Contacts of the strand formed by residues 203 - 210 (chain A) in PDB entry 1I9R
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 ARG 203 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A CYS* 3.5 7.4 - - - +
195A LEU* 3.0 36.9 + - + +
201A PHE 4.3 2.5 - - - +
202A GLU* 1.3 82.6 - - - +
204A ILE* 1.3 88.3 + - - +
205A LEU* 4.4 4.7 + - + -
127C ILE* 6.0 1.0 - - - +
144C GLY* 4.1 4.9 - - - -
145C TYR* 3.1 63.0 - - + +
251C THR* 4.6 13.1 + - - -
97Y GLU* 4.2 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A SER* 4.2 8.7 - - - +
193A LEU 4.0 4.7 - - - +
194A CYS* 4.1 13.5 - - - +
203A ARG* 1.3 105.2 + - - +
205A LEU* 1.3 66.6 + - - +
206A LEU 3.8 20.4 - - - +
207A ARG* 3.7 39.0 - - + +
251C THR* 4.1 19.9 + - - +
252C GLY* 4.5 2.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ILE* 4.8 2.2 - - + -
193A LEU* 3.0 24.3 + - + +
195A LEU* 3.6 36.8 - - + +
203A ARG* 4.4 2.7 - - + +
204A ILE* 1.3 82.7 - - - +
206A LEU* 1.3 70.1 + - + +
229A PHE* 3.8 42.2 - - + -
231A LEU* 5.2 0.9 - - + -
237A VAL* 4.5 8.3 - - + -
125C HIS* 5.3 1.7 + - - -
145C TYR* 3.5 44.0 - - + -
252C GLY* 3.3 14.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A SER* 3.3 0.9 - - - -
193A LEU* 2.8 63.8 + - + +
204A ILE* 3.8 1.1 - - - +
205A LEU* 1.3 81.7 - - - +
207A ARG* 1.3 70.5 + - - +
225A LEU* 3.8 25.4 - - + +
226A GLY 3.1 30.1 - - - +
229A PHE* 2.9 35.2 - - + -
125C HIS* 4.2 11.2 - - + +
174C GLN* 5.2 3.4 - - + +
252C GLY 3.1 8.7 - - - +
255C SER* 4.6 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ILE* 2.8 35.8 - - + +
191A ALA 3.1 6.5 - - - +
192A SER* 3.1 23.2 + - - +
204A ILE* 3.7 24.1 - - + +
206A LEU* 1.3 85.0 - - - +
208A ALA* 1.3 60.0 + - - +
225A LEU* 3.7 6.0 - - - +
174C GLN* 3.6 8.4 + - - +
250C GLY 5.6 0.2 - - - -
251C THR* 3.8 19.1 + - - +
252C GLY 2.6 21.0 + - - +
253C PHE* 3.4 45.8 - - + +
59X ASN* 5.7 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PHE 3.9 0.2 - - - +
190A ILE* 3.2 1.9 - - - +
191A ALA 2.8 29.7 + - - +
207A ARG* 1.3 73.1 - - - +
209A ALA* 1.3 65.2 + - - +
223A ILE* 3.6 27.8 - - + -
224A HIS 4.8 2.7 - - - +
225A LEU* 3.2 22.8 - - + +
174C GLN* 3.6 8.3 - - - +
222C SER* 3.2 15.3 - - - +
253C PHE* 4.4 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PRO* 4.7 2.5 - - + -
189A PHE 3.3 7.0 - - - +
190A ILE* 3.6 26.5 - - + -
208A ALA* 1.3 78.1 - - - +
210A ASN* 1.3 63.9 + - - +
223A ILE* 4.0 1.7 - - - +
176C THR* 4.9 0.6 + - - +
220C GLN* 3.3 14.5 - - + +
221C GLN* 3.1 29.3 + - - -
222C SER* 3.2 8.3 + - - -
253C PHE* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PHE* 4.1 9.9 - - + -
188A PRO* 2.9 21.6 - - - +
189A PHE* 3.1 15.8 + - - -
209A ALA* 1.3 81.3 + - - +
211A THR* 1.3 64.7 + - - +
212A HIS 4.0 0.4 + - - -
221A GLN* 3.0 36.7 + - - +
222A SER 4.2 15.1 + - - +
223A ILE* 3.6 19.0 - - - +
210B ASN* 5.0 5.5 - - - +
210C ASN* 5.1 4.6 - - - +
220C GLN 3.7 5.8 - - - -
221C GLN* 4.3 11.9 + - - +
222C SER* 3.8 16.3 + - - +
----------------------------------------------------------
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