Contacts of the helix formed by residues 211 - 218 (chain B) in PDB entry 1OFY
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 ASP 211 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ARG* 2.5 38.9 + - - +
207B ARG 5.7 0.2 - - - +
208B ILE* 3.3 15.8 + - - +
210B ASP* 1.3 75.7 - - - +
212B LYS* 1.3 59.3 + - - +
213B LEU* 2.9 16.1 + - - +
214B ALA* 2.8 30.2 + - + +
215B GLN* 2.8 34.0 + - - +
1295B HEC 4.3 9.0 - - - +
1296B HEC 3.5 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 4.2 27.4 - - + -
43B LYS* 6.1 0.2 - - - +
210B ASP 3.2 11.9 + - - +
211B ASP* 1.3 72.4 + - - +
213B LEU* 1.3 65.8 + - - +
215B GLN* 3.9 12.7 - - - +
216B ALA* 3.2 16.3 + - - +
1295B HEC 3.3 57.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B HIS* 3.7 36.1 - - + +
104B GLN* 3.9 21.5 - - + +
108B ARG* 5.3 1.3 - - - +
211B ASP* 2.9 9.2 + - - +
212B LYS* 1.3 76.5 - - - +
214B ALA* 1.3 66.4 + - - +
216B ALA* 3.2 9.4 + - - +
217B PHE* 3.2 48.7 + - + +
1295B HEC 3.7 40.5 - - + +
1296B HEC 3.9 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE* 4.4 10.3 - - + +
211B ASP* 2.8 27.1 + - + +
213B LEU* 1.3 72.2 - - - +
215B GLN* 1.3 58.3 + - - +
218B HIS* 2.7 63.8 + - + +
1296B HEC 3.9 25.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B THR* 3.4 37.8 + - + +
169B VAL 4.7 5.2 + - - +
208B ILE 5.0 3.6 - - - +
209B LYS 3.1 24.7 + - - +
210B ASP* 3.7 13.2 + - - +
211B ASP 2.8 28.1 + - - +
212B LYS* 3.9 14.7 - - - +
214B ALA* 1.3 76.6 - - - +
216B ALA* 1.3 63.2 + - - +
218B HIS* 3.7 15.0 - - - +
219B ASN* 4.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B THR* 3.7 21.8 - - + +
168B THR* 5.5 0.9 - - - -
212B LYS 3.2 8.3 + - - +
213B LEU 3.2 3.1 + - - +
215B GLN* 1.3 77.0 - - - +
217B PHE* 1.3 60.7 + - + +
219B ASN* 3.3 25.8 + - - +
1295B HEC 3.5 39.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B HIS* 3.8 17.7 - + + -
126B TRP* 3.5 42.0 - + - -
129B THR* 3.6 33.2 - - + -
130B CYS* 4.1 15.9 - - - -
213B LEU* 3.2 41.8 + - + +
216B ALA* 1.3 74.4 - - + +
218B HIS* 1.3 64.8 + - - +
219B ASN* 3.0 19.0 + - - +
223B ILE* 4.0 8.1 - - - +
1295B HEC 4.6 6.7 - + - -
1296B HEC 3.4 41.0 - - + +
1297B HEC 4.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B VAL* 4.1 13.0 - - - +
171B PRO* 5.9 2.7 - - + +
208B ILE* 3.7 9.8 - - + +
214B ALA* 2.7 39.0 + - + +
215B GLN* 3.7 11.5 - - - +
217B PHE* 1.3 69.5 - - - +
219B ASN* 1.3 57.5 + - - +
220B LYS 3.6 4.8 + - - +
223B ILE* 3.9 19.9 - - + +
224B LEU* 3.8 16.3 - - + +
1296B HEC 1.9 94.5 + + + -
----------------------------------------------------------
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