Contacts of the helix formed by residues 263 - 275 (chain B) in PDB entry 1RC5
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 263 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS 5.0 9.9 + - - -
35A HIS* 5.1 10.3 - - - -
37A GLU* 3.0 20.9 - - - +
38A THR* 4.9 0.2 - - - -
261B ASN* 4.2 16.1 - - - +
262B LYS* 1.4 84.4 - - + +
264B GLU* 1.3 65.8 + - - +
265B GLY* 4.3 5.2 - - - +
266B PHE* 3.1 14.9 + - - +
267B LEU* 3.3 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLU* 2.5 28.5 + - + +
40A GLU* 6.1 0.4 - - - +
41A PHE* 3.3 34.0 - - + -
262B LYS 3.7 1.5 + - - -
263B ARG* 1.3 71.5 - - - +
265B GLY* 1.3 58.4 + - - +
267B LEU* 4.2 5.8 - - - -
268B SER* 3.0 52.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ARG* 3.2 5.1 - - - +
264B GLU* 1.3 83.1 + - - +
266B PHE* 1.3 56.3 + - - +
268B SER* 4.7 1.3 - - - -
269B PRO* 3.2 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B SER* 5.0 5.6 + - - -
260B PRO* 5.6 8.1 - - + -
261B ASN* 3.0 47.7 - - + +
263B ARG* 3.1 5.7 + - - +
265B GLY* 1.3 76.4 - - - +
267B LEU* 1.3 63.8 + - - +
268B SER 3.7 0.2 - - - -
269B PRO* 4.1 7.7 - - - +
270B LEU* 3.9 24.8 - - + +
346B GLY* 6.2 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 4.9 1.6 - - + -
41A PHE* 3.6 41.1 - - + -
255B LEU* 3.2 39.4 - - + +
256B VAL* 4.7 12.3 - - + -
259B SER* 3.7 21.1 - - - +
261B ASN* 5.6 0.2 - - + -
262B LYS* 3.5 30.7 - - + +
263B ARG 3.5 12.3 - - - +
264B GLU* 3.2 3.8 + - - +
266B PHE* 1.3 82.8 - - + +
268B SER* 1.3 55.4 + - - +
269B PRO 3.6 0.2 - - - -
270B LEU* 3.4 2.0 + - + -
271B LYS* 2.7 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.8 7.8 - - - -
264B GLU* 3.0 38.1 + - - -
265B GLY* 4.7 1.6 - - - -
267B LEU* 1.3 74.9 - - - +
269B PRO* 1.3 72.7 - - - +
271B LYS* 3.1 8.8 + - - +
272B ALA* 2.9 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B GLY 3.2 23.3 - - - +
266B PHE* 4.3 8.1 - - + +
267B LEU 3.7 1.3 - - - -
268B SER* 1.3 95.1 - - - +
270B LEU* 1.3 60.9 + - + +
272B ALA* 3.7 7.6 + - + +
273B TYR 3.6 7.6 + - - -
348B HIS* 3.2 42.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 3.8 24.5 - - + -
259B SER* 4.7 7.9 - - - +
260B PRO* 6.1 0.2 - - + -
266B PHE* 3.9 24.7 - - + +
267B LEU 3.4 7.4 + - - +
268B SER 3.2 0.6 - - - -
269B PRO* 1.3 78.2 - - - +
271B LYS* 1.3 64.8 - - - +
273B TYR* 3.4 3.7 + - + +
274B LEU* 3.3 33.2 + - + +
342B ALA 4.4 5.4 - - - +
343B ILE* 3.9 27.1 - - + +
346B GLY* 3.6 30.5 - - - -
347B ARG 3.6 17.3 - - - +
348B HIS 3.9 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 4.2 15.3 - - + -
248B ASN* 3.1 25.0 + - - +
251B ILE* 5.0 3.1 - - + -
252B VAL* 3.8 27.7 - - + +
255B LEU* 4.1 11.6 - - + +
267B LEU 2.7 23.3 + - - +
268B SER* 3.1 9.4 + - - +
270B LEU* 1.3 72.0 - - - +
272B ALA* 1.3 67.5 + - - +
273B TYR 3.2 0.7 + - - -
274B LEU* 3.4 4.9 + - - +
275B ILE* 3.3 42.6 + - + +
632D LYS* 4.4 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B SER 2.9 15.5 + - - +
269B PRO* 3.8 9.4 - - + +
270B LEU 3.3 0.4 - - - -
271B LYS* 1.3 80.7 - - - +
273B TYR* 1.3 61.4 + - - +
275B ILE* 3.6 9.7 + - - +
276B SER* 3.4 21.0 + - - -
348B HIS* 4.9 5.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PRO 3.6 1.6 + - - +
270B LEU* 3.4 6.7 + - + +
271B LYS 3.1 1.0 - - - -
272B ALA* 1.3 76.8 - - - +
274B LEU* 1.3 81.7 + - + +
275B ILE 3.0 8.2 + - - -
276B SER* 2.8 30.5 + - - -
278B GLU* 5.1 12.6 - - + -
279B PHE* 3.3 38.4 - + + +
282B LEU* 5.6 2.9 - - - +
342B ALA* 4.2 12.7 - - + +
347B ARG* 3.5 52.3 - - + +
348B HIS* 3.6 32.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ILE* 3.8 31.4 - - + +
255B LEU* 4.4 11.0 - - + -
270B LEU* 3.3 24.7 + - + +
271B LYS* 3.4 2.2 + - - +
273B TYR* 1.3 83.4 - - + +
275B ILE* 1.3 61.2 + - - +
276B SER 3.6 0.7 - - - -
279B PHE* 3.3 31.5 - - + -
280B PHE* 3.1 17.0 - - - -
339B ILE* 4.2 10.8 - - + +
342B ALA* 3.5 33.0 - - + +
343B ILE* 4.1 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ASP* 5.8 3.1 - - - +
248B ASN* 3.4 32.3 - - + +
251B ILE* 3.8 25.4 - - + -
271B LYS* 3.3 37.6 + - + +
272B ALA* 3.7 9.4 - - - +
273B TYR 3.0 1.2 - - - -
274B LEU* 1.3 85.5 - - - +
276B SER* 1.3 59.4 + - - +
277B GLU 4.1 0.7 + - - -
280B PHE* 3.4 24.6 - - + -
632D LYS* 5.6 8.1 - - + +
----------------------------------------------------------
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