Contacts of the helix formed by residues 177 - 190 (chain B) in PDB entry 5I1U
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 ALA 177 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TYR* 3.5 40.4 - - + +
146B TYR* 3.6 19.5 - - + -
173B ARG 4.1 1.9 + - - -
174B GLY 3.2 11.1 + - - -
175B THR 3.2 2.6 - - - -
176B ALA* 1.3 79.3 - - - +
178B MET* 1.3 64.6 + - - +
179B GLU 3.2 3.6 - - - +
180B SER* 3.2 7.4 + - - +
181B ILE* 3.0 22.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ARG 4.5 5.9 + - - +
176B ALA* 3.1 19.0 - - + +
177B ALA* 1.3 77.6 - - - +
179B GLU* 1.3 59.1 + - + +
181B ILE* 3.7 18.3 - - + +
182B PHE* 2.9 69.4 + - + +
210B ALA 4.1 7.6 - - - +
211B ALA* 3.5 36.3 - - + +
214B PRO* 4.2 8.5 - - + -
215B SER* 5.4 0.4 - - - +
299B TRP* 3.5 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ASN* 3.6 26.8 + - + +
145B TYR* 4.1 26.0 - - + -
173B ARG 5.3 3.5 + - - +
177B ALA 3.2 1.4 - - - -
178B MET* 1.3 78.3 - - + +
180B SER* 1.4 57.2 + - - +
182B PHE* 3.4 0.6 + - - -
183B ASP* 2.9 33.5 + - - +
207B ARG* 3.1 42.9 + - - +
208B GLN* 4.3 15.4 + - - +
211B ALA* 4.5 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 6.0 0.2 - - - -
76B TYR* 3.4 21.8 - - - -
142B ASN* 3.6 27.4 + - - +
143B TRP* 3.7 25.6 + - - -
146B TYR* 5.3 2.3 - - - +
177B ALA* 3.2 7.4 + - - +
179B GLU* 1.4 75.4 - - - +
181B ILE* 1.3 66.7 + - - +
183B ASP* 3.1 12.2 + - - +
184B MET* 3.1 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 2.8 27.0 + - - +
72B LEU* 5.3 2.7 - - + -
73B MET* 4.3 19.7 - - + -
76B TYR* 4.0 27.6 - - + -
176B ALA 3.9 15.9 - - - +
177B ALA 3.0 21.8 + - - +
178B MET* 3.3 23.5 + - + +
180B SER* 1.3 77.2 - - - +
182B PHE* 1.3 62.7 + - + +
184B MET* 3.4 11.6 + - - +
185B ILE* 3.8 1.7 + - - +
299B TRP* 3.2 42.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B MET* 2.9 44.6 + - + +
179B GLU* 5.4 0.7 - - - -
181B ILE* 1.3 81.1 - - + +
183B ASP* 1.3 65.0 + - - +
184B MET 3.0 1.6 - - - -
185B ILE* 3.1 39.1 + - + +
186B GLU* 4.2 2.1 + - - +
207B ARG* 3.6 51.8 + - + +
210B ALA* 3.6 24.2 - - + -
211B ALA* 3.6 26.5 - - + -
292B TYR* 5.0 2.0 - - + -
296B MET* 4.4 12.8 - - + -
299B TRP* 3.9 28.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TRP* 3.4 27.3 - - + -
138B ARG* 2.8 40.3 + - - +
139B ALA* 3.5 20.6 - - + +
142B ASN* 2.8 27.6 + - - +
179B GLU 2.9 17.4 + - - +
180B SER* 3.1 11.9 + - - +
182B PHE* 1.3 76.4 - - - +
184B MET* 1.3 67.5 + - + +
186B GLU* 3.1 17.5 + - - +
187B ARG 3.5 0.5 + - - -
207B ARG* 3.7 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 3.6 14.6 - - + +
68B LEU* 5.6 2.5 - - - -
72B LEU* 3.8 25.1 - - + -
127B ILE* 3.4 51.1 - - + -
135B TRP* 3.5 20.6 - - + -
139B ALA* 5.7 0.4 - - + -
143B TRP* 5.8 2.9 - - - +
180B SER* 3.1 15.7 + - - +
181B ILE 3.4 10.5 - - - +
182B PHE 3.0 0.8 - - - -
183B ASP* 1.3 78.5 - - + +
185B ILE* 1.3 65.1 + - - +
186B GLU 3.2 0.2 - - - -
187B ARG* 3.7 13.2 - - + +
188B LEU* 2.8 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 4.3 17.0 - - + -
181B ILE 3.8 3.1 + - - +
182B PHE* 3.1 35.0 + - + +
184B MET* 1.3 76.7 - - - +
186B GLU* 1.3 57.9 + - - +
188B LEU* 4.6 0.8 - - - +
189B GLY* 3.0 26.5 + - - -
191B PHE* 3.6 21.0 - - + -
291B ARG 4.3 4.3 - - - +
292B TYR* 4.3 13.9 - - + +
295B GLY* 3.6 21.8 - - - +
296B MET* 3.5 43.1 - - + +
299B TRP* 5.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B MET* 4.3 2.4 - - - +
135B TRP* 3.0 24.8 + - + +
138B ARG* 2.8 31.7 + - - -
182B PHE 4.9 1.7 - - - +
183B ASP* 3.1 11.2 + - - +
185B ILE* 1.3 77.2 - - + +
187B ARG* 1.3 59.2 + - - +
190B HIS* 2.8 26.3 + - - -
191B PHE* 3.1 36.7 + - + +
192B GLU* 3.4 6.0 - - + +
193B VAL* 2.9 47.4 + - + +
198B MET* 4.1 4.7 - - - +
207B ARG* 4.5 2.2 + - - -
292B TYR* 5.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLU* 5.0 7.9 + - - -
65B ASP* 2.9 27.7 + - - -
68B LEU* 3.6 18.5 - - + +
126B ARG* 3.0 31.7 + - - +
127B ILE* 3.0 22.2 + - - +
129B LEU* 3.4 13.5 + - - +
131B MET* 3.4 25.4 - - - +
135B TRP* 4.1 9.8 - - + -
183B ASP 3.5 2.2 + - - -
184B MET* 3.3 30.3 + - + +
186B GLU* 1.3 78.8 - - - +
188B LEU* 1.3 69.3 - - + +
190B HIS* 3.4 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 3.6 47.6 - - + -
61B SER* 4.4 17.6 - - - -
62B SER 5.2 0.3 + - - -
65B ASP* 3.5 53.5 - - + +
68B LEU* 3.9 25.6 - - + -
69B ALA* 3.8 14.4 - - + +
72B LEU* 6.5 0.2 - - + -
184B MET* 2.8 31.8 + - + +
185B ILE* 4.6 0.9 - - - +
187B ARG* 1.3 77.5 - - + +
189B GLY* 1.3 56.2 + - - +
190B HIS* 3.4 4.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ILE 3.0 18.9 + - - -
188B LEU* 1.3 75.2 - - - +
190B HIS* 1.3 71.9 + - - +
191B PHE* 3.3 8.1 + - - -
291B ARG* 2.9 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASP* 2.7 30.4 + - - -
129B LEU 5.9 0.4 - - - -
130B GLY* 6.2 0.2 - - - -
131B MET* 4.4 16.4 - - + +
186B GLU 2.8 9.6 + - - -
187B ARG* 3.4 26.8 + - - -
188B LEU 3.5 9.2 - - - -
189B GLY* 1.3 80.1 - - - +
191B PHE* 1.3 58.1 + - - +
291B ARG* 4.8 1.4 + - - -
----------------------------------------------------------
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