Contacts of the helix formed by residues 171 - 182 (chain B) in PDB entry 2X1L
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 TYR 171 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ASP* 2.6 34.6 + - - -
166B PHE* 3.8 21.1 - + - -
167B ARG 3.3 25.4 - - - -
168B LEU 3.0 7.8 + - - +
170B ALA* 1.3 80.1 - - - +
172B THR* 1.3 57.3 + - - +
173B ASP 3.4 2.0 - - - -
174B ARG* 3.2 34.4 + - - -
175B LEU* 2.8 38.5 + - + +
276B ALA* 4.2 17.3 - - + -
279B MET* 3.7 30.6 - - + -
280B SER* 3.3 16.6 - - - -
602B CXS 3.5 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU 3.7 2.3 + - - -
169B SER* 3.6 15.7 + - - -
170B ALA 3.6 1.6 - - - -
171B TYR* 1.3 76.9 - - - +
173B ASP* 1.3 68.2 + - - +
175B LEU* 3.3 3.1 + - - +
176B LEU* 3.0 32.7 + - + +
199B VAL* 3.4 30.5 - - + +
200B SER 5.7 0.4 - - - -
202B GLY* 4.4 9.6 - - - -
203B LEU* 3.5 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ALA 5.4 0.6 + - - -
171B TYR 3.4 0.6 - - - -
172B THR* 1.3 83.6 - - - +
174B ARG* 1.3 59.2 - - - +
176B LEU* 3.4 20.9 + - - +
177B ALA* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ALA 5.6 0.2 + - - -
171B TYR* 3.2 25.9 + - - +
173B ASP* 1.3 78.3 - - - +
175B LEU* 1.3 60.1 + - - +
177B ALA* 3.7 7.3 + - + +
178B LEU* 3.3 19.9 + - - +
279B MET* 3.7 54.3 + - + +
602B CXS 2.8 49.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
168B LEU* 4.5 1.1 - - + -
171B TYR* 2.8 32.5 + - + +
172B THR 3.5 4.5 - - - +
174B ARG* 1.3 76.7 - - - +
176B LEU* 1.3 63.1 + - - +
178B LEU* 3.2 17.4 + - + +
179B TYR* 3.2 38.4 + - + +
199B VAL* 4.3 2.5 - - + -
203B LEU* 3.8 26.0 - - + -
272B VAL* 3.7 22.7 - - + +
275B PRO* 3.7 36.1 - - + -
276B ALA* 4.1 7.2 - - + +
279B MET* 4.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B THR* 3.0 20.9 + - + +
173B ASP* 3.4 27.6 + - - +
175B LEU* 1.3 72.1 - - - +
177B ALA* 1.3 65.1 + - - +
179B TYR* 3.5 14.1 + - + +
180B GLU* 3.2 22.5 + - - +
196B VAL* 3.8 17.7 - - + +
199B VAL* 3.8 17.3 - - + -
200B SER* 3.5 35.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASP 3.0 17.9 + - - +
174B ARG* 3.8 9.2 - - + +
175B LEU 3.3 0.2 - - - -
176B LEU* 1.3 75.1 - - - +
178B LEU* 1.3 59.3 + - - +
180B GLU* 3.4 5.3 + - - +
181B GLU* 2.9 51.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ARG 3.3 11.1 + - - +
175B LEU* 3.2 11.7 + - + +
177B ALA* 1.3 77.5 - - - +
179B TYR* 1.3 61.7 + - + +
181B GLU* 4.8 3.4 - - - -
182B HIS* 2.8 57.9 + - + +
185B PHE* 3.8 42.0 - - + -
275B PRO* 4.2 6.7 - - + -
279B MET* 4.1 11.9 - - + -
285B LEU* 3.8 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 3.2 31.8 + - + +
176B LEU* 3.5 13.9 + - + +
177B ALA 3.4 0.2 - - - -
178B LEU* 1.3 82.5 - - + +
180B GLU* 1.3 60.8 + - - +
182B HIS 4.2 4.9 - - - -
183B PRO* 3.4 26.0 - - - +
185B PHE* 4.1 15.9 - + + -
186B ILE* 3.7 23.3 - - + -
192B ARG* 4.3 9.7 + - + +
195B ILE* 3.6 16.5 - - + +
196B VAL* 3.9 31.6 - - + -
199B VAL* 3.7 31.0 - - + +
271B THR 2.7 30.4 + - - -
272B VAL* 3.8 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU 3.2 16.5 + - - +
177B ALA* 3.8 6.3 - - - +
179B TYR* 1.3 79.4 - - - +
181B GLU* 1.3 65.2 + - + +
183B PRO* 3.7 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ALA* 2.9 33.0 + - - +
178B LEU* 4.3 1.1 - - - +
180B GLU* 1.3 79.8 - - + +
182B HIS* 1.3 83.3 + - + +
183B PRO* 3.5 6.4 - - - +
184B GLU* 4.8 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 2.8 42.9 + - + +
179B TYR* 3.7 2.6 - - - +
181B GLU* 1.3 95.3 + - + +
183B PRO* 1.4 65.0 - - - +
184B GLU* 3.1 28.0 + - - +
185B PHE* 3.1 22.3 + - + +
192B ARG* 5.3 0.2 - - - -
287B LYS 6.0 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