Contacts of the strand formed by residues 171 - 189 (chain C) 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 LEU 171 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C CYS* 3.5 27.0 - - + +
167C ASN 5.2 1.3 - - - +
168C SER* 3.9 28.6 - - - +
169C GLU 3.0 9.7 + - - +
170C GLY* 1.3 78.9 + - - +
172C GLN* 1.3 59.7 + - - +
211C CYS* 4.0 23.3 - - + +
212C MET* 3.0 26.5 - - - +
213C SER* 3.8 9.4 - - - +
214C LYS* 4.1 3.0 + - - -
193L SER* 5.1 1.3 - - - +
194L TYR* 4.5 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C CYS* 3.5 4.9 - - - -
170C GLY 3.9 0.2 + - - -
171C LEU* 1.3 75.2 - - - +
173C CYS* 1.3 71.4 + - - +
174C MET* 3.2 34.9 + - + +
212C MET 2.6 30.6 + - - +
214C LYS* 3.1 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C CYS* 2.0 58.1 - - + -
132C MET 3.9 1.1 - - - -
162C CYS* 3.9 16.3 - - - +
163C GLY* 3.6 26.5 - - - -
164C GLY 4.3 16.2 - - - +
166C CYS* 3.4 9.3 - - - -
172C GLN* 1.3 77.6 + - - +
174C MET* 1.3 62.8 + - - +
210C ARG 4.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C CYS* 3.8 5.8 - - - -
172C GLN* 3.2 47.1 - - + +
173C CYS* 1.3 79.7 - - - +
175C ASN* 1.3 65.1 + - - +
176C THR* 3.6 1.6 + - - +
209C CYS* 3.3 2.1 - - - -
210C ARG 3.0 33.3 + - - +
212C MET* 3.6 33.9 - - + -
213C SER 4.7 6.5 - - - +
214C LYS* 4.4 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C CYS* 3.4 19.6 - - - +
174C MET* 1.3 77.8 - - - +
176C THR* 1.3 61.1 + - - +
177C SER 4.1 3.4 - - - +
178C THR* 4.1 1.4 - - - -
206C HIS* 3.3 29.5 + - + +
208C SER 3.3 7.2 - - - +
212C MET* 5.3 2.9 - - - +
1I NAG 1.4 80.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C MET 3.6 0.6 + - - +
175C ASN* 1.3 75.2 - - - +
177C SER* 1.3 63.9 + - - +
208C SER* 2.7 34.0 + - - -
209C CYS* 3.6 4.3 + - - -
210C ARG* 3.4 51.5 + - + +
212C MET* 4.3 9.9 - - - -
1I NAG 3.6 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ASN* 4.1 2.1 - - - +
176C THR* 1.3 83.3 - - - +
178C THR* 1.3 64.3 + - - +
206C HIS* 3.8 2.4 - - - -
207C THR* 2.7 41.3 + - - -
208C SER* 2.6 26.7 + - - +
1I NAG 3.2 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C SER* 1.3 78.3 - - - +
179C SER* 1.3 65.3 + - - +
180C TYR* 4.2 20.8 - - + -
204C ALA* 3.9 2.1 - - - +
205C ASN 2.6 31.7 + - - -
206C HIS* 3.5 16.4 - - - -
207C THR* 3.8 7.2 + - - -
1I NAG 3.4 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C THR* 1.3 79.3 + - - +
180C TYR* 1.3 77.4 + - - +
181C LEU* 4.9 0.5 - - - +
204C ALA* 3.5 3.5 - - - -
205C ASN* 2.7 39.4 + - - -
207C THR* 4.2 6.1 - - - -
1J NAG 3.7 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C THR* 4.2 17.3 - - + -
179C SER* 1.3 88.8 + - - +
181C LEU* 1.3 65.0 + - - +
182C SER 4.2 0.9 + - - -
202C SER* 4.2 19.5 - - - +
203C PHE* 3.3 21.5 - - - -
204C ALA* 3.7 19.7 - - + -
1I NAG 4.1 6.4 - - - -
2I NAG 3.3 49.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C SER 4.9 1.1 - - - +
159C VAL* 4.3 14.8 - - + -
179C SER* 4.9 1.6 - - - +
180C TYR* 1.3 78.4 - - - +
182C SER* 1.3 63.0 + - - +
183C LYS* 3.7 26.9 + - - +
201C ILE 3.5 1.2 - - - +
202C SER* 3.3 4.4 - - - -
203C PHE* 2.9 32.5 + - - +
205C ASN* 3.7 36.6 - - + +
1J NAG 3.7 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C TYR 4.2 1.6 + - - -
181C LEU* 1.3 73.6 - - - +
183C LYS* 1.3 66.6 + - - +
200C THR* 4.1 18.7 - - - +
201C ILE 3.7 4.7 - - - -
202C SER* 3.4 15.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C VAL* 3.5 26.0 - - + -
158C SER 3.2 24.9 + - - -
159C VAL* 3.7 15.5 - - - -
181C LEU* 4.0 24.7 - - - +
182C SER* 1.3 81.7 + - - +
184C THR* 1.3 64.0 + - - +
185C LEU* 3.7 9.8 - - + +
200C THR* 3.3 4.9 - - - -
201C ILE 3.0 33.9 + - - +
203C PHE* 4.1 11.7 - - + -
125D GLU* 3.3 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C LYS* 1.3 73.9 - - - +
185C LEU* 1.3 73.0 + - - +
186C PHE* 5.4 3.1 - - + -
198C PRO* 4.8 10.5 - - + -
199C VAL 3.5 13.5 - - - +
200C THR* 3.6 17.3 + - - +
118D ILE* 4.2 26.5 - - + +
121D SER* 6.0 1.3 + - - -
122D ILE* 3.8 36.6 - - + +
125D GLU* 5.9 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C VAL* 4.7 12.3 - - + -
152C PHE* 4.4 10.3 - - + -
153C LYS 4.2 2.5 - - - +
154C PRO* 3.7 36.6 - - + +
156C CYS 4.6 0.4 - - - +
157C VAL* 3.6 24.2 - - + -
183C LYS* 3.7 17.9 - - + +
184C THR* 1.3 81.1 - - - +
186C PHE* 1.3 67.3 + - - +
187C GLU 4.2 0.2 - - - -
198C PRO* 3.6 4.2 - - - +
199C VAL* 2.9 41.3 + - + +
201C ILE* 4.5 8.7 - - + -
203C PHE* 3.9 27.4 - - + -
125D GLU* 5.1 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C PHE* 3.4 5.9 - - - -
153C LYS* 2.7 55.5 + - + +
184C THR* 5.4 2.9 - - + -
185C LEU* 1.3 76.5 - - - +
187C GLU* 1.3 62.5 + - - +
188C ILE* 5.2 0.2 - - - -
196C PRO* 4.0 22.2 - - + -
197C LYS 3.4 3.4 - - - -
198C PRO* 4.0 34.5 - - + -
119D LEU* 5.4 5.4 - - + -
122D ILE* 4.0 37.2 - - + -
126D TRP* 4.8 3.6 - + - -
133O HIS* 3.9 30.7 - + + -
213O MET* 5.3 4.0 - - + -
215O ILE* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C VAL* 5.4 0.5 - - - +
150C THR* 3.4 32.1 + - + +
151C PHE 3.6 4.3 - - - +
152C PHE* 3.5 24.6 - - + -
185C LEU 4.2 0.6 - - - -
186C PHE* 1.3 73.7 - - - +
188C ILE* 1.3 67.8 + - - +
189C THR* 4.4 4.7 + - - +
195C GLY 4.3 1.2 - - - +
196C PRO* 3.3 5.2 - - - +
197C LYS* 2.7 74.4 + - + +
199C VAL* 4.2 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ASN 3.8 0.2 - - - +
150C THR* 3.4 3.8 - - - +
151C PHE* 2.8 43.2 + - + +
153C LYS* 3.9 23.8 - - + -
186C PHE 5.0 0.2 - - - +
187C GLU* 1.3 81.7 - - - +
189C THR* 1.3 69.6 + - - +
190C VAL* 4.6 7.0 - - + -
192C LEU* 3.2 29.8 - - + -
194C GLN 5.9 0.7 - - - -
195C GLY 4.8 2.7 - - - -
196C PRO* 3.7 32.8 - - + -
137O TYR* 5.8 0.4 - - + -
217O VAL* 3.8 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 189 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ASN* 3.4 39.7 - - - +
150C THR* 3.8 10.7 + - - +
187C GLU* 4.4 8.8 + - - +
188C ILE* 1.3 79.0 + - - +
190C VAL* 1.3 68.1 + - - +
191C PRO 3.2 14.7 - - - +
192C LEU* 3.4 14.1 - - - +
193C SER 4.5 1.2 + - - -
194C GLN* 5.3 5.0 + - - +
197C LYS* 5.7 2.8 + - - -
----------------------------------------------------------
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