Contacts of the helix formed by residues 173 - 186 (chain B) in PDB entry 2I62
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 ASP 173 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B CYS* 3.3 1.7 - - - +
172B PRO* 1.3 87.8 - - - +
174B LEU* 1.3 64.2 + - - +
175B PRO* 3.4 17.0 - - + +
176B ALA* 2.9 35.5 + - - +
177B TYR 3.0 17.0 + - - -
215B LEU* 3.5 18.4 - - - +
154C SER* 4.3 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASP* 1.3 75.0 - - - +
175B PRO* 1.4 69.4 - - + +
177B TYR* 3.1 27.5 + - + +
178B ARG* 2.9 64.5 + - + +
215B LEU* 3.9 5.4 - - - +
217B LEU* 4.3 10.8 - - + -
221B THR* 4.0 31.9 - - + -
225B ALA* 4.6 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASP* 3.4 16.4 - - + +
174B LEU* 1.4 92.4 - - + +
176B ALA* 1.3 59.6 + - - +
178B ARG* 3.4 23.3 + - + +
179B THR* 3.0 28.8 + - - -
154C SER* 5.2 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B CYS* 3.8 6.5 - - + -
172B PRO* 3.6 28.9 - - + -
173B ASP* 2.9 26.8 + - - +
175B PRO* 1.3 74.1 - - - +
177B TYR* 1.3 52.9 + - - +
179B THR* 3.1 8.4 + - - -
180B ALA* 2.8 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU* 3.7 37.8 - - + +
168B ASP* 3.5 21.3 + - - -
171B CYS* 3.7 9.8 - - + +
173B ASP 3.0 12.3 + - - +
174B LEU* 3.1 14.3 + - + +
176B ALA* 1.3 72.1 - - - +
178B ARG* 1.3 65.8 + - - +
180B ALA* 3.3 2.8 + - - +
181B LEU* 3.0 42.3 + - + +
196B MET* 4.1 10.2 - - - -
198B ASP* 4.9 1.1 + - - -
215B LEU* 4.0 13.5 - - + -
217B LEU* 3.7 25.7 - - + +
222B VAL* 4.0 23.4 - - + +
225B ALA* 4.0 21.5 - - + -
226B VAL* 5.3 1.0 - - + +
254B PHE* 4.0 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 2.9 57.0 + - + +
175B PRO* 3.6 27.4 - - - +
177B TYR* 1.3 74.9 - - - +
179B THR* 1.3 58.1 + - - +
181B LEU* 3.2 13.2 + - - +
182B ARG* 2.9 43.7 + - - +
225B ALA* 4.9 12.6 - - + +
228B GLU* 4.3 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B THR* 5.2 4.7 - - - +
175B PRO 3.0 16.1 + - - -
176B ALA* 3.1 11.4 + - - -
178B ARG* 1.3 74.2 - - - +
180B ALA* 1.3 53.0 + - - +
182B ARG* 3.0 33.2 + - - +
183B ASN* 2.8 54.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B VAL* 3.7 28.7 - - + +
145B THR* 5.5 2.2 - - + +
167B LEU* 4.1 14.8 - - + -
171B CYS* 3.6 20.9 - - - -
176B ALA 2.8 19.4 + - - +
177B TYR 3.3 5.1 + - - +
179B THR* 1.3 72.8 - - - +
181B LEU* 1.3 61.8 + - - +
183B ASN* 3.2 3.2 + - - +
184B LEU* 3.1 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU* 3.9 9.8 - - + +
177B TYR* 3.0 39.0 + - + +
178B ARG* 3.2 10.3 + - - +
180B ALA* 1.3 74.3 - - - +
182B ARG* 1.3 62.6 + - - +
184B LEU* 3.4 5.4 + - + +
185B GLY* 3.3 18.9 + - - -
194B LEU* 4.2 17.0 - - + -
196B MET* 3.8 35.7 - - + -
225B ALA* 3.9 31.9 - - + +
226B VAL* 4.2 9.9 - - + +
229B ALA* 4.4 14.8 - - + -
231B TYR* 4.5 9.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B PRO 5.1 0.2 + - - -
178B ARG* 2.9 22.9 + - - +
179B THR* 3.2 54.1 + - - +
181B LEU* 1.3 76.0 - - - +
183B ASN* 1.3 67.2 + - - +
185B GLY* 3.3 11.5 + - - -
186B SER* 3.7 7.3 + - - -
229B ALA* 5.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B VAL 2.9 26.5 + - - +
145B THR* 3.3 17.8 + - - +
146B GLN 3.3 25.9 + - - +
147B SER* 3.6 17.6 - - - +
149B PRO* 3.6 10.2 - - + +
179B THR* 2.8 35.3 + - - +
180B ALA 3.5 3.1 - - - +
182B ARG* 1.3 77.6 - - - +
184B LEU* 1.3 57.8 + - + +
186B SER* 2.6 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 3.9 26.7 - - + -
144B VAL* 3.8 25.1 - - + -
149B PRO* 3.9 23.1 - - + -
161B LEU* 2.9 33.6 - - + +
163B SER* 4.9 1.8 - - - -
167B LEU* 3.8 33.7 - - + -
180B ALA 3.1 15.7 + - - +
181B LEU* 4.0 5.2 - - + +
182B ARG 3.4 0.2 - - - -
183B ASN* 1.3 69.9 - - - +
185B GLY* 1.3 60.8 + - - +
186B SER 3.0 2.7 - - - -
187B LEU* 2.9 22.1 + - + +
188B LEU 3.9 0.2 + - - -
194B LEU* 5.4 2.9 - - + -
196B MET* 4.5 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 4.7 0.7 - - - -
181B LEU 3.3 9.7 + - - -
182B ARG 3.3 6.2 + - - -
183B ASN 3.3 0.6 - - - -
184B LEU* 1.3 76.8 - - - +
186B SER* 1.3 60.6 + - - +
187B LEU 3.1 1.8 + - - -
188B LEU* 3.3 11.0 + - - +
231B TYR* 3.8 21.0 + - - -
260B LYS* 2.7 31.1 + - - -
265B GLU* 4.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B SER 3.5 15.8 + - - -
148B GLN* 4.8 3.5 - - - +
149B PRO* 3.8 8.3 - - - +
182B ARG 3.7 5.6 + - - -
183B ASN* 2.6 23.1 + - - -
184B LEU 3.0 1.0 - - - -
185B GLY* 1.3 77.4 - - - +
187B LEU* 1.3 61.5 + - - +
188B LEU 3.5 1.1 + - - +
265B GLU* 5.4 4.0 - - - -
----------------------------------------------------------
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