Contacts of the strand formed by residues 213 - 218 (chain K) 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 K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98K TYR* 4.3 16.2 - - + +
100K THR* 3.9 19.5 - - + +
103K LEU* 3.5 35.0 - - + -
211K ASP* 6.2 0.2 - - + -
212K VAL* 1.3 86.8 - - - +
214K THR* 1.3 71.5 + - - +
215K LYS* 4.9 4.7 - - + -
245K PRO* 4.7 11.2 - - + +
246K GLY* 4.4 19.1 - - - +
252K TRP* 4.0 20.9 - - + +
283K VAL* 3.8 1.2 - - - -
284K PHE* 2.8 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 214 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202K CYS* 4.2 2.9 - - - +
204K VAL* 5.5 0.2 - - - +
212K VAL* 5.4 0.4 - - - -
213K ILE* 1.3 79.8 - - - +
215K LYS* 1.3 64.7 + - - +
216K TRP* 3.8 10.4 - - + +
239K ARG* 5.5 3.8 - - - +
252K TRP* 3.5 28.4 - - + -
265K LEU* 5.1 8.7 - - - +
267K ASP* 2.8 34.8 - - - +
281K CYS* 3.3 26.2 - - - -
282K VAL 3.4 4.1 + - - -
283K VAL* 4.2 7.0 - - - +
284K PHE* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 215 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103K LEU* 4.2 23.3 - - - +
213K ILE* 4.9 3.6 - - + -
214K THR* 1.3 79.1 - - - +
216K TRP* 1.3 62.0 + - - +
217K ILE* 4.5 9.2 - - + -
228K TYR* 3.9 21.0 + - + +
236K GLU* 3.2 43.3 + - + +
280K VAL 3.6 0.2 - - - +
281K CYS* 3.8 0.9 - - - -
282K VAL* 2.8 46.9 + - + +
284K PHE* 3.4 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 216 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188K VAL* 4.1 9.6 - - + -
200K LEU* 3.8 33.2 - - + -
202K CYS* 3.4 38.4 - - + -
214K THR* 3.8 8.2 - - + +
215K LYS* 1.3 74.4 - - - +
217K ILE* 1.3 60.7 + - - +
236K GLU 2.7 33.8 + - - +
237K TRP* 3.4 20.2 + - + +
239K ARG* 5.2 8.1 - - + -
267K ASP* 2.7 34.7 + - - -
269K VAL* 3.0 31.6 - - + +
279K PRO* 3.7 30.7 - - + -
280K VAL 3.5 12.6 - - - -
281K CYS* 3.8 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 217 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215K LYS* 4.5 9.9 - - + +
216K TRP* 1.3 82.4 - - - +
218K GLU* 1.3 73.7 + - - +
221K HIS* 3.9 14.8 - - + -
222K PHE* 3.7 19.3 - - + -
228K TYR* 4.0 16.4 - - + -
234K TYR* 3.8 25.1 - - + -
235K PRO 3.5 21.3 - - - +
236K GLU* 4.2 8.3 - - + +
279K PRO* 3.8 4.3 - - - -
280K VAL* 2.8 40.6 + - + +
282K VAL* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217K ILE* 1.3 76.5 - - - +
219K SER* 1.3 67.1 + - - +
220K GLU* 3.0 22.2 + - + +
221K HIS* 3.1 34.8 + - + +
222K PHE* 4.0 0.9 - - - -
235K PRO 5.1 0.4 + - - -
237K TRP* 3.7 36.4 - - + +
275K MET* 3.8 21.7 - - + +
276K SER* 3.5 16.0 + - - -
277K SER* 3.5 15.5 + - - +
278K GLN 4.6 3.4 - - - +
279K PRO* 3.9 9.1 - - - +
----------------------------------------------------------
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