* 5.1 0.9 - - + -
234B ILE 3.7 10.1 - - - -
235B GLY 4.1 0.2 - - - +
241B ASP* 3.3 8.6 + - - +
242B ARG* 1.3 78.6 - - - +
244B GLY* 1.3 59.6 + - - +
246B ILE* 3.6 5.7 + - - +
247B MET* 3.2 62.0 + - + +
262B LEU* 5.7 0.2 - - + -
316B VAL* 4.6 7.6 - - + -
317B MET* 4.4 17.3 - - + -
320B HIS* 3.3 67.8 - + + +
321B TYR* 4.4 12.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B GLY* 3.3 29.5 + - - -
241B ASP 4.5 1.0 + - - -
242B ARG* 3.4 0.4 - - - +
243B PHE* 1.3 78.9 - - - +
245B ALA* 1.3 61.4 + - - +
247B MET 3.7 0.2 + - - -
248B GLN* 3.4 32.1 + - - +
262B LEU* 3.7 10.5 - - - +
263B MET* 3.8 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ASP 5.2 0.6 + - - +
242B ARG* 3.7 22.7 + - + +
243B PHE 3.4 0.2 - - - -
244B GLY* 1.3 76.7 - - - +
246B ILE* 1.3 60.3 + - + +
248B GLN* 4.6 3.5 - - - +
249B SER* 3.0 30.0 + - - -
263B MET* 3.6 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ARG* 3.1 55.9 + - + +
243B PHE* 4.1 4.3 - - - +
244B GLY 3.3 0.2 - - - -
245B ALA* 1.3 75.6 - - + +
247B MET* 1.3 62.3 + - - +
249B SER* 3.7 4.8 + - - +
250B ASN* 3.1 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B PRO* 4.1 11.0 - - + -
243B PHE* 3.2 48.1 + - + +
244B GLY 4.1 0.2 - - - +
245B ALA 3.4 0.2 - - - -
246B ILE* 1.3 79.3 - - - +
248B GLN* 1.3 62.4 + - - +
250B ASN* 4.4 1.3 - - - +
251B LEU* 3.2 37.3 + - + +
259B MET* 3.8 34.5 - - + +
262B LEU* 4.0 13.5 - - + -
321B TYR* 3.5 27.6 - - + +
335B BME 4.4 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLY 3.4 16.6 + - - +
245B ALA* 4.6 3.5 - - - +
247B MET* 1.3 77.5 - - - +
249B SER* 1.3 62.0 + - - +
251B LEU* 3.5 5.3 + - - +
252B LYS* 3.2 23.9 + - - +
257B LEU 4.6 3.0 - - - +
258B GLU* 6.0 0.6 - - - +
259B MET* 2.7 39.4 + - + +
260B PRO* 4.5 7.9 + - - +
262B LEU* 3.9 18.1 - - + +
263B MET* 3.4 31.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ALA 3.0 21.6 + - - -
246B ILE* 3.7 6.9 + - - +
248B GLN* 1.3 77.5 - - - +
250B ASN* 1.3 66.8 + - - +
252B LYS* 3.5 6.1 + - - +
253B GLU* 3.4 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ILE* 3.1 24.2 + - + +
247B MET* 4.4 2.5 - - - +
249B SER* 1.3 79.5 + - - +
251B LEU* 1.3 66.8 + - + +
253B GLU* 4.5 3.2 - - - +
254B SER* 2.8 44.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B THR* 5.9 1.3 - - + -
206B TYR* 4.5 14.1 - - + +
247B MET* 3.2 27.4 + - + +
248B GLN* 3.9 4.5 - - - +
249B SER 3.4 0.2 - - - -
250B ASN* 1.3 88.3 - - + +
252B LYS* 1.3 58.0 + - - +
254B SER* 5.3 0.4 - - - +
255B ARG* 3.2 31.9 + - + +
256B ASN 3.0 21.0 + - - -
257B LEU* 3.3 30.7 + - + +
258B GLU* 5.4 0.4 - - - -
259B MET* 4.1 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B GLN 3.2 16.7 + - - +
249B SER* 3.8 8.3 - - - +
250B ASN 3.3 0.4 - - - -
251B LEU* 1.3 77.2 - - - +
253B GLU* 1.3 64.3 + - + +
256B ASN* 3.4 59.7 + - - +
257B LEU 4.1 10.5 - - - +
258B GLU* 4.2 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B SER* 3.4 17.7 + - - +
250B ASN* 4.5 3.6 - - - +
251B LEU 3.5 0.2 - - - -
252B LYS* 1.3 79.9 - - + +
254B SER* 1.3 60.6 + - - +
255B ARG 3.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ASN* 2.8 32.0 + - - -
251B LEU* 4.5 0.3 - - - +
253B GLU* 1.3 77.9 - - - +
255B ARG* 1.3 72.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 3.4 38.2 + - + +
7B GLN* 3.4 45.7 + - - +
8B THR* 3.5 15.0 - - - +
11B ASP* 3.7 30.1 + - - -
251B LEU* 3.2 34.7 + - + +
254B SER* 1.3 95.8 + - - +
256B ASN* 1.3 70.1 + - - +
257B LEU* 3.4 11.6 + - + +
----------------------------------------------------------
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