Contacts of the helix formed by residues 258 - 270 (chain B) in PDB entry 2O5C
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 HIS 258 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B PHE* 4.0 2.9 - - - -
248B PRO 5.6 0.6 + - - -
249B TYR* 4.0 36.8 - + + +
256B LEU* 3.5 11.7 - - - +
257B LEU* 1.3 99.9 + - + +
259B ARG* 1.3 65.3 + - - +
260B PRO* 3.4 9.3 - - + +
261B LEU* 3.4 20.6 + - + +
262B ALA 3.8 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B PHE* 3.6 39.9 - - + -
258B HIS* 1.3 70.2 - - - +
260B PRO* 1.4 74.4 - - + +
262B ALA* 2.9 13.9 + - - +
263B GLU* 2.9 42.9 + - - +
480B VAL* 3.8 35.1 + - + +
482B GLU* 3.9 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B HIS* 3.4 13.0 - - + +
259B ARG* 1.4 91.0 - - + +
261B LEU* 1.3 51.0 + - - +
263B GLU* 3.1 9.4 + - + +
264B HIS* 2.8 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B TRP* 4.3 15.9 - - + -
246B CYS* 4.4 17.9 - - - -
249B TYR* 4.0 31.9 - - + -
256B LEU* 3.9 21.8 - - + -
258B HIS* 3.4 15.1 + - + +
259B ARG 3.1 0.8 - - - -
260B PRO* 1.3 79.2 - - - +
262B ALA* 1.3 60.9 + - - +
264B HIS* 3.6 15.6 + - + +
265B VAL* 3.3 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B PHE* 4.2 9.6 - - + -
223B GLU 5.0 0.7 - - - +
224B VAL* 3.5 23.8 - - + +
240B TRP* 4.7 0.9 - - - -
256B LEU* 4.1 18.3 - - + +
258B HIS 3.8 1.4 + - - -
259B ARG* 2.9 12.1 + - - +
261B LEU* 1.3 79.9 - - - +
263B GLU* 1.3 56.9 + - - +
265B VAL 3.6 0.3 + - - -
266B VAL* 3.1 30.3 + - - +
480B VAL* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ARG* 2.9 42.1 + - + +
260B PRO* 3.6 10.8 - - + +
262B ALA* 1.3 75.7 - - - +
264B HIS* 1.3 59.3 + - - +
266B VAL* 3.2 18.7 + - - +
267B ASN* 3.0 44.4 + - - +
480B VAL* 3.2 18.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B PRO 2.8 19.1 + - - +
261B LEU* 3.9 18.6 - - + +
262B ALA 3.4 0.2 - - - -
263B GLU* 1.3 72.7 - - - +
265B VAL* 1.3 62.9 + - + +
267B ASN* 3.6 14.5 + - - +
268B ARG* 3.3 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B VAL* 4.1 22.4 - - + -
240B TRP* 3.7 40.2 - - + +
261B LEU* 3.3 24.5 + - + +
262B ALA 3.9 4.3 - - - +
263B GLU 3.2 0.6 - - - -
264B HIS* 1.3 80.7 - - + +
266B VAL* 1.3 63.1 + - - +
267B ASN 3.2 0.4 - - - -
268B ARG* 3.1 21.0 + - + +
269B ILE* 3.2 15.6 + - + +
434B PHE* 4.1 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B VAL* 3.9 12.8 - - + -
262B ALA 3.1 18.7 + - - +
263B GLU* 3.2 21.5 + - - +
265B VAL* 1.3 76.4 - - - +
267B ASN* 1.3 62.9 + - - +
269B ILE* 3.5 7.0 + - - +
270B SER* 2.7 37.1 + - - +
478B GLY 3.4 21.1 - - - +
479B GLU* 3.6 23.6 - - - +
480B VAL* 3.7 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B GLU* 3.0 29.2 + - - +
264B HIS* 3.6 18.5 + - - +
265B VAL 3.2 0.2 - - - -
266B VAL* 1.3 82.9 - - - +
268B ARG* 1.3 61.3 - - + +
269B ILE 3.4 0.5 + - - -
270B SER* 3.9 11.8 + - - +
272B GLN* 5.6 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B HIS* 3.3 34.5 + - + +
265B VAL* 3.1 17.8 + - + +
267B ASN* 1.3 80.9 - - + +
269B ILE* 1.3 58.8 + - + +
272B GLN* 3.2 24.0 + - - +
430B ALA* 2.7 57.3 + - + +
431B LYS* 4.3 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B VAL* 3.9 13.7 - - + -
226B ALA* 4.1 13.0 - - + -
265B VAL* 3.3 20.0 - - + +
266B VAL* 3.6 8.3 - - - +
268B ARG* 1.3 82.0 - - + +
270B SER* 1.3 65.6 + - - +
272B GLN* 3.2 17.5 + - - +
429B ILE* 3.7 29.4 - - + +
430B ALA* 4.3 2.7 - - + -
434B PHE* 3.7 44.2 - - + -
475B CYS* 3.3 19.0 - - - +
478B GLY* 3.8 22.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B VAL* 2.7 27.5 + - - +
267B ASN* 3.9 9.8 + - - +
268B ARG 3.6 1.2 - - - -
269B ILE* 1.3 74.4 - - - +
271B GLY* 1.3 57.4 + - - +
272B GLN* 3.2 9.5 + - - +
475B CYS 4.3 0.2 - - - -
476B GLU 3.9 4.0 - - - -
477B LYS* 4.1 5.4 - - - +
478B GLY* 3.0 23.5 + - - +
----------------------------------------------------------
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