Contacts of the strand formed by residues 214 - 218 (chain B) in PDB entry 6YB9
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 TRP 214 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ILE* 4.0 20.0 - - + -
64B ILE* 3.9 25.6 - - + -
176B LEU* 4.1 11.0 - - + -
180B TRP* 3.6 37.2 - + - -
187B LEU* 3.7 23.8 - - + -
189B ASP 3.4 14.6 - - - +
190B MET* 3.9 5.6 - - + -
209B ILE* 3.8 27.4 - - + -
210B ASP 3.7 11.9 - - - -
211B ASN* 3.1 27.4 + - - +
212B ASP 3.4 1.6 + - - +
213B SER* 1.3 76.8 - - - +
215B ARG* 1.3 60.8 + - - +
216B LEU* 4.0 14.7 - - + +
227B ASP* 3.2 29.2 - - + +
228B LYS 4.8 0.2 + - - -
232B ARG* 5.2 0.3 + - - -
252B VAL* 4.1 9.0 - - + -
256B VAL* 4.8 0.4 - - + -
703B OK8 3.5 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B THR* 3.8 20.7 + - - +
106B GLY* 3.9 14.1 - - - -
187B LEU* 3.7 7.4 - - - +
188B VAL* 3.0 38.8 + - + -
189B ASP* 2.8 41.4 + - - +
214B TRP* 1.3 75.1 - - - +
216B LEU* 1.3 60.5 + - - +
217B TRP* 4.2 11.7 - - - +
225B GLN* 5.9 0.2 - - - -
227B ASP* 3.3 21.1 - - - +
229B GLN* 3.0 36.7 + - + +
232B ARG* 4.6 2.8 - - - +
703B OK8 3.1 52.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
180B TRP* 3.7 53.4 - - + -
185B CYS* 3.7 25.1 - - + -
186B THR 3.6 10.1 - - - +
187B LEU* 4.4 6.1 - - + -
214B TRP* 4.0 22.0 - - + +
215B ARG* 1.3 70.7 - - - +
217B TRP* 1.3 67.7 + - - +
218B PRO* 3.6 3.8 - - + +
225B GLN* 3.5 0.5 - - - -
226B LYS* 3.1 29.8 + - + -
227B ASP* 3.1 11.3 + - + +
251B TRP* 4.9 7.9 - - + -
252B VAL* 4.1 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ILE* 4.5 24.2 - - + -
105B THR* 4.5 13.5 - - + -
117B GLU* 4.4 16.6 - - + -
118B GLY* 6.3 0.4 - - - -
185B CYS* 4.4 1.3 - - - -
186B THR* 2.9 36.4 + - + +
188B VAL* 3.3 36.3 - - + +
215B ARG* 4.4 13.0 - - - +
216B LEU* 1.3 83.6 - - - +
218B PRO* 1.4 66.3 - - - +
220B GLY* 3.1 28.7 + - - -
221B ASP 3.7 14.6 - - - +
222B ARG* 3.6 41.4 - - + +
225B GLN* 3.9 23.1 + - + +
227B ASP* 4.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASN 3.6 9.0 - - - +
185B CYS* 4.2 5.6 - - - -
216B LEU 3.6 7.9 - - - +
217B TRP* 1.4 81.3 - - - +
219B SER* 1.3 62.0 + - - +
221B ASP* 3.0 25.6 + - - +
224B GLN* 3.1 48.9 - - + +
226B LYS* 3.7 21.5 - - + +
251B TRP* 4.0 24.0 - - + -
----------------------------------------------------------
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