Contacts of the helix formed by residues 176 - 184 (chain M) in PDB entry 5IYB
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 176 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165M TYR* 4.1 3.1 - - - -
175M ARG* 1.3 74.4 - - - +
177M PHE* 1.3 58.2 + - - +
178M LYS* 3.5 13.0 + - - +
179M GLU* 2.8 61.9 + - + +
180M ILE* 3.2 7.6 + - - +
214M PHE* 3.9 11.9 - - + -
217M ARG* 5.2 0.2 - - - +
218M PHE* 5.2 6.1 - - + -
251M ILE* 3.7 39.3 - - + -
278M ALA 4.8 7.7 + - - +
286P GLU* 5.1 8.1 - - - -
154T LYS* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 177 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165M TYR* 3.4 53.4 - + - -
175M ARG 4.0 0.6 + - - -
176M THR* 1.3 71.8 - - - +
178M LYS* 1.3 64.0 + - - +
180M ILE* 2.9 8.4 + - + +
181M CYS* 2.9 27.5 + - - -
188M LYS* 4.5 21.1 - - + -
191M ILE* 4.1 27.9 - - + +
192M GLY* 4.6 11.2 - - - -
195M PHE* 4.2 22.4 - + + -
284P GLU* 3.5 22.4 - - + -
286P GLU* 3.1 37.0 + - + +
287P LEU* 5.1 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 178 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176M THR* 3.6 10.7 - - - +
177M PHE* 1.3 77.5 - - - +
179M GLU* 1.3 58.4 + - - +
181M CYS* 3.4 8.5 + - - +
182M ALA 3.1 11.3 + - - -
188M LYS* 4.4 16.4 - - + +
251M ILE* 6.6 0.2 - - + -
278M ALA 4.5 6.3 - - - +
279M GLY* 2.3 47.3 + - - +
280M VAL* 3.4 2.2 - - - +
286P GLU* 4.9 3.1 + - - +
154T LYS* 2.3 37.7 - - + +
156T VAL* 3.5 38.6 - - + +
86Y C 2.4 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 179 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128M ILE* 5.0 13.0 - - + +
175M ARG* 3.4 15.3 - - + -
176M THR* 2.8 50.3 + - - +
178M LYS* 1.3 76.3 - - - +
180M ILE* 1.3 62.1 + - + +
182M ALA* 3.3 16.5 + - - +
183M VAL* 3.5 12.0 + - - +
217M ARG* 2.7 46.1 + - - -
218M PHE* 6.1 2.5 - - - -
154T LYS* 3.2 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 180 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124M MET* 5.7 0.7 - - - -
128M ILE* 4.8 12.3 - - + -
161M SER* 4.1 24.9 - - - +
164M LEU* 4.7 19.1 - - + -
165M TYR* 3.8 38.4 - - + -
168M CYS* 5.5 1.3 - - - -
175M ARG* 4.6 13.5 - - + -
176M THR 3.2 6.9 + - - +
177M PHE* 2.9 9.4 + - + +
179M GLU* 1.3 79.1 - - + +
181M CYS* 1.3 58.2 + - - +
183M VAL* 3.3 7.9 - - + +
184M SER* 2.9 28.5 + - - -
191M ILE* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 181 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LEU* 5.7 0.2 - - - +
177M PHE 2.9 16.2 + - - -
178M LYS 3.8 7.2 - - - +
179M GLU 3.3 0.2 - - - -
180M ILE* 1.3 73.3 - - - +
182M ALA* 1.3 65.1 + - - +
184M SER 2.8 22.1 - - - +
186M ILE 3.7 16.4 - - - +
188M LYS* 3.4 24.7 - - - -
191M ILE* 4.1 5.2 - - - -
155T PRO* 4.7 5.3 - - + +
156T VAL* 3.1 44.0 - - - +
157T ALA* 4.4 3.8 - - - +
158T ASN 5.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B ASN* 5.5 2.4 + - - -
433B LEU* 3.7 13.2 - - - +
127M ARG* 5.6 0.2 - - - -
178M LYS 3.1 5.9 + - - -
179M GLU 3.3 6.5 + - - +
181M CYS* 1.3 78.2 - - - +
183M VAL* 1.3 62.4 + - + +
152T ASN* 4.1 26.9 + - + +
153T TYR 4.1 5.4 - - - -
154T LYS* 3.3 43.7 - - + +
155T PRO* 4.6 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LEU* 3.2 18.7 - - - +
124M MET* 4.0 26.8 - - + +
127M ARG* 3.4 42.5 + - + +
128M ILE* 3.6 33.7 - - + -
164M LEU* 5.4 1.8 - - + -
179M GLU 3.5 8.3 + - - +
180M ILE* 3.3 22.0 - - + +
182M ALA* 1.3 81.0 - - + +
184M SER* 1.3 63.4 + - - +
152T ASN* 3.9 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LEU* 4.1 9.4 - - - +
124M MET* 3.7 15.5 - - - -
157M ASP* 4.5 2.1 + - - +
161M SER* 2.9 30.6 + - - -
180M ILE* 2.9 18.9 + - - -
181M CYS* 2.8 17.5 - - - +
183M VAL* 1.3 79.9 - - - +
185M ARG* 1.3 66.3 + - - +
186M ILE* 3.2 23.1 + - - +
191M ILE* 5.0 0.4 - - - -
----------------------------------------------------------
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