Contacts of the helix formed by residues 154 - 169 (chain F) in PDB entry 4GTU
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 PHE 154 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F LEU* 3.6 26.7 - - + -
73F ASN* 6.2 0.4 - - - -
76F LEU* 4.3 21.0 - - + +
77F CYS* 3.7 26.0 - - - -
80F ALA* 3.9 7.9 - - + -
85F LEU* 2.9 29.3 + - - +
86F CYS* 3.6 27.8 - - - -
96F VAL* 3.6 29.6 - - + -
100F GLU* 4.0 15.3 - - + -
153F THR* 1.3 72.0 - - - +
155F VAL* 1.3 69.4 + - + +
157F PHE* 2.9 33.3 + - - +
158F LEU* 3.2 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F ARG 5.5 0.4 - - - +
96F VAL* 3.8 37.9 - - + +
99F LEU* 3.8 24.0 - - + +
100F GLU* 4.4 6.7 - - - +
147F PHE* 4.7 6.3 - - + -
148F VAL* 4.5 10.1 - - + -
153F THR* 3.0 26.3 - - - +
154F PHE* 1.3 101.0 - - + +
156F ASP* 1.3 62.7 - - - +
158F LEU* 3.7 9.2 - - + +
159F ALA* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 156 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146F TRP* 3.2 21.3 - - + +
147F PHE* 3.0 29.5 + - - -
148F VAL 4.2 1.2 + - - -
151F LYS 4.2 0.7 - - - +
152F ILE* 3.8 15.3 - - + -
153F THR* 2.8 45.5 + - - +
155F VAL* 1.3 81.7 - - - +
157F PHE* 1.3 58.2 + - + +
159F ALA* 3.7 6.4 - - - +
160F TYR* 3.2 24.3 + - - +
183F PHE* 3.4 20.5 - - + -
187F PHE* 4.0 8.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 157 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F ALA* 4.3 16.4 - - + +
18F LEU* 3.4 30.6 - - + +
19F LEU* 3.5 39.3 - - + -
22F TYR* 3.5 35.4 - + + -
76F LEU* 5.8 0.4 - - + -
85F LEU* 4.7 8.3 - - + -
152F ILE* 4.6 11.4 - - + -
153F THR 3.6 19.7 - - - -
154F PHE* 2.9 14.1 + - - +
156F ASP* 1.3 75.0 - - - +
158F LEU* 1.3 67.0 + - - +
159F ALA 3.1 1.6 - - - -
160F TYR* 3.1 7.7 + - - +
161F ASP* 3.0 22.2 + - - +
187F PHE* 3.2 33.0 - + - -
190F LEU* 6.0 0.2 - - + -
193F ILE* 4.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F ALA* 4.4 14.7 - - + +
72F SER* 6.5 0.2 - - - -
73F ASN* 4.3 9.0 - - - +
76F LEU* 3.7 28.5 - - + -
100F GLU* 4.1 31.2 - - - +
103F ALA* 4.0 16.6 - - + -
104F MET* 5.0 13.0 - - + +
154F PHE* 3.2 31.2 + - + +
155F VAL* 3.7 11.2 - - + +
157F PHE* 1.3 78.3 - - - +
159F ALA* 1.3 64.0 + - - +
161F ASP* 3.2 4.8 + - + +
162F VAL* 3.2 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F LEU* 4.5 8.1 - - + -
103F ALA* 4.8 2.4 - - - +
137F PHE* 6.1 4.5 - - + -
147F PHE* 3.9 33.0 - - + -
155F VAL 3.0 18.0 + - - +
156F ASP 3.7 6.3 - - - +
158F LEU* 1.3 76.4 - - - +
160F TYR* 1.3 66.3 + - - +
162F VAL* 3.0 9.3 + - - +
163F LEU* 2.9 29.5 + - + +
183F PHE* 4.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 160 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F ARG* 6.1 0.7 - - - -
14F HIS* 5.9 3.4 - + - -
18F LEU* 4.3 17.5 - - + -
156F ASP 3.2 12.4 + - - +
157F PHE* 3.1 9.5 + - - +
159F ALA* 1.3 78.8 - - - +
161F ASP* 1.3 61.3 + - - +
163F LEU* 3.3 3.9 + - - -
164F ASP* 2.9 39.8 + - + +
167F ARG* 4.0 8.0 + - - -
183F PHE* 4.3 7.5 - - + -
184F ILE* 3.3 33.0 - - + -
187F PHE* 3.2 43.5 - + + -
188F GLU* 3.6 26.9 + - + +
193F ILE* 5.1 0.2 - - + -
197F MET* 3.9 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 161 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F ARG* 3.1 27.7 + - - +
11F GLY 4.4 6.4 - - - +
12F LEU* 5.7 1.4 - - - -
14F HIS* 3.2 10.7 - - - +
15F ALA* 3.2 34.2 + - + +
18F LEU* 5.0 3.3 - - + +
107F SER* 6.0 0.9 - - - -
157F PHE 3.0 11.1 + - - +
158F LEU* 3.3 10.5 - - - +
159F ALA 3.1 0.2 - - - -
160F TYR* 1.3 75.4 - - - +
162F VAL* 1.3 65.8 + - + +
164F ASP* 3.0 19.1 - - - +
165F LEU* 3.0 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 162 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F ALA* 3.5 23.8 - - + +
106F VAL* 3.7 31.9 - - + -
107F SER* 3.5 23.6 - - - +
137F PHE* 5.5 7.4 - - + -
158F LEU* 3.3 16.2 - - + +
159F ALA* 3.0 6.9 + - - +
161F ASP* 1.3 75.8 - - + +
163F LEU* 1.3 65.3 + - + +
165F LEU* 3.3 10.7 - - - +
166F HIS* 2.9 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F MET* 5.2 4.9 - - + -
137F PHE* 5.3 12.1 - - + -
147F PHE* 4.7 7.6 - - + -
159F ALA* 2.9 25.4 + - + +
160F TYR 3.7 3.4 - - - +
162F VAL* 1.3 79.1 - - + +
164F ASP* 1.3 61.0 + - - +
165F LEU 3.3 0.2 + - - -
166F HIS* 3.6 1.0 + - - -
167F ARG* 3.0 25.9 + - - +
174F LEU* 3.6 36.6 - - + +
180F LEU* 4.4 24.2 - - + +
183F PHE* 3.7 31.6 - - + -
184F ILE* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 164 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F ARG* 2.8 39.9 + - - -
160F TYR* 2.9 48.4 + - + +
161F ASP* 3.0 4.7 - - - +
163F LEU* 1.3 73.9 - - - +
165F LEU* 1.3 67.5 + - - +
167F ARG* 3.1 38.0 - - - +
168F ILE* 3.1 19.2 + - + +
184F ILE* 4.9 0.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F ARG* 3.0 33.0 - - - +
107F SER* 5.7 6.7 - - - +
110F LEU* 3.3 30.7 - - + -
161F ASP* 3.0 19.2 + - - +
162F VAL* 3.3 16.8 - - - +
163F LEU 3.1 0.2 - - - -
164F ASP* 1.3 77.1 - - - +
166F HIS* 1.3 62.0 + - + +
168F ILE* 3.0 9.2 + - - +
169F PHE* 3.0 23.4 + - - +
207F LEU* 4.1 27.6 - - + +
208F TYR* 3.8 13.9 - - + +
214F TRP* 5.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 166 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F VAL* 3.7 31.7 - - + +
107F SER* 5.8 0.7 - - - -
110F LEU* 3.9 18.4 - - + +
126F TYR* 2.9 23.2 + + - -
130F LEU* 3.5 32.9 - - + +
134F MET* 5.1 7.1 - - + +
162F VAL* 2.9 32.8 + - + +
163F LEU 4.2 2.7 - - - +
165F LEU* 1.3 78.2 - - + +
167F ARG* 1.3 60.1 + - - +
169F PHE* 4.0 9.6 - - + -
170F GLU* 2.7 37.2 + - - +
173F CYS* 3.6 16.9 - - - -
174F LEU* 4.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 167 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F TYR* 4.0 17.6 + - - -
163F LEU 3.0 15.3 + - - +
164F ASP* 3.1 32.1 - - - +
166F HIS* 1.3 75.8 - - - +
168F ILE* 1.3 66.1 + - + +
170F GLU 4.4 2.9 - - - -
171F PRO* 3.0 35.7 - - + +
174F LEU* 4.3 13.2 - - + +
184F ILE* 4.3 24.5 - - + +
185F SER* 6.3 0.2 - - - +
188F GLU* 3.2 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 168 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164F ASP* 3.2 20.4 - - + +
165F LEU* 3.0 6.9 + - - +
167F ARG* 1.3 90.0 - - + +
169F PHE* 1.3 64.3 + - - +
170F GLU 3.2 1.3 - - - -
171F PRO* 4.2 6.5 - - - +
205F LYS* 6.1 2.5 - - - +
207F LEU* 5.6 10.5 - - + -
214F TRP* 4.6 15.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 169 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F LEU* 3.8 29.2 - - + -
113F VAL* 5.1 2.7 - - + -
114F CYS* 3.6 25.6 - - - -
119F PHE* 4.0 10.5 - + - -
123F LYS* 3.7 43.2 - - + -
126F TYR* 5.2 5.8 - + - -
127F LEU* 4.6 11.7 - - + -
130F LEU* 5.6 1.8 - - + -
165F LEU 3.0 15.9 + - - +
166F HIS* 3.1 11.6 + + + +
168F ILE* 1.3 78.2 - - - +
170F GLU* 1.3 68.3 + - + +
171F PRO* 4.2 1.3 - - - +
214F TRP* 3.4 43.1 - + + -
----------------------------------------------------------
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