Contacts of the helix formed by residues 163 - 178 (chain F) in PDB entry 3EBL
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 163 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F ARG 4.2 0.4 - - - +
162F TYR* 1.4 112.3 - - + +
164F CYS* 1.3 71.4 + - - +
165F ALA 3.3 2.2 - - - -
166F TYR* 3.0 11.9 + - + +
167F ASP* 3.0 40.0 + - - +
258F TYR* 3.9 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 164 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F ARG* 3.5 37.6 + - + +
160F HIS* 4.0 29.2 - - + +
161F ARG 3.0 21.1 + - - +
162F TYR* 3.8 0.2 - - - +
163F PRO* 1.3 81.4 - - - +
165F ALA* 1.3 63.8 + - - +
167F ASP* 3.3 6.2 + - - -
168F ASP* 3.0 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F PHE* 4.5 2.7 - - + -
154F TYR* 3.7 34.7 - - + +
155F ARG 3.8 12.0 + - - +
163F PRO 3.3 0.4 - - - -
164F CYS* 1.3 78.0 - - - +
166F TYR* 1.3 59.7 + - - +
168F ASP* 3.3 6.0 + - - +
169F GLY* 3.0 23.9 + - - -
203F ILE* 3.9 20.3 - - + +
258F TYR* 3.9 22.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 166 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124F PHE* 4.2 0.8 - + - -
162F TYR* 3.4 38.4 - + - -
163F PRO* 3.0 11.7 + - + +
165F ALA* 1.3 73.9 - - - +
167F ASP* 1.3 65.8 + - - +
169F GLY* 3.3 2.2 + - - +
170F TRP* 3.0 22.7 + - - +
202F ASN* 2.6 29.6 + - - -
203F ILE* 3.9 32.8 - - + -
206F HIS* 3.2 39.5 + + + -
207F VAL* 4.0 6.8 - - + +
210F ARG* 5.2 1.1 + - - -
255F TRP* 5.6 0.2 - - - -
258F TYR* 3.4 23.4 - + - -
269F ALA* 3.4 17.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 167 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F ARG* 4.3 10.6 + - - +
163F PRO* 3.0 39.3 + - - +
164F CYS* 3.7 9.3 - - - +
166F TYR* 1.3 74.7 - - - +
168F ASP* 1.3 57.9 + - - +
170F TRP* 3.3 7.8 + - - +
171F THR* 2.8 35.0 + - - +
210F ARG* 4.2 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 168 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F ASP* 5.7 0.3 - - - +
74F VAL* 4.8 3.8 - - - +
76F LEU* 3.4 40.9 - - + +
152F VAL* 4.3 2.8 - - + +
154F TYR* 3.8 10.6 - - + -
155F ARG* 2.9 60.9 + - - +
164F CYS 3.0 13.1 + - - +
165F ALA 3.4 8.7 - - - +
166F TYR 3.2 0.2 - - - -
167F ASP* 1.3 77.7 - - - +
169F GLY* 1.3 56.0 + - - +
171F THR* 4.3 1.7 + - - -
172F ALA* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 169 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F PHE* 3.4 34.1 - - - -
165F ALA 3.0 12.3 + - - -
166F TYR 3.3 3.5 + - - -
168F ASP* 1.3 73.1 - - - +
170F TRP* 1.3 60.3 + - - +
172F ALA* 3.1 4.0 + - - +
173F LEU* 2.9 28.6 + - - +
203F ILE* 4.8 0.2 - - - -
207F VAL* 3.8 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 170 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166F TYR 3.0 12.9 + - - +
167F ASP 3.4 8.7 - - - +
169F GLY* 1.3 72.3 - - - +
171F THR* 1.3 67.3 + - - +
173F LEU* 3.1 26.5 + - + +
174F LYS* 2.9 62.6 + - + +
207F VAL* 3.8 9.6 - - + +
210F ARG* 3.3 62.8 - - + +
211F ALA* 3.6 34.1 - - - -
214F GLU* 3.5 25.2 + - + -
216F VAL* 4.1 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 171 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ILE* 4.3 8.5 - - + +
71F ASP* 3.9 27.8 + - + +
76F LEU* 3.9 19.1 - - + -
167F ASP* 2.8 25.2 + - - +
168F ASP* 3.6 7.3 + - - -
169F GLY 3.4 0.2 - - - -
170F TRP* 1.3 72.4 - - - +
172F ALA* 1.3 57.0 + - - +
174F LYS* 3.8 9.9 - - - +
175F TRP* 3.0 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ILE* 3.7 20.2 - - + +
78F VAL* 4.9 2.0 - - + -
117F ILE* 4.3 7.6 - - + -
150F VAL* 5.5 2.5 - - + -
152F VAL* 3.7 31.2 - - + -
168F ASP 3.0 15.3 + - - +
169F GLY* 3.1 8.5 + - - +
171F THR* 1.3 75.0 - - - +
173F LEU* 1.3 64.9 + - - +
175F TRP* 3.4 2.3 + - - +
176F VAL* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ILE* 3.7 13.2 - - + +
169F GLY 2.9 16.0 + - - +
170F TRP* 3.1 34.7 + - + +
172F ALA* 1.3 73.4 - - - +
174F LYS* 1.3 64.7 + - + +
176F VAL* 3.4 1.6 + - - +
177F MET* 3.1 46.2 + - + +
192F VAL* 3.9 27.6 - - + -
194F LEU* 4.6 3.1 - - + -
207F VAL* 3.8 20.2 - - + -
211F ALA* 3.8 16.6 - - + -
216F VAL* 4.4 9.4 - - + -
218F VAL* 4.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 174 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170F TRP* 2.9 63.2 + - + +
171F THR* 3.8 8.1 - - - +
173F LEU* 1.3 76.0 - - + +
175F TRP* 1.3 62.3 + - - +
177F MET* 3.3 10.2 + - - +
178F SER* 3.2 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 175 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F HIS* 3.5 27.4 + + - -
70F ILE* 3.5 48.6 - - + +
78F VAL* 4.6 5.2 - - + -
80F ILE* 3.8 26.2 - - + -
150F VAL* 4.6 5.8 - - + -
171F THR* 3.0 19.0 + - + +
172F ALA* 3.7 4.0 - - - +
174F LYS* 1.3 73.4 - - - +
176F VAL* 1.3 89.7 + - + +
178F SER* 2.8 23.3 + - - -
179F GLN* 3.1 46.6 + - + +
182F MET* 3.9 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 176 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F VAL* 3.7 23.6 - - + -
117F ILE* 3.8 20.2 - - + -
150F VAL* 4.1 18.2 - - + -
172F ALA 3.0 20.3 + - - +
173F LEU 3.8 3.4 - - - +
175F TRP* 1.3 97.5 - - + +
177F MET* 1.3 64.8 + - - +
178F SER 3.1 0.9 + - - -
179F GLN 3.2 10.6 + - - +
182F MET* 3.6 27.4 - - + +
190F ALA* 4.2 2.4 - - + +
192F VAL* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 177 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173F LEU* 3.1 26.6 + - + +
174F LYS* 3.3 12.5 + - - +
176F VAL* 1.3 77.0 - - - +
178F SER* 1.3 57.2 + - - +
179F GLN 3.4 0.4 + - - -
183F ARG* 3.0 24.4 + - - -
190F ALA* 4.2 25.9 + - - +
192F VAL* 3.8 25.6 - - + -
216F VAL* 3.6 22.9 - - + -
217F LYS* 3.4 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 178 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F LYS 3.2 12.3 + - - -
175F TRP* 2.8 24.1 + - - -
176F VAL 3.1 0.2 - - - -
177F MET* 1.3 76.8 - - - +
179F GLN* 1.3 69.9 + - - +
180F PRO* 3.4 10.7 - - - +
183F ARG* 3.9 9.4 + - - +
----------------------------------------------------------
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