Contacts of the strand formed by residues 211 - 219 (chain C) in PDB entry 4LEZ
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 GLU 211 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C TYR* 3.8 18.0 + - - +
205C LYS* 3.9 20.4 - - + +
209C PRO 3.7 1.2 - - - -
210C ASN* 1.3 95.8 + - - +
212C PHE* 1.3 66.9 + - - +
213C ASP* 4.9 6.3 - - - +
305C SER* 3.3 19.0 + - - +
406C GLU* 5.8 0.3 - - - +
602C 1SY 4.1 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C ALA* 4.0 15.7 - - + -
168C ALA* 4.4 10.1 - - - -
171C VAL* 3.7 29.2 - - + -
172C ASN* 6.0 0.4 - - - -
200C TYR* 3.5 47.8 - + - -
201C TYR* 3.4 25.1 - - + +
209C PRO* 3.3 30.1 - - + -
211C GLU* 1.3 77.4 - - - +
213C ASP* 1.3 66.0 + - - +
214C VAL* 5.2 1.3 - - + -
304C ILE* 3.6 24.2 - - + -
305C SER 2.9 8.7 + - - +
306C VAL* 3.3 8.8 - - + +
307C ASP 2.9 25.1 + - - -
11J G 4.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C ASN* 3.6 2.8 - - - -
197C THR* 3.0 52.8 + - - +
198C GLY* 4.3 9.9 - - - -
199C SER 5.4 0.8 + - - -
200C TYR* 5.9 0.2 - - - +
201C TYR* 3.7 5.6 - - - -
211C GLU* 4.9 6.2 - - - +
212C PHE* 1.3 82.6 + - - +
214C VAL* 1.3 66.2 + - - +
307C ASP* 3.8 12.8 - - - +
309C ILE* 4.4 2.5 - - + -
602C 1SY 2.9 47.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C VAL* 5.6 0.4 - - + -
175C VAL* 4.3 23.3 - - + -
194C GLN* 3.9 11.7 - - + -
195C LEU 3.8 3.6 - - - +
196C ASN* 3.3 22.4 - - - +
197C THR* 4.9 0.2 - - - -
201C TYR* 4.9 5.8 - - - +
212C PHE* 4.9 2.7 - - + -
213C ASP* 1.3 83.2 - - - +
215C MET* 1.3 73.2 + - - +
216C PHE* 3.8 22.6 + - + -
306C VAL* 4.6 7.6 - - + -
307C ASP 2.9 11.8 + - - +
308C ILE* 3.6 7.4 - - + +
309C ILE* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C GLU 3.3 2.9 - - - +
195C LEU* 2.8 53.6 + - + +
197C THR* 4.2 9.5 + - + -
214C VAL* 1.3 72.9 - - - +
216C PHE* 1.3 69.9 + - - +
217C LYS* 3.7 2.9 - - + +
309C ILE* 3.2 28.3 - - + +
311C ALA* 3.5 18.6 - - + -
346C TYR* 3.5 46.0 - - + -
366C SER* 4.2 9.9 - - - +
368C SER* 4.2 26.0 - - - -
369C HIS 5.6 0.4 - - - +
602C 1SY 4.4 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C VAL* 4.2 15.7 - - + -
178C LEU* 4.3 10.3 - - + -
179C LEU* 3.8 35.0 - - + -
182C MET* 3.7 27.6 - - + -
192C VAL* 3.9 19.3 - - + -
193C GLU 3.5 6.3 - - - -
194C GLN* 4.7 3.4 - - + -
214C VAL* 3.8 20.1 + - + -
215C MET* 1.3 79.4 - - - +
217C LYS* 1.3 60.9 + - - +
266C PHE* 3.7 33.2 - + + -
270C ILE* 5.2 1.6 - - + -
308C ILE* 3.9 22.7 - - + -
309C ILE 2.9 7.9 + - - -
310C LEU* 3.5 5.9 - - - +
311C ALA 2.9 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 217 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C GLY 4.1 1.7 - - - +
192C VAL* 3.3 4.0 - - - -
193C GLU* 2.9 76.6 + - - +
194C GLN 4.7 3.4 - - - -
195C LEU* 3.9 30.1 - - + -
215C MET* 4.7 4.5 - - + -
216C PHE* 1.3 75.6 - - - +
218C LEU* 1.3 61.1 + - - +
219C GLU 4.2 0.4 - - - -
311C ALA* 3.3 9.9 - - + +
313C GLU* 2.7 30.5 + - + +
346C TYR* 3.6 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C GLU 4.3 13.2 - - - +
189C PHE* 4.3 9.0 - - + +
190C LYS 3.6 23.6 - - - +
191C GLY* 4.1 3.8 - - - -
192C VAL* 3.8 23.8 - - + +
217C LYS* 1.3 75.3 - - - +
219C GLU* 1.3 69.5 + - - +
220C VAL* 2.9 12.6 + - + +
248C LEU* 4.7 11.4 - - + -
262C MET* 3.9 27.1 - - + -
310C LEU* 5.2 3.6 - - + -
311C ALA 2.9 13.5 + - - +
312C LEU* 3.6 9.7 - - + -
313C GLU* 2.9 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C GLY 4.9 1.6 + - - +
193C GLU* 4.8 12.6 + - - +
217C LYS 4.2 1.2 + - - -
218C LEU* 1.3 82.0 - - - +
220C VAL* 1.3 66.7 + - - +
221C PRO* 4.0 6.1 - - + +
313C GLU* 3.8 27.7 - - - +
315C LYS* 3.3 35.1 - - + +
----------------------------------------------------------
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