Contacts of the strand formed by residues 213 - 218 (chain J) in PDB entry 3IT8
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 ILE 213 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98J TYR* 4.3 16.2 - - + +
100J THR* 4.2 18.4 - - + +
103J LEU* 3.5 35.0 - - + -
211J ASP* 6.3 0.2 - - + -
212J VAL* 1.3 84.4 - - - +
214J THR* 1.3 73.4 + - - +
215J LYS* 4.9 4.5 - - + -
245J PRO* 4.6 11.2 - - + -
246J GLY* 4.3 20.6 - - - +
252J TRP* 4.0 21.1 - - + +
283J VAL* 3.8 1.7 - - - -
284J PHE* 2.8 38.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 214 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202J CYS* 4.2 2.9 - - - +
212J VAL* 5.4 0.2 - - - -
213J ILE* 1.3 80.2 - - - +
215J LYS* 1.3 65.7 + - - +
216J TRP* 3.8 11.5 - - + +
236J GLU* 5.3 0.2 - - - +
239J ARG* 5.5 3.6 - - - +
252J TRP* 3.5 27.5 - - + -
265J LEU* 5.1 9.2 - - - +
267J ASP* 2.8 35.7 - - - +
281J CYS* 3.4 26.9 - - - -
282J VAL 3.4 4.4 + - - -
283J VAL* 4.2 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 215 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J LEU* 4.2 22.4 - - - +
213J ILE* 4.9 3.8 - - + -
214J THR* 1.3 78.7 - - - +
216J TRP* 1.3 63.7 + - - +
217J ILE* 3.9 10.5 - - + -
228J TYR* 3.9 20.0 + - + +
236J GLU* 3.1 42.5 + - + +
280J VAL 3.6 0.2 - - - +
281J CYS* 3.8 1.1 - - - -
282J VAL* 2.8 46.2 + - + +
284J PHE* 3.4 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 216 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188J VAL* 4.0 9.0 - - + -
200J LEU* 3.8 34.1 - - + -
202J CYS* 3.3 42.8 - - + -
214J THR* 3.8 7.5 - - + +
215J LYS* 1.3 73.6 - - - +
217J ILE* 1.3 60.4 + - - +
236J GLU 2.7 33.7 + - - +
237J TRP* 3.4 21.1 + - + +
239J ARG* 5.2 7.9 - - + -
267J ASP* 2.8 30.7 + - - -
269J VAL* 3.0 31.6 - - + +
279J PRO* 3.7 29.8 - - + -
280J VAL 3.5 13.2 - - - -
281J CYS* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 217 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215J LYS* 4.5 8.1 - - + +
216J TRP* 1.3 82.2 - - - +
218J GLU* 1.3 75.7 + - - +
221J HIS* 3.9 14.4 - - + -
222J PHE* 3.7 19.7 - - + -
228J TYR* 4.0 16.2 - - + -
234J TYR* 3.8 25.6 - - + -
235J PRO 3.5 21.1 - - - +
236J GLU* 4.2 8.7 - - + +
279J PRO* 3.8 3.6 - - - -
280J VAL* 2.8 39.9 + - + +
282J VAL* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217J ILE* 1.3 77.3 - - - +
219J SER* 1.3 64.8 + - - +
220J GLU* 3.0 23.1 + - + +
221J HIS* 3.1 34.9 + - + +
222J PHE* 4.0 1.2 - - - -
235J PRO 5.1 0.4 + - - -
237J TRP* 3.7 37.1 - - + +
275J MET* 3.7 20.4 - - + +
276J SER* 3.5 16.2 + - - -
277J SER* 3.5 15.2 + - - +
278J GLN 4.6 2.9 - - - +
279J PRO* 4.0 8.9 - - - +
----------------------------------------------------------
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