Contacts of the helix formed by residues 167 - 181 (chain B) in PDB entry 3FCL
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 PRO 167 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B TYR* 3.5 44.4 - - + +
152B GLN* 3.8 20.9 - - - +
160B VAL* 3.7 23.6 - - + -
165B PRO 3.3 8.3 - - - +
166B PRO* 1.3 84.3 - - + +
168B PRO* 1.3 78.8 - - + +
169B SER 3.2 1.1 - - - +
170B LEU* 2.8 18.0 + - + -
171B GLU* 3.0 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PRO 3.9 0.6 - - - +
167B PRO* 1.3 86.7 - - + +
169B SER* 1.3 62.1 + - - +
171B GLU* 3.3 8.0 + - + +
172B ASN* 3.1 30.8 + - - +
271B PRO* 3.5 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B 3FL 3.6 23.5 - - - -
147B TYR* 4.2 5.6 - - - -
158B PHE* 4.0 23.8 - - - -
167B PRO 3.0 1.0 + - - -
168B PRO* 1.3 79.0 - - - +
170B LEU* 1.3 58.0 + - - +
172B ASN* 3.3 4.5 + - - +
173B ILE* 3.1 30.8 + - - +
268B HIS* 3.7 1.9 - - - -
269B PRO* 3.8 12.8 - - - +
270B SER* 3.4 25.6 + - - +
271B PRO* 4.4 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B TYR* 4.0 4.6 + - - +
158B PHE 3.3 21.1 - - - +
159B SER* 4.6 0.2 - - - -
160B VAL* 4.6 0.4 - - + -
166B PRO* 3.9 12.6 - - + -
167B PRO* 2.8 18.0 + - + +
169B SER* 1.3 73.4 - - - +
171B GLU* 1.3 59.2 + - - +
173B ILE* 3.2 20.0 + - + -
174B TYR* 2.9 44.3 + - + +
190B GLY* 3.3 43.5 - - - +
192B LEU* 4.0 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PRO* 3.7 41.4 - - + +
167B PRO 3.0 9.1 + - - +
168B PRO* 4.0 8.3 - - + +
170B LEU* 1.3 74.6 - - - +
172B ASN* 1.3 61.7 + - - +
174B TYR* 3.4 6.4 + - - +
175B LYS* 2.8 29.1 + - - +
186B HIS* 3.1 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PRO 3.1 14.6 + - - +
169B SER 3.5 3.4 - - - +
170B LEU 3.2 0.2 - - - -
171B GLU* 1.3 78.2 - - - +
173B ILE* 1.3 64.4 + - - +
175B LYS* 3.1 8.5 + - - +
176B GLU* 2.9 22.5 + - - +
269B PRO* 2.8 30.6 + - + +
271B PRO* 3.8 15.6 - - - +
274B VAL* 3.7 27.0 - - + +
278B PHE* 4.1 2.7 - - - -
279B PHE* 3.5 21.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PHE* 3.7 35.4 - - + -
169B SER 3.1 20.2 + - - +
170B LEU* 3.2 18.8 + - + +
172B ASN* 1.3 75.5 - - - +
174B TYR* 1.3 58.1 + - + +
176B GLU* 3.3 2.8 + - - +
177B LEU* 3.0 28.8 + - + +
192B LEU* 5.6 0.9 - - + -
195B TRP* 3.9 29.6 - - + -
245B TRP* 3.6 21.5 - - + -
269B PRO* 3.9 4.9 - - + -
278B PHE* 3.8 22.7 - - + -
284B PHE* 3.9 15.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PRO* 4.2 5.2 - - + -
170B LEU* 2.9 42.8 + - + +
171B GLU* 3.7 11.9 - - - +
173B ILE* 1.3 77.8 - - + +
175B LYS* 1.3 62.1 + - - +
177B LEU* 3.4 9.5 + - + +
178B SER* 3.1 21.8 + - - -
184B PHE* 3.7 23.8 - + + -
186B HIS* 3.2 39.0 - + + +
187B PRO* 3.5 11.5 - - + +
189B HIS 2.8 28.3 + - - -
190B GLY* 3.7 5.5 - - - -
191B ASP 4.4 1.0 + - - -
192B LEU* 3.6 19.8 - - + +
195B TRP* 4.6 3.8 - + - -
304B LEU* 4.0 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B GLU 2.8 21.9 + - - +
172B ASN* 3.1 8.7 + - - +
174B TYR* 1.3 70.1 - - - +
176B GLU* 1.3 62.7 + - - +
178B SER* 2.7 29.0 + - - +
179B THR* 3.3 30.5 + - + +
275B TYR* 6.2 0.7 - - - -
279B PHE* 3.5 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ASN 2.9 7.7 + - - +
173B ILE 3.7 2.5 - - - +
175B LYS* 1.3 76.8 - - - +
177B LEU* 1.3 57.4 + - - +
179B THR* 3.0 13.7 + - - -
180B ASP* 2.8 33.5 + - + +
278B PHE* 3.6 35.2 - - + +
279B PHE* 3.4 12.3 - - + +
280B GLY* 2.8 31.6 + - - -
281B CYS* 4.3 4.7 - - - -
282B ARG* 2.9 32.1 + - - +
284B PHE* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ILE* 3.0 17.0 + - + +
174B TYR* 3.6 11.4 - - + +
175B LYS 3.2 0.2 - - - -
176B GLU* 1.3 77.2 - - - +
178B SER* 1.3 56.8 + - - +
180B ASP* 4.2 3.1 - - - -
181B ILE* 2.8 42.2 + - + +
184B PHE* 3.7 30.6 - - + +
195B TRP* 3.5 37.9 - - + -
284B PHE* 3.5 40.6 - - + -
301B TRP* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TYR 3.1 12.7 + - - -
175B LYS* 2.7 28.9 + - - +
177B LEU* 1.3 76.1 - - - +
179B THR* 1.3 66.0 + - - +
181B ILE 3.4 16.9 - - - +
182B GLU* 4.2 6.8 + - - +
184B PHE* 4.0 14.1 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
175B LYS* 3.3 33.2 + - + +
176B GLU* 3.0 26.5 + - - -
178B SER* 1.3 83.8 + - - +
180B ASP* 1.3 65.0 + - - +
181B ILE 5.0 0.9 - - - -
182B GLU* 5.0 1.2 + - - -
280B GLY* 5.8 0.3 - - - -
282B ARG* 5.1 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLU* 2.8 28.5 + - - +
177B LEU* 3.8 4.5 - - - +
179B THR* 1.3 81.5 + - - +
181B ILE* 1.3 61.5 + - + +
182B GLU 4.1 1.2 + - - -
282B ARG* 2.7 69.5 + - - +
284B PHE* 3.2 20.5 + - + +
285B SER* 2.7 39.7 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
3B SCN 3.7 30.5 - - - +
177B LEU* 2.8 26.9 + - + +
178B SER* 3.4 7.0 - - - +
180B ASP* 1.3 84.2 - - + +
182B GLU* 1.3 66.3 + - - +
183B ASP* 3.9 11.4 - - + +
184B PHE* 3.0 14.4 + - + +
284B PHE* 4.0 14.1 - - + -
285B SER* 4.0 15.5 - - - +
288B ASN* 4.7 2.5 - - - +
301B TRP* 3.5 32.3 - - + -
----------------------------------------------------------
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