Contacts of the strand formed by residues 213 - 217 (chain B) in PDB entry 2Q5E
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 THR 213 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE* 4.3 0.2 - - - +
103B CYS* 3.1 13.5 - - + +
105B VAL* 4.7 1.1 - - + -
203B LEU* 4.0 16.6 - - + -
206B LEU* 4.0 24.6 - - + +
208B ARG* 3.7 15.9 - - - +
209B ASP 3.0 16.9 + - - -
210B LEU* 3.6 12.1 + - - +
211B ARG 3.7 0.4 - - - -
212B LYS* 1.3 78.7 + - - +
214B LEU* 1.3 80.9 + - - +
229B ASN* 2.5 31.6 + - - -
261B VAL* 3.6 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE* 4.1 20.0 - - + -
103B CYS 2.8 9.1 + - - +
104B VAL* 3.6 11.2 - - + -
105B VAL* 2.7 34.1 + - - +
157B PHE* 4.7 1.3 - - + -
203B LEU* 4.7 0.7 - - - -
213B THR* 1.3 88.1 - - - +
215B ILE* 1.3 58.6 + - - +
229B ASN* 3.4 14.6 - - - +
231B VAL* 4.3 10.5 - - + -
252B PHE* 3.8 26.7 - - + -
255B LEU* 3.8 22.2 - - + -
261B VAL* 3.9 16.4 - - + -
265B LEU* 3.8 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B VAL* 3.3 27.1 - - + +
201B LYS* 4.0 30.7 - - + +
203B LEU* 4.0 22.0 - - + -
214B LEU* 1.3 79.7 - - - +
216B LEU* 1.3 61.4 + - - +
217B ASP* 4.0 21.6 + - + +
222B SER 4.6 0.4 - - - +
223B TYR* 3.9 27.4 - - + -
226B HIS 4.8 0.2 - - - +
229B ASN* 3.0 16.9 + - + +
230B ALA* 3.5 11.8 - - + +
231B VAL* 2.9 26.7 + - - +
252B PHE* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 4.7 2.3 - - + +
105B VAL 2.8 13.3 + - - +
106B ILE* 4.0 20.4 - - + -
107B ASP 3.1 24.8 + - - -
111B THR* 4.0 9.2 - - + +
149B PHE* 3.5 37.0 - - + -
214B LEU 4.3 0.2 - - - -
215B ILE* 1.3 71.6 - - - +
217B ASP* 1.3 60.3 + - - +
231B VAL* 3.4 24.7 - - + +
233B VAL* 3.5 29.4 - - + -
245B LEU* 5.0 3.6 - - + -
248B LEU* 3.6 18.4 - - + -
252B PHE* 4.4 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ASP* 3.3 13.1 - - - +
111B THR* 4.0 5.8 - - - -
201B LYS* 2.8 30.7 + - - +
215B ILE* 4.0 15.1 + - + +
216B LEU* 1.3 76.3 - - - +
218B ASN* 1.3 69.8 + - - +
219B SER* 2.9 26.0 + - - -
222B SER* 3.2 24.0 + - - -
223B TYR* 4.1 17.9 + - + -
231B VAL 3.9 4.0 + - - -
232B PRO* 4.0 7.1 - - - +
233B VAL* 3.7 19.7 + - - +
----------------------------------------------------------
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