Contacts of the helix formed by residues 203 - 212 (chain U) in PDB entry 5IYB
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 ASN 203 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197U ASN 5.2 1.6 - - - +
200U ASP* 3.5 28.4 + - + +
202U LYS* 1.3 82.8 - - - +
204U PRO* 1.3 61.8 - - - +
205U ASN* 3.4 11.6 + - - +
206U LEU* 3.2 41.7 + - + +
207U ARG* 4.2 2.9 + - - +
228U MET 4.9 0.4 + - - -
229U ALA* 4.1 17.0 + - - +
230U SER 3.2 23.1 + - - -
231U ASP* 3.7 12.2 - - - +
232U GLU 5.8 1.1 - - - -
233U LEU* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 204 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157U ASP* 4.4 1.1 - - - +
200U ASP 4.1 1.5 - - - +
201U ALA* 3.9 11.2 - - - +
202U LYS 3.7 5.6 - - - +
203U ASN* 1.3 87.3 - - - +
205U ASN* 1.3 62.8 + - + +
206U LEU 3.1 2.9 - - - -
207U ARG* 3.1 37.5 + - - +
208U LYS* 2.9 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 205 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203U ASN* 3.2 5.1 - - - +
204U PRO* 1.3 80.2 - - + +
206U LEU* 1.3 56.8 + - - +
208U LYS* 3.9 21.5 - - + +
209U ASN* 2.6 53.0 + - - +
231U ASP* 3.1 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197U ASN* 3.1 37.0 - - - +
198U LEU* 5.5 5.4 - - + -
200U ASP* 6.5 0.2 - - + -
203U ASN* 3.2 33.0 + - + +
205U ASN* 1.3 75.7 - - - +
207U ARG* 1.3 60.7 + - - +
209U ASN* 3.0 8.6 + - + +
210U VAL* 2.9 31.7 + - + +
215U ILE* 4.3 14.1 - - + -
220U PHE* 6.1 1.6 - - + -
228U MET* 3.8 42.4 - - + +
229U ALA* 5.5 0.2 - - - -
230U SER* 5.2 9.0 - - - +
231U ASP* 3.9 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 207 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151U ALA 4.3 7.4 - - - -
152U LEU* 3.9 30.3 - - + +
154U THR* 3.2 32.1 + - - +
155U GLY* 4.7 3.2 - - - -
157U ASP* 2.7 28.7 + - - +
198U LEU* 3.0 40.7 + - + +
199U LYS 4.9 0.6 - - - -
200U ASP 3.9 15.2 + - - -
203U ASN 4.2 1.6 + - - +
204U PRO* 3.1 26.6 + - - +
206U LEU* 1.3 75.4 - - - +
208U LYS* 1.3 55.5 + - - +
210U VAL* 3.2 7.2 + - - +
211U LEU* 2.7 53.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 208 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157U ASP* 2.4 41.8 + - + +
161U ILE* 4.0 8.9 - - + +
204U PRO* 2.9 34.1 + - - +
205U ASN* 3.8 22.2 - - - +
207U ARG* 1.3 75.3 - - - +
209U ASN* 1.3 57.8 + - - +
211U LEU* 3.8 9.5 - - - +
212U CYS* 3.0 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 209 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205U ASN* 2.6 42.2 + - - +
206U LEU* 3.0 13.9 + - + +
208U LYS* 1.3 77.8 - - - +
210U VAL* 1.3 60.6 + - - +
212U CYS* 3.2 21.5 - - - -
214U ASN* 3.3 40.1 + - - +
215U ILE* 3.7 17.1 + - + +
231U ASP* 3.5 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 210 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152U LEU* 4.7 12.6 - - + -
168U LEU* 3.8 26.5 - - + +
172U ILE* 5.1 7.0 - - + -
198U LEU* 4.6 8.5 - - + -
206U LEU* 2.9 25.3 + - + +
207U ARG* 3.5 7.6 - - - +
209U ASN* 1.3 76.6 - - - +
211U LEU* 1.3 62.8 + - + +
213U GLY* 3.2 14.4 + - - -
215U ILE* 4.1 35.4 - - + +
220U PHE* 4.3 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152U LEU* 4.3 22.9 - - + +
157U ASP* 3.8 13.0 - - + -
158U TYR* 3.6 43.7 - - + +
161U ILE* 3.7 18.1 - - + +
163U ALA* 3.5 29.1 - - + +
165U GLU* 4.3 13.7 - - + -
168U LEU* 4.7 10.3 - - + +
207U ARG* 2.7 45.3 + - + +
208U LYS* 3.8 2.7 - - - +
210U VAL* 1.3 73.3 - - - +
212U CYS* 1.3 58.6 + - - +
213U GLY 3.2 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 212 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161U ILE* 4.1 19.5 - - + -
208U LYS 3.0 16.0 + - - +
209U ASN* 3.2 26.2 - - - -
210U VAL 3.2 0.4 - - - -
211U LEU* 1.3 76.7 - - - +
213U GLY* 1.3 58.7 + - - +
214U ASN* 3.5 16.6 + - - -
----------------------------------------------------------
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