Contacts of the strand formed by residues 181 - 193 (chain A) in PDB entry 5IXM
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 PHE 181 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ASP* 3.3 2.4 + - - -
178A VAL* 2.9 41.5 + - - +
179A GLY 3.2 1.8 - - - -
180A PRO* 1.3 92.3 - - + +
182A ASP* 1.3 68.6 - - - +
183A MET* 4.2 11.9 - - + -
211A VAL* 3.7 28.0 - - + -
212A ASN 3.2 16.4 - - - +
213A LEU* 3.9 15.5 - - + -
601A C8E 3.1 87.9 - - + -
386C THR* 5.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LYS 3.7 3.4 - - - -
176A ASN* 3.4 17.1 - - - +
177A ASP* 3.2 13.0 + - - -
180A PRO 4.3 0.2 + - - -
181A PHE* 1.3 73.8 - - - +
183A MET* 1.3 62.0 + - - +
210A THR 3.9 0.5 - - - +
211A VAL* 3.8 1.0 - - - -
212A ASN* 2.9 46.4 + - + +
214A PRO* 3.6 14.1 - - + +
37B ARG* 2.4 49.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A TYR* 4.7 2.0 - - + -
174A TYR* 3.7 1.9 - - - +
175A LYS* 2.9 42.0 + - + +
176A ASN* 5.3 0.7 - - - +
178A VAL* 3.6 40.8 - - + -
181A PHE* 4.6 11.4 - - + -
182A ASP* 1.3 78.5 - - - +
184A HIS* 1.3 63.7 + - - +
185A VAL* 5.8 3.6 - - + -
210A THR 3.3 4.5 - - - +
211A VAL* 4.0 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASN* 3.0 25.6 + - - -
173A TYR* 3.3 12.6 - - - +
174A TYR* 3.3 37.7 - + + -
183A MET* 1.3 77.9 - - - +
185A VAL* 1.3 72.3 + - - +
186A TYR* 4.1 14.1 - - + -
208A GLU* 3.8 3.2 - - - +
209A PRO 3.7 0.7 - - - -
210A THR* 2.9 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A MET 3.9 0.5 - - - +
172A ASN* 3.5 3.5 - - - -
173A TYR* 2.9 52.8 + - + +
183A MET* 5.8 2.7 - - + -
184A HIS* 1.3 82.0 - - - +
186A TYR* 1.3 63.3 + - - +
207A ILE* 3.6 30.1 - - + -
208A GLU 3.6 6.3 - - - +
209A PRO* 4.3 16.8 - - + -
210A THR 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ASP* 2.6 34.6 + - + -
171A MET 3.3 10.5 - - - -
172A ASN* 3.2 31.6 - - - +
184A HIS* 4.0 13.2 - + + +
185A VAL* 1.3 75.7 - - - +
187A GLY* 1.3 71.9 + - - +
188A GLN* 2.9 18.1 + - + -
206A HIS* 4.2 17.5 - + - -
207A ILE* 3.5 6.0 - - - +
208A GLU* 2.9 58.3 + - + +
324A LEU* 5.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU 4.4 0.2 - - - -
170A ASP* 3.5 2.1 - - - -
171A MET* 2.9 40.6 + - - +
186A TYR* 1.3 82.8 - - - +
188A GLN* 1.3 63.0 + - - +
206A HIS 3.2 9.9 - - - -
207A ILE* 4.2 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLN* 4.2 18.4 + - + +
169A LEU 3.1 7.9 - - - +
170A ASP* 2.7 29.3 + - - +
186A TYR* 2.9 20.4 + - + +
187A GLY* 1.3 75.5 - - - +
189A ALA* 1.3 71.0 + - - +
190A ALA* 4.2 4.6 - - - +
204A ARG* 2.7 38.0 + - - +
205A PHE* 3.4 4.3 - - - +
206A HIS* 2.9 46.4 + - + +
304A ASP* 5.6 0.4 + - - -
324A LEU* 3.8 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A PRO* 3.8 2.4 - - - +
168A GLN* 3.6 1.9 - - - -
169A LEU* 2.9 51.0 + - + +
188A GLN* 1.3 75.8 - - - +
190A ALA* 1.3 59.2 + - - +
204A ARG 3.4 4.7 - - - -
205A PHE* 4.0 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ALA* 5.4 0.7 - - + -
167A PRO 3.4 5.2 - - - +
168A GLN* 3.8 21.1 - - + -
188A GLN* 4.2 10.2 - - - +
189A ALA* 1.3 74.8 - - - +
191A LYS* 1.3 60.2 + - - +
192A PHE* 3.7 31.8 - - + -
202A ALA 3.9 0.3 - - - +
203A SER* 3.4 5.0 - - - -
204A ARG* 2.9 36.2 + - - +
205A PHE* 5.7 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ARG 3.4 2.8 - - - +
165A ALA* 3.7 0.3 - - - -
166A GLN* 2.9 49.0 + - - +
167A PRO* 3.1 14.0 + - + -
190A ALA* 1.3 72.9 - - - +
192A PHE* 1.3 62.5 + - - +
193A THR* 3.7 27.2 + - + +
201A GLU* 3.6 26.3 + - - +
202A ALA 3.4 12.4 - - - +
203A SER* 3.4 24.3 + - - +
236A ASP* 4.0 13.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A TYR* 4.0 6.3 - - + -
164A ARG 3.3 15.9 - - - +
165A ALA* 4.1 9.9 - - + -
168A GLN* 4.5 3.6 - - - -
190A ALA* 3.7 22.0 - - + -
191A LYS* 1.3 72.7 - - - +
193A THR* 1.3 65.7 + - - +
201A GLU* 3.4 4.0 - - - -
202A ALA* 2.9 45.3 + - + +
204A ARG* 3.3 59.2 - - + -
303A TYR* 3.7 39.5 - + + -
304A ASP* 4.0 9.6 - - + -
114B LEU* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A TYR* 3.6 5.1 - - - -
164A ARG* 2.8 54.2 + - - +
166A GLN* 5.3 5.2 + - - +
191A LYS* 3.7 23.3 + - + -
192A PHE* 1.3 81.0 - - - +
194A SER* 1.3 62.6 + - - +
201A GLU* 3.5 35.7 - - - +
----------------------------------------------------------
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