Contacts of the strand formed by residues 180 - 193 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B TYR* 3.4 6.3 - - - -
177B VAL 2.9 31.8 + - - +
178B ASP* 4.2 7.6 - - + +
179B GLY* 1.3 79.2 - - - +
181B PRO* 1.3 79.0 - - + +
182B HIS* 3.3 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLU* 4.2 24.2 - - + +
140B LEU* 3.7 32.1 - - + -
174B VAL* 4.0 7.4 - - + -
175B ARG 3.6 7.0 - - - +
176B TYR* 3.9 23.3 - - + -
180B LYS* 1.3 88.6 - - + +
182B HIS* 1.3 60.3 + - - +
219B LEU* 4.0 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ARG* 2.8 36.7 + - + +
177B VAL* 3.7 37.5 - - + +
180B LYS 3.3 0.6 + - - +
181B PRO* 1.3 74.2 - - - +
183B SER* 1.3 65.0 + - - +
219B LEU* 3.8 9.5 - - - +
221B LYS* 2.8 52.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B VAL* 3.4 9.3 - - - +
175B ARG* 2.9 45.1 + - - +
182B HIS* 1.3 92.2 + - - +
184B ILE* 1.3 68.6 + - - +
185B ASP* 4.0 1.4 + - - -
219B LEU* 3.2 19.0 - - - +
221B LYS* 3.8 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 3.5 23.8 - - + -
172B VAL* 4.1 6.1 - - + -
173B THR 3.8 11.7 - - - +
174B VAL* 4.6 6.5 - - + -
183B SER* 1.3 77.6 - - - +
185B ASP* 1.3 67.1 + - - +
186B THR 4.3 2.7 - - - +
187B VAL* 3.6 29.4 - - + -
215B LEU* 3.4 32.3 - - + -
216B PRO* 4.3 10.3 - - + +
219B LEU* 3.1 24.3 + - + +
220B ILE* 5.7 0.4 - - + -
221B LYS 5.5 1.0 + - - -
223B ASP 4.6 0.9 - - - +
224B ILE* 3.4 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A THR* 5.1 3.8 - - - +
6B LEU* 3.8 42.1 - - + +
173B THR* 2.9 18.5 + - + +
175B ARG* 4.6 3.5 - - + +
183B SER* 4.0 5.6 + - - -
184B ILE* 1.3 73.6 - - - +
186B THR* 1.3 80.7 + - - +
223B ASP* 3.5 9.5 - - - +
224B ILE* 3.4 2.4 - - - -
225B LYS* 2.9 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A THR* 6.1 1.8 - - - -
171B GLN* 3.9 1.6 - - - +
172B VAL* 3.7 1.6 - - - -
173B THR* 2.8 42.1 + - - +
184B ILE* 4.3 0.6 - - - +
185B ASP* 1.3 97.4 + - - +
187B VAL* 1.3 69.3 + - - +
188B VAL* 3.8 26.0 - - + -
224B ILE* 5.3 0.2 - - - -
225B LYS* 3.3 30.1 + - + +
227B LEU* 4.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 3.3 32.5 - - + -
171B GLN 3.4 6.7 - - - +
172B VAL* 4.2 3.6 - - + -
184B ILE* 3.6 23.8 - - + -
186B THR* 1.3 76.9 - - - +
188B VAL* 1.3 67.6 + - - +
189B LEU* 4.2 1.1 + - + -
211B ILE* 4.0 27.7 - - + +
215B LEU* 3.9 22.9 - - + -
224B ILE* 4.7 5.2 - - + -
225B LYS 3.1 8.7 + - - +
226B PHE* 3.7 4.7 - - + +
227B LEU 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLN* 3.9 15.5 - - + +
305A ALA* 4.9 7.0 - - + -
306A ILE* 5.2 4.9 - - + +
169B LYS 5.6 0.2 - - - +
170B SER* 3.3 4.0 - - - -
171B GLN* 2.7 63.4 + - + +
186B THR* 3.8 9.9 - - + -
187B VAL* 1.3 77.5 - - - +
189B LEU* 1.3 65.6 + - - +
190B SER* 4.6 4.0 - - - +
227B LEU* 3.3 37.5 - - + +
230B PRO* 4.1 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 4.2 24.0 - - + +
149B VAL* 5.6 2.0 - - + -
152B GLN* 5.2 5.4 - - + -
168B ALA* 5.0 5.2 - - + -
169B LYS 3.3 10.5 - - - +
170B SER* 4.7 2.9 - - - -
187B VAL* 4.2 2.0 + - + -
188B VAL* 1.3 74.1 - - - +
190B SER* 1.3 76.3 + - - +
191B THR* 4.0 15.0 - - + -
206B VAL* 4.0 24.5 - - + -
210B VAL* 3.5 32.5 - - + -
211B ILE* 4.3 15.0 - - + -
227B LEU 3.0 8.5 + - - -
228B VAL* 3.3 11.7 - - + +
229B ASN 3.1 19.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLN* 5.5 0.5 + - - -
306A ILE* 4.0 16.6 - - - +
168B ALA* 3.3 3.6 - - - +
169B LYS* 2.8 46.2 + - - +
188B VAL* 4.3 3.6 - - - +
189B LEU* 1.3 73.6 - - - +
191B THR* 1.3 60.8 + - - +
229B ASN* 3.3 10.7 - - - +
230B PRO* 3.6 22.5 - - - +
231B THR* 5.6 1.4 + - - -
234B PHE* 4.3 15.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLN* 3.0 28.9 + - - -
164B LEU* 3.4 18.8 - - + +
167B ASP 3.8 4.9 + - - -
168B ALA* 4.1 1.1 - - - -
189B LEU* 4.0 10.1 - - + -
190B SER* 1.3 75.5 - - - +
192B GLN* 1.3 75.2 + - - +
193B HIS* 3.7 2.8 - - - -
202B LEU* 4.2 11.9 - - + -
206B VAL* 4.1 20.4 - - + -
229B ASN* 2.8 33.5 + - - +
234B PHE* 3.2 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TYR* 3.6 15.5 + - - -
164B LEU* 4.0 1.6 - - - -
165B ARG* 3.2 39.5 + - + +
166B PRO* 3.5 4.0 - - - +
167B ASP* 2.8 44.1 + - + +
191B THR* 1.3 86.9 + - - +
193B HIS* 1.3 66.2 - - - +
234B PHE* 3.1 27.5 - - + +
235B VAL 2.9 24.4 + - - +
236B ILE* 4.0 0.2 - - - +
237B GLY* 3.0 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B TRP* 3.2 20.2 - - + +
165B ARG* 3.5 16.1 + - - -
191B THR 3.7 9.6 - - - -
192B GLN* 1.3 77.7 - - - +
194B ALA* 1.3 86.0 + - - +
195B PRO* 3.8 1.7 - - + -
197B ILE* 3.5 18.8 - - + +
199B LEU* 4.3 9.4 - - + +
202B LEU* 3.4 31.9 - - + +
229B ASN* 4.0 2.4 + - - -
233B ARG* 3.8 11.3 - - + -
234B PHE* 2.9 42.3 + - + -
235B VAL* 3.5 33.3 - - + -
----------------------------------------------------------
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