Contacts of the helix formed by residues 145 - 161 (chain E) in PDB entry 1W88
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 GLY 145 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E ILE* 1.3 76.3 - - - +
146E ALA* 1.3 63.9 + - - +
147E GLN* 3.0 21.7 + - - +
148E TYR* 3.0 22.0 + - - +
171E THR* 4.3 5.4 + - - -
175E GLY 5.1 4.3 - - - -
178E GLN* 4.9 7.0 - - - -
180E ASN* 3.2 24.0 - - - +
181E PHE* 5.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E GLN* 3.9 5.4 - - - -
143E ILE* 3.1 20.4 + - + +
144E ILE 3.3 3.0 + - - -
145E GLY* 1.3 75.5 - - - +
147E GLN* 1.3 61.4 - - - +
148E TYR 3.2 0.9 + - - -
149E ILE* 3.5 7.8 - - + +
150E GLN* 3.4 26.9 + - - +
180E ASN* 3.8 18.3 - - - +
91F ASP* 4.9 2.0 - - - +
96F GLN* 3.4 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 147 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E LEU* 3.7 20.5 - - + +
100E PRO 4.2 2.0 - - - +
101E GLY* 3.7 16.8 - - - -
138E LEU* 6.4 0.4 - - + -
141E GLN* 3.6 26.2 - - + +
143E ILE 3.6 0.5 - - - +
144E ILE* 4.5 1.5 - - - +
145E GLY* 3.0 23.2 + - - +
146E ALA* 1.3 80.0 + - - +
148E TYR* 1.3 63.0 + - + +
149E ILE 3.6 0.2 - - - -
150E GLN* 3.6 10.5 + - - +
151E ALA* 3.1 24.8 + - - +
169E THR* 3.1 25.3 + - - +
170E TYR 2.9 24.2 + - - +
171E THR* 3.5 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 148 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E GLY* 3.0 15.4 + - - +
147E GLN* 1.3 80.0 - - + +
149E ILE* 1.3 64.5 + - - +
151E ALA* 3.4 1.4 + - - +
152E ALA 3.4 15.6 + - - -
169E THR* 3.7 21.8 - - + -
170E TYR 4.2 0.7 - - - -
171E THR* 3.5 33.8 - - + +
180E ASN 3.6 11.2 - - - +
181E PHE* 3.3 44.9 - + - -
184E GLY* 3.7 5.2 - - - -
185E ILE* 4.1 3.6 - - + -
197E PHE* 3.5 50.2 - + + +
198E VAL 2.8 28.1 + - - -
199E VAL* 3.4 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 149 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E GLY 4.1 0.6 + - - -
146E ALA* 3.5 11.9 + - - +
148E TYR* 1.3 76.3 - - - +
150E GLN* 1.3 68.9 + - + +
152E ALA* 3.3 6.4 + - + -
153E GLY 3.3 14.2 + - - -
180E ASN* 3.4 31.8 + - - +
183E GLN* 4.0 8.7 - - + +
184E GLY* 3.9 7.1 - - - +
187E PHE* 3.8 34.1 - - + -
60F SER 4.8 2.2 - - - +
61F GLY* 3.5 36.1 - - - +
64F GLY* 3.5 21.4 - - - +
65F LEU* 4.3 2.0 - - - +
92F SER* 6.1 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 150 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E LEU* 3.7 13.6 - - + +
138E LEU* 3.6 24.8 - - - +
141E GLN* 3.6 13.1 + - - +
146E ALA* 3.4 17.7 + - - +
147E GLN* 3.8 3.0 - - - +
148E TYR 3.3 0.4 - - - -
149E ILE* 1.3 78.5 - - + +
151E ALA* 1.3 57.0 + - - +
153E GLY 3.2 2.4 + - - -
154E VAL* 2.9 24.4 + - - +
64F GLY* 3.5 11.9 - - - +
67F ILE* 3.8 34.6 - - + +
68F GLY* 3.3 10.9 - - - +
71F LEU* 5.3 0.7 - - + -
96F GLN* 3.3 42.6 + - - +
100F ILE* 4.8 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E LEU* 3.6 26.0 - - + +
147E GLN 3.1 17.4 + - - +
148E TYR 3.6 6.1 - - - +
150E GLN* 1.3 74.9 - - - +
152E ALA* 1.3 57.1 + - - +
154E VAL* 3.6 1.6 - - - +
155E ALA* 2.7 37.8 + - - +
167E ALA* 3.7 7.2 - - + +
168E ILE 5.3 0.2 - - - -
169E THR* 4.0 19.5 - - + +
195E ALA* 4.8 4.0 - - + -
197E PHE* 4.3 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E TYR 3.4 5.2 + - - +
149E ILE* 3.3 23.5 + - + +
151E ALA* 1.3 77.4 - - - +
153E GLY* 1.3 56.3 + - - +
155E ALA* 3.7 4.6 - - - +
156E LEU* 2.9 29.5 + - - +
184E GLY 3.7 23.3 - - - +
187E PHE* 4.0 4.0 - - + -
188E ALA* 3.9 23.8 - - + +
191E PHE* 6.1 0.4 - - + -
193E ALA* 4.1 3.8 - - - +
197E PHE* 4.6 2.0 - - - -
65F LEU* 4.1 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 153 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149E ILE 3.3 4.4 + - - -
150E GLN 3.2 8.0 + - - -
152E ALA* 1.3 76.9 - - - +
154E VAL* 1.3 58.8 + - - +
156E LEU* 3.4 2.9 + - - +
157E GLY* 2.9 23.7 + - - -
65F LEU* 3.6 36.2 - - - +
68F GLY* 3.5 13.6 - - - -
69F LEU* 3.6 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E PHE* 3.8 26.9 - - + -
99E LEU* 4.2 13.0 - - + -
150E GLN 2.9 19.3 + - - +
151E ALA* 3.1 6.5 + - - +
153E GLY* 1.3 71.4 - - - +
155E ALA* 1.3 62.0 + - - +
157E GLY* 3.0 3.6 + - - -
158E LEU* 2.8 34.7 + - + +
167E ALA* 3.7 17.7 - - + -
68F GLY* 3.7 21.1 - - - +
71F LEU* 4.0 20.6 - - + -
72F GLN* 3.7 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E ALA 2.7 20.1 + - - +
152E ALA 3.7 1.1 - - - +
154E VAL* 1.3 72.4 - - - +
156E LEU* 1.3 56.7 + - - +
158E LEU* 3.1 7.8 + - - +
159E LYS 2.9 25.1 + - - -
167E ALA* 3.7 6.9 - - + +
193E ALA* 3.7 14.8 - - + -
194E PRO* 3.4 42.8 - - - +
195E ALA* 3.7 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E ALA 2.9 18.6 + - - +
153E GLY* 3.7 5.2 - - - +
155E ALA* 1.3 75.1 - - - +
157E GLY* 1.3 57.7 + - - +
159E LYS* 3.2 20.8 + - + +
160E MET* 2.9 53.4 + - + +
191E PHE* 3.9 36.8 - - + +
193E ALA* 3.9 6.4 - - + +
53F PHE* 4.1 19.7 - - + -
65F LEU* 3.9 32.3 - - + -
69F LEU* 4.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 157 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E GLY 2.9 13.4 + - - -
154E VAL 3.0 4.2 + - - -
156E LEU* 1.3 74.6 - - - +
158E LEU* 1.3 57.0 + - - +
160E MET* 3.3 2.5 + - - +
161E ARG* 3.0 33.7 + - - +
69F LEU* 3.7 19.2 - - - +
72F GLN* 4.1 13.9 - - - -
74F PHE* 3.8 10.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E GLU 4.6 6.5 - - - +
97E PHE* 4.7 3.4 - - + +
154E VAL* 2.8 29.0 + - + +
155E ALA* 3.3 9.6 - - - +
157E GLY* 1.3 76.1 - - - +
159E LYS* 1.3 61.2 + - - +
161E ARG* 3.3 3.2 + - - +
162E GLY 3.3 2.8 + - - -
163E LYS* 3.2 48.0 + - + +
165E ALA* 4.0 28.5 - - + +
166E VAL* 3.4 38.8 - - - +
167E ALA 3.7 3.8 - - - +
194E PRO* 4.5 1.3 - - + -
72F GLN* 3.7 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 159 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E ALA 2.9 12.9 + - - +
156E LEU* 3.4 20.7 - - + +
158E LEU* 1.3 76.8 - - - +
160E MET* 1.3 62.1 + - + +
162E GLY* 3.2 13.5 + - - -
163E LYS 5.1 2.7 - - - -
191E PHE 2.7 27.6 + - - +
192E LYS* 3.9 25.3 + - - +
193E ALA* 4.6 0.2 - - - -
194E PRO* 3.9 15.3 - - + +
255E GLY* 5.9 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 160 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E LEU* 2.9 38.1 + - + +
157E GLY 3.7 4.9 - - - +
158E LEU 3.3 0.4 - - - -
159E LYS* 1.3 74.5 - - + +
161E ARG* 1.3 60.8 + - - +
162E GLY 3.1 5.2 + - - -
24F LEU* 4.2 11.2 - - - -
49F GLU 5.4 0.4 - - - +
50F ASP* 4.0 23.1 - - + +
53F PHE* 3.6 39.0 - - + -
69F LEU* 4.0 21.5 - - - -
74F PHE* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 161 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E GLY 3.0 21.8 + - - +
158E LEU 3.3 3.8 + - - +
160E MET* 1.3 75.8 - - - +
162E GLY* 1.3 56.9 + - - +
163E LYS* 3.1 41.5 + - + +
22F ASN* 3.3 19.6 + - - -
72F GLN* 3.0 29.5 + - - +
73F GLY* 3.2 25.7 + - - -
74F PHE* 3.6 25.0 - - + +
----------------------------------------------------------
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