Contacts of the helix formed by residues 172 - 182 (chain B) in PDB entry 4G1U
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 172 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B SER* 4.2 2.6 + - - -
171B ASP* 1.3 89.0 + - - +
173B GLN* 1.3 67.3 + - - +
174B GLN* 3.1 28.3 + - + +
175B LEU* 3.3 32.7 + - - +
176B ARG* 3.5 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ASP* 1.3 74.8 - - - +
174B GLN* 1.3 69.5 + - - +
176B ARG* 3.5 5.5 + - - +
177B GLN* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 4.3 17.5 - - + +
172B ASP* 3.1 27.5 + - + +
173B GLN* 1.3 86.2 + - - +
175B LEU* 1.3 59.1 + - + +
177B GLN* 3.8 8.2 - - - +
178B PHE* 2.9 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 4.6 14.8 - - + -
105B VAL* 4.9 11.7 - - + -
166B LEU* 3.7 37.0 - - + +
167B THR* 5.4 8.1 - - - +
170B SER* 3.4 40.6 - - - +
172B ASP* 3.3 18.3 + - - +
174B GLN* 1.3 80.5 - - + +
176B ARG* 1.3 62.0 + - - +
178B PHE* 3.8 10.0 - - + +
179B SER* 2.9 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B THR* 6.0 4.7 - - + -
171B ASP* 5.8 2.2 - - - +
172B ASP 3.5 9.6 + - - +
173B GLN* 4.1 7.0 - - - +
174B GLN 3.4 0.4 - - - -
175B LEU* 1.3 74.9 - - - +
177B GLN* 1.3 66.7 + - - +
179B SER* 3.2 7.0 + - - -
180B LEU* 2.9 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B GLN* 2.9 23.3 + - + +
174B GLN* 3.8 8.1 - - - +
176B ARG* 1.3 76.2 - - - +
178B PHE* 1.3 56.8 + - - +
180B LEU* 3.5 8.7 + - - +
181B TRP* 2.9 30.0 + - + +
188B GLN* 2.5 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA 3.3 24.7 - - - -
98B LEU* 5.1 4.0 - - + -
100B VAL* 3.5 18.6 - - + -
101B GLY* 3.4 29.6 - - - -
104B ILE* 3.9 22.0 - - + -
163B VAL* 4.4 22.7 - - + -
174B GLN 2.9 19.1 + - - +
175B LEU* 3.8 14.4 - - + +
177B GLN* 1.3 75.0 - - - +
179B SER* 1.3 62.8 + - - +
181B TRP* 3.6 22.3 - + - +
182B SER* 2.8 34.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL* 3.2 28.6 - - - +
167B THR* 3.3 16.4 + - - -
175B LEU* 2.9 22.9 + - - +
176B ARG* 3.2 7.6 + - - -
178B PHE* 1.3 78.5 - - - +
180B LEU* 1.3 65.8 + - - +
182B SER* 3.3 16.2 + - - -
183B MET* 3.4 16.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 3.7 26.5 - - + +
176B ARG* 2.9 46.1 + - + +
177B GLN* 3.9 7.9 - - - +
179B SER* 1.3 80.5 - - - +
181B TRP* 1.3 61.1 + - - +
183B MET* 3.3 31.1 - - + +
184B GLY 4.2 0.3 + - - -
185B SER* 3.8 9.6 + - - -
308B PRO* 4.1 7.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA* 5.0 6.7 - - + -
100B VAL* 3.8 32.3 - - + -
177B GLN* 2.9 19.9 + - + +
178B PHE* 3.2 26.2 + + - +
180B LEU* 1.3 74.9 - - - +
182B SER* 1.3 61.9 + - - +
183B MET 3.0 4.9 - - - -
184B GLY* 3.0 17.5 + - - -
185B SER* 3.9 17.9 + - - -
188B GLN* 3.2 31.7 - - + +
251B VAL* 3.4 23.8 - - + -
252B ALA* 3.4 30.5 - - - -
253B VAL 3.9 14.8 + - - -
254B SER 3.7 3.9 - - - +
255B GLY* 3.6 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA* 4.8 13.2 - - - -
163B VAL* 4.6 13.3 - - - +
178B PHE* 2.8 25.0 + - - -
179B SER* 3.3 16.5 + - - -
181B TRP* 1.3 82.9 - - - +
183B MET* 1.3 61.4 + - - +
184B GLY* 3.0 6.7 + - - -
255B GLY* 4.4 5.6 - - - -
256B VAL* 3.3 23.5 - - - +
----------------------------------------------------------
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