Contacts of the strand formed by residues 172 - 188 (chain A) in PDB entry 2X1W
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 GLN 172 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A CYS* 3.7 5.1 - - - -
170A GLY 5.0 3.4 - - - +
171A LEU* 1.3 75.9 - - - +
173A CYS* 1.3 71.7 + - - +
174A MET* 3.2 22.7 + - + +
212A MET 2.7 32.0 + - - +
213A SER 6.0 0.9 - - - -
281N SER* 5.7 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A CYS* 2.0 58.1 - - + -
132A MET 3.8 2.0 - - - -
162A CYS* 4.0 16.1 - - - +
163A GLY* 3.6 27.1 - - - -
164A GLY 4.3 14.1 - - - +
166A CYS* 3.5 11.3 - - - -
172A GLN* 1.3 75.6 + - - +
174A MET* 1.3 61.9 + - - +
210A ARG 4.0 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A CYS* 3.7 6.3 - - - -
172A GLN* 3.6 25.1 - - + +
173A CYS* 1.3 80.1 - - - +
175A ASN* 1.3 68.5 + - - +
176A THR* 4.3 1.3 - - - +
209A CYS* 3.1 3.6 - - - -
210A ARG 2.9 35.2 + - - +
212A MET* 3.4 50.0 - - + +
213A SER 3.9 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A CYS* 3.4 8.6 - - - +
174A MET* 1.3 79.7 - - - +
176A THR* 1.3 62.1 + - - +
177A SER 4.4 1.1 - - - +
178A THR* 2.7 11.8 + - - +
206A HIS* 3.4 36.6 + - + +
208A SER 3.3 6.3 - - - +
212A MET* 5.1 2.3 - - - +
1E NAG 1.4 74.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASN* 1.3 77.6 - - - +
177A SER* 1.3 61.5 + - - +
208A SER* 2.7 34.6 + - - -
209A CYS* 3.8 1.7 + - - -
210A ARG* 3.8 48.9 + - + +
212A MET* 4.2 16.2 - - - -
1E NAG 3.6 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASN* 4.4 1.2 - - - +
176A THR* 1.3 82.6 + - - +
178A THR* 1.3 65.0 + - - +
206A HIS* 3.9 2.3 - - - -
207A THR* 2.8 35.4 + - - -
208A SER* 2.7 24.7 + - - +
1E NAG 3.4 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASN* 2.7 31.2 + - - -
177A SER* 1.3 74.8 + - - +
179A SER* 1.3 83.9 + - - +
180A TYR* 4.1 22.0 - - + -
204A ALA* 3.7 17.5 - - + -
205A ASN 3.5 21.1 - - - +
206A HIS* 3.8 4.2 - - + -
207A THR* 4.4 1.3 - - - -
1E NAG 3.0 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR* 1.3 80.7 - - - +
180A TYR* 1.3 75.9 + - - +
181A LEU* 4.7 0.2 - - - +
205A ASN* 2.8 38.7 + - - -
207A THR* 4.0 11.0 + - - +
1F NAG 3.4 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR* 4.1 24.7 - - + +
179A SER* 1.3 80.9 + - - +
181A LEU* 1.3 67.6 + - - +
182A SER 4.0 1.4 + - - -
202A SER* 4.8 16.4 - - - +
203A PHE* 3.6 8.1 - - - -
204A ALA* 3.8 27.6 - - + -
1E NAG 3.8 10.4 + - - -
2E NAG 3.7 40.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A SER 5.0 1.6 - - - +
159A VAL* 4.6 6.3 - - + -
179A SER* 4.7 0.9 - - - +
180A TYR* 1.3 79.3 - - - +
182A SER* 1.3 65.2 + - - +
183A LYS* 3.5 30.3 + - + +
201A ILE 3.5 1.4 - - - +
202A SER* 3.2 5.7 - - - -
203A PHE* 3.0 36.7 + - + +
205A ASN* 3.9 31.6 - - + +
1F NAG 3.4 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A TYR 4.0 2.2 + - - -
181A LEU* 1.3 73.0 - - - +
183A LYS* 1.3 64.9 + - - +
200A THR* 3.8 19.2 - - - +
201A ILE 3.6 4.5 - - - -
202A SER* 3.7 13.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A VAL* 3.7 26.5 - - + -
158A SER 3.4 24.6 + - - -
159A VAL* 4.0 13.2 - - - -
181A LEU* 4.1 25.1 - - + +
182A SER* 1.3 79.5 - - - +
184A THR* 1.3 64.6 + - - +
185A LEU* 4.2 2.2 + - + +
199A VAL 3.8 0.5 - - - +
200A THR* 3.6 2.9 - - - +
201A ILE* 2.9 33.5 + - - +
203A PHE* 4.0 19.2 - - + -
125B GLU* 2.9 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LYS* 1.3 76.3 - - - +
185A LEU* 1.3 74.1 + - - +
186A PHE* 6.3 0.4 - - + -
198A PRO* 4.6 14.6 - - + -
199A VAL 3.5 9.6 - - - +
200A THR* 3.1 21.1 + - - +
118B ILE* 5.1 12.1 - - + +
121B SER* 4.3 11.9 + - - -
122B ILE* 3.4 27.3 - - + +
125B GLU* 5.3 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A VAL* 4.0 9.0 - - + -
152A PHE* 4.0 18.8 - - + -
153A LYS 3.4 9.4 - - - +
154A PRO* 3.5 35.0 - - + +
157A VAL* 3.6 31.2 - - + -
183A LYS* 5.1 3.6 - - + +
184A THR* 1.3 81.1 - - - +
186A PHE* 1.3 65.8 + - - +
198A PRO* 3.4 4.7 - - - +
199A VAL* 2.9 47.8 + - + +
201A ILE* 4.3 13.2 - - + -
203A PHE* 5.2 2.7 - - + -
122B ILE* 4.4 7.0 - - + -
125B GLU* 5.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PHE* 3.6 6.8 - - - -
153A LYS* 2.9 43.9 + - + +
184A THR* 6.3 0.7 - - + -
185A LEU* 1.3 74.2 - - - +
187A GLU* 1.3 60.6 + - - +
188A ILE 4.2 0.4 - - - -
196A PRO* 3.9 24.2 - - + -
197A LYS 3.4 4.3 - - - -
198A PRO* 3.6 42.2 - - + -
199A VAL* 4.5 1.6 - - - -
118B ILE 5.9 0.2 - - - -
119B LEU* 5.4 9.9 - - + -
122B ILE* 3.3 35.0 - - + -
126B TRP* 5.8 0.4 - + - -
215M ILE* 3.5 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A THR* 3.6 32.6 + - + +
151A PHE 3.5 4.3 - - - -
152A PHE* 4.3 10.1 - - + -
186A PHE* 1.3 74.4 - - - +
188A ILE* 1.3 64.5 + - - +
189A THR* 3.9 3.8 + - - +
195A GLY 4.5 0.3 - - - +
196A PRO* 3.5 1.8 - - - +
197A LYS* 2.7 64.4 + - - +
199A VAL* 3.1 32.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ASN 3.7 0.3 - - - +
150A THR* 3.2 5.5 - - - +
151A PHE* 2.7 49.6 + - + +
153A LYS* 3.7 26.2 - - + -
186A PHE 4.2 0.2 - - - -
187A GLU* 1.3 74.0 - - - +
189A THR* 1.3 73.9 + - - +
190A VAL* 5.4 2.5 - - + -
192A LEU* 4.2 16.6 - - + -
194A GLN 5.8 2.5 - - - +
195A GLY 5.7 0.4 - - - -
196A PRO* 4.0 28.7 - - + -
135M VAL* 5.1 0.7 - - + -
137M TYR* 4.8 6.1 - - - +
215M ILE* 4.7 0.4 - - + -
217M VAL* 3.1 45.3 - - + -
----------------------------------------------------------
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