Contacts of the helix formed by residues 178 - 194 (chain A) in PDB entry 4I5L
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 THR 178 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PHE* 3.7 18.4 - - + +
144A ARG* 3.6 8.4 + - - -
176A ASP* 2.7 27.5 + - - +
177A ASP* 1.3 71.1 - - - +
179A PRO* 1.3 68.8 - - - +
180A MET* 3.3 38.8 - - + +
181A VAL* 3.2 10.8 + - - +
182A ARG* 3.4 9.9 + - - +
357B SER 3.6 11.1 + - - +
358B GLY* 4.1 2.9 - - - -
367B GLN* 3.1 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ASP 3.7 7.2 - - - +
178A THR* 1.3 87.7 - - + +
180A MET* 1.3 71.1 + - - +
182A ARG* 3.3 20.8 + - - +
183A ARG* 2.9 23.9 + - - +
217A GLN* 3.7 39.3 - - + +
220A VAL* 4.1 2.8 - - - +
354B ARG* 4.4 10.1 - - - +
357B SER* 4.0 12.8 - - - +
402B LEU 5.2 4.3 - - - +
403B ASP* 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PHE* 3.7 33.0 - - + -
145A THR* 3.9 4.3 + - - +
178A THR* 3.3 27.2 - - + -
179A PRO* 1.3 82.8 - - - +
181A VAL* 1.3 57.0 + - - +
183A ARG* 3.5 9.6 + - - +
184A ALA* 3.1 25.8 + - - +
354B ARG* 3.6 24.7 - - - +
357B SER* 4.4 1.8 - - - +
359B ALA* 3.7 36.8 - - + +
398B ARG 5.2 0.2 - - - +
401B ASP 4.2 2.5 - - - +
402B LEU 3.3 19.1 - - - +
403B ASP 3.9 11.9 - - - +
404B GLY* 3.7 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PHE* 3.6 42.8 - - + +
144A ARG* 3.9 14.1 - - + +
145A THR* 4.2 6.7 - - - +
148A CYS* 4.6 1.1 - - - -
173A LEU* 3.9 29.2 - - + +
176A ASP* 3.6 39.3 - - + +
178A THR* 3.2 3.0 + - - +
180A MET* 1.3 75.0 - - - +
182A ARG* 1.3 66.9 + - - +
184A ALA* 3.1 3.5 + - - +
185A ALA* 2.9 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU 4.0 7.0 - - - +
174A CYS 3.1 30.1 - - - +
175A SER* 4.6 3.1 - - - +
176A ASP 2.8 27.8 + - - +
177A ASP* 3.6 18.4 + - - +
178A THR 3.4 1.8 + - - +
179A PRO* 3.3 34.1 + - - +
181A VAL* 1.3 77.5 - - - +
183A ARG* 1.3 57.1 + - - +
185A ALA* 3.2 3.6 + - - +
186A ALA* 2.8 30.7 + - - +
212A LEU* 4.2 6.0 - - + +
215A ASP* 3.0 40.0 + - - -
216A GLU* 4.3 18.6 + - - +
217A GLN* 3.9 10.3 - - - +
220A VAL* 4.0 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A THR* 5.1 5.5 + - - +
179A PRO 2.9 14.0 + - - +
180A MET 3.5 19.8 + - - +
182A ARG* 1.3 76.0 - - - +
184A ALA* 1.3 81.8 + - - +
186A ALA* 3.3 1.9 + - - -
187A SER* 3.0 33.1 + - - -
219A SER* 4.0 13.0 - - - +
220A VAL* 3.8 12.7 - - + +
223A LEU* 3.3 33.6 - - + +
403B ASP* 2.4 60.0 + - + +
404B GLY 3.1 19.5 + - - -
405B ASP* 4.4 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A THR* 3.9 24.9 - - + +
148A CYS* 3.9 16.6 - - + -
180A MET 3.1 10.3 + - - +
181A VAL 3.1 8.6 + - - +
183A ARG* 1.3 99.8 - - - +
185A ALA* 1.3 60.1 + - - +
187A SER* 2.7 21.0 + - - -
188A LYS* 3.4 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A CYS* 3.6 17.8 - - - -
170A PHE* 3.8 12.8 - - + -
173A LEU* 4.1 4.7 - - + -
174A CYS* 3.9 37.0 - - - +
181A VAL 2.9 12.6 + - - +
182A ARG 3.7 6.3 - - - +
184A ALA* 1.3 75.0 - - - +
186A ALA* 1.3 66.4 + - - +
188A LYS* 2.9 13.2 + - - -
189A LEU* 3.0 11.3 + - - +
212A LEU* 4.7 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ARG 2.8 17.4 + - - +
183A ARG 3.4 9.2 - - - +
185A ALA* 1.3 71.8 - - - +
187A SER* 1.3 61.5 + - - +
188A LYS 3.2 0.7 + - - -
189A LEU* 3.3 16.8 + - - +
190A GLY 4.6 1.2 + - - -
212A LEU* 3.8 25.4 - - + +
220A VAL* 4.1 16.2 - - + +
223A LEU* 3.9 30.9 - - + +
224A ALA* 5.4 0.7 - - - +
227A ALA* 4.8 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ARG* 3.0 22.9 + - - -
184A ALA* 2.7 22.6 + - - -
186A ALA* 1.3 75.8 - - - +
188A LYS* 1.3 76.2 + - - +
189A LEU 3.5 0.4 + - - -
190A GLY 5.0 1.8 + - - -
191A GLU* 5.4 1.7 + - - +
223A LEU* 4.0 24.2 - - - +
226A GLU* 6.0 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A VAL* 6.0 2.6 - - - +
113A ARG* 5.5 4.4 - - - +
148A CYS* 3.6 29.8 - - + +
149A GLY* 4.1 13.4 - - - +
170A PHE* 4.3 8.5 - - + -
184A ALA 3.4 12.8 - - - +
185A ALA 2.9 7.8 + - - +
187A SER* 1.3 90.2 - - - +
189A LEU* 1.3 66.0 + - - +
190A GLY 3.4 2.5 - - - -
191A GLU* 3.4 34.5 + - + +
192A PHE* 3.0 24.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PHE* 3.8 25.1 - - + -
174A CYS* 4.9 2.2 - - - -
185A ALA 3.0 9.8 + - - +
186A ALA* 3.3 14.7 + - - +
188A LYS* 1.3 77.4 - - - +
190A GLY* 1.3 58.6 + - - +
192A PHE* 3.2 2.4 + - - +
193A ALA* 2.8 31.4 + - - +
205A ILE* 3.8 28.5 - - + -
208A MET* 4.3 13.7 - - + -
209A PHE* 3.6 36.8 - - + +
212A LEU* 4.1 13.5 - - + -
224A ALA* 6.3 0.4 - - - -
227A ALA* 4.0 17.9 - - + -
231A ILE* 4.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ALA 4.6 1.0 + - - -
187A SER 5.0 2.0 + - - -
188A LYS 3.4 0.6 - - - -
189A LEU* 1.3 79.0 - - - +
191A GLU* 1.3 61.9 + - - +
193A ALA* 3.2 8.2 + - - +
194A LYS* 3.1 25.7 + - - +
227A ALA* 4.5 12.6 - - - +
230A ASN* 3.7 33.6 - - - +
231A ILE* 5.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ARG* 2.9 38.0 + - - -
148A CYS 4.9 0.5 - - - +
149A GLY* 4.0 5.5 - - - +
152A SER* 3.6 28.4 + - - +
187A SER 5.4 1.5 + - - +
188A LYS* 3.4 42.6 + - + +
189A LEU 3.3 0.4 - - - -
190A GLY* 1.3 76.2 - - - +
192A PHE* 1.3 65.7 + - - +
194A LYS* 3.3 24.5 + - + +
195A VAL* 3.9 5.0 + - - +
230A ASN* 4.7 1.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
151A PHE* 3.8 27.4 - + + -
152A SER* 4.1 9.0 - - - -
155A TYR* 4.0 21.3 - + + -
166A LEU 4.4 8.3 - - - -
167A ARG* 4.4 10.3 - - + -
170A PHE* 3.5 55.9 - + + -
188A LYS* 3.0 18.7 + - + +
189A LEU 3.6 3.1 - - - +
191A GLU* 1.3 74.9 - - + +
193A ALA* 1.3 65.6 + - - +
195A VAL* 3.1 27.2 + - + +
196A LEU* 3.5 36.1 + - + +
205A ILE* 4.1 12.6 - - + -
208A MET* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU 2.8 17.6 + - - +
190A GLY* 3.5 8.7 - - - +
192A PHE* 1.3 78.3 - - - +
194A LYS* 1.3 60.5 + - - +
195A VAL 3.1 2.0 + - - -
196A LEU* 3.3 11.5 + - - +
201A VAL* 3.5 18.4 - - + +
205A ILE* 3.9 36.5 - - + +
231A ILE* 4.5 6.7 - - + -
234A LEU* 3.6 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A GLY 3.1 11.5 + - - +
191A GLU* 3.6 16.8 - - + +
192A PHE 3.2 0.8 - - - -
193A ALA* 1.3 76.3 - - - +
195A VAL* 1.3 62.8 + - + +
196A LEU 4.8 1.7 - - - +
230A ASN* 3.3 41.0 + - - +
233A GLN* 3.1 25.8 + - - +
234A LEU* 3.8 30.7 - - + +
----------------------------------------------------------
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