Contacts of the strand formed by residues 180 - 193 (chain C) in PDB entry 3IML
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 LYS 180 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C TYR* 3.5 5.5 - - - -
177C VAL 3.1 28.7 + - - +
178C ASP 3.2 6.5 + - - +
179C GLY* 1.3 79.3 - - - +
181C PRO* 1.3 79.7 - - + +
182C HIS* 4.2 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C GLU* 4.1 28.7 - - + +
140C LEU* 3.7 31.4 - - + -
174C VAL* 4.2 6.7 - - + -
175C ARG 4.0 2.7 - - - +
176C TYR* 3.6 25.3 - - + -
180C LYS* 1.3 88.9 - - + +
182C HIS* 1.3 59.8 + - - +
219C LEU* 4.2 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ARG* 3.0 31.9 + - + +
177C VAL* 3.6 41.4 - - + +
180C LYS 3.2 0.6 + - - +
181C PRO* 1.3 74.1 - - - +
183C SER* 1.3 71.6 + - - +
218C ASP 4.4 0.2 - - - +
219C LEU* 3.5 16.6 - - - +
221C LYS* 3.7 38.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C VAL* 3.4 8.8 - - - +
175C ARG* 2.9 49.7 + - - +
181C PRO 4.0 0.2 - - - -
182C HIS* 1.3 94.0 - - - +
184C ILE* 1.3 69.1 + - - +
185C ASP* 4.2 2.3 + - - -
219C LEU* 3.4 10.0 - - - +
221C LYS* 3.7 22.9 - - - -
223C ASP* 5.4 7.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 3.8 20.0 - - + -
172C VAL* 4.4 5.8 - - + -
173C THR 3.9 9.9 - - - +
174C VAL* 4.6 7.6 - - + +
183C SER* 1.3 75.9 + - - +
185C ASP* 1.3 62.7 + - - +
186C THR 4.2 4.0 - - - +
187C VAL* 3.7 28.0 - - + -
215C LEU* 3.4 37.0 - - + -
216C PRO* 4.1 7.4 - - + -
219C LEU* 3.0 29.4 + - + +
220C ILE* 4.4 1.8 - - + -
221C LYS* 5.4 1.2 + - - +
223C ASP* 4.8 1.0 - - - +
224C ILE* 3.4 34.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 3.8 36.6 - - + +
173C THR* 2.9 21.8 + - + +
175C ARG* 4.5 4.7 - - + +
183C SER* 3.6 6.2 + - - +
184C ILE* 1.3 73.3 - - - +
186C THR* 1.3 82.1 + - - +
223C ASP* 3.4 20.8 - - - +
224C ILE* 3.7 2.5 - - - -
225C LYS* 3.0 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C GLN 5.2 0.2 - - - +
172C VAL* 3.5 3.3 - - - -
173C THR* 2.8 42.6 + - - +
184C ILE* 4.2 1.0 - - - +
185C ASP* 1.3 100.7 + - - +
187C VAL* 1.3 70.1 + - - +
188C VAL* 3.8 25.6 - - + -
224C ILE* 5.4 0.2 - - - -
225C LYS* 3.4 26.5 - - + +
227C LEU* 4.4 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C LEU* 3.5 28.0 - - + -
171C GLN 3.5 3.6 - - - +
172C VAL* 4.7 7.9 - - + -
184C ILE* 3.7 21.8 - - + -
186C THR* 1.3 78.6 - - - +
188C VAL* 1.3 69.1 + - - +
189C LEU* 5.1 0.2 - - + -
211C ILE* 3.7 32.8 - - + +
215C LEU* 4.0 21.8 - - + -
224C ILE* 5.0 0.6 - - + +
225C LYS 3.0 9.1 + - - +
226C PHE* 3.5 9.8 - - + -
227C LEU 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C LYS 5.6 0.7 - - - +
170C SER* 3.4 4.2 - - - -
171C GLN* 2.8 54.9 + - + +
186C THR* 3.8 19.1 - - + -
187C VAL* 1.3 81.5 - - - +
189C LEU* 1.3 67.3 + - - +
190C SER* 4.5 6.7 - - - +
227C LEU* 3.2 22.4 - - + +
230C PRO* 4.3 21.8 - - + -
123D GLN* 5.8 5.8 - - + -
304D TYR 5.4 1.3 - - - +
305D ALA* 4.7 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C LEU* 4.0 24.9 - - + +
149C VAL* 5.0 2.9 - - + +
152C GLN* 5.1 7.6 - - + -
168C ALA* 5.2 2.5 - - + -
169C LYS 3.5 9.9 - - - +
170C SER* 4.6 5.2 - - - -
187C VAL* 4.2 0.6 - - + -
188C VAL* 1.3 74.5 - - - +
190C SER* 1.3 65.4 + - - +
191C THR* 4.0 24.0 - - + -
206C VAL* 3.6 20.4 - - + -
210C VAL* 3.4 30.3 - - + -
211C ILE* 4.1 21.3 - - + +
227C LEU 2.9 9.5 + - - -
228C VAL* 3.2 12.2 - - + +
229C ASN* 3.0 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 190 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C ALA* 3.2 5.0 - - - +
169C LYS* 2.8 46.1 + - - +
188C VAL* 4.3 6.0 - - - +
189C LEU* 1.3 72.1 - - - +
191C THR* 1.3 60.0 + - - +
229C ASN* 3.4 8.6 - - - -
230C PRO* 3.6 23.7 - - - +
231C THR* 5.6 2.4 + - - +
234C PHE* 4.1 18.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 191 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C GLN* 2.9 30.1 + - - -
164C LEU* 3.3 19.4 - - + +
167C ASP 3.9 2.7 - - - -
168C ALA* 4.2 0.4 - - - -
189C LEU* 4.0 11.0 - - + -
190C SER* 1.3 74.5 - - - +
192C GLN* 1.3 73.2 + - - +
193C HIS* 3.5 2.1 - - - -
202C LEU* 4.2 15.9 - - + -
206C VAL* 4.2 16.6 - - + -
228C VAL* 5.3 0.2 - - + -
229C ASN* 2.9 36.8 + - - +
234C PHE* 3.4 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 192 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C TYR* 3.6 12.7 + - - -
164C LEU* 4.0 1.7 - - - -
165C ARG* 3.1 41.5 + - + +
166C PRO* 3.5 4.2 - - - +
167C ASP* 2.9 46.5 + - + +
191C THR* 1.3 86.4 + - - +
193C HIS* 1.3 63.0 + - - +
234C PHE* 3.1 24.1 - - + +
235C VAL 3.1 21.9 + - - +
236C ILE* 4.1 0.4 - - - +
237C GLY* 3.1 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 193 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C TRP* 3.1 18.8 - - + +
165C ARG* 3.6 12.8 + - - -
191C THR 3.5 14.1 - - - -
192C GLN* 1.3 78.1 - - - +
194C ALA* 1.3 86.0 + - - +
195C PRO 3.8 0.3 - - - -
197C ILE* 3.8 8.9 - - + +
199C LEU* 4.6 4.2 - - + +
202C LEU* 3.4 30.0 - - + +
229C ASN* 3.8 4.5 + - - -
233C ARG* 3.7 37.9 - - + -
234C PHE 2.9 37.1 + - - -
235C VAL* 3.5 24.7 - - + -
----------------------------------------------------------
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