Contacts of the helix formed by residues 140 - 156 (chain B) in PDB entry 1OFD
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 ALA 140 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ASP* 3.1 21.1 - - + +
71B ARG* 3.9 14.6 - - + +
138B GLY 3.8 4.7 + - - +
139B CYS* 1.3 78.0 - - - +
141B GLY* 1.3 68.7 + - - +
142B ASP 3.2 2.8 + - - -
143B GLU* 3.2 14.3 + - - +
144B LEU* 3.3 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ASP* 2.9 22.4 + - - -
140B ALA* 1.3 71.7 - - - +
142B ASP* 1.3 63.5 + - - -
145B ASP* 2.9 25.5 + - - +
170B CYS* 3.7 12.8 - - - -
171B ARG* 3.4 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ALA 3.2 1.6 + - - -
141B GLY* 1.3 71.5 - - - +
143B GLU* 1.3 58.5 + - - +
145B ASP* 3.4 3.0 + - - +
146B ARG* 2.9 29.3 + - - +
171B ARG* 2.9 27.1 + - - +
283B ARG* 5.2 3.1 + - - +
338B LYS* 3.0 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B CYS* 3.3 28.5 - - - -
140B ALA 3.2 8.2 + - - +
142B ASP* 1.3 76.2 - - - +
144B LEU* 1.3 66.1 + - - +
146B ARG* 3.0 45.0 + - - +
147B ARG* 3.0 49.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ASP 3.7 10.8 - - - +
71B ARG* 3.7 34.3 - - - +
73B GLY* 4.1 6.1 - - - +
102B LEU* 3.8 29.4 - - + -
133B VAL* 4.9 5.8 - - + +
135B CYS* 4.7 7.6 - - + +
139B CYS* 4.2 10.3 - - - +
140B ALA* 3.3 25.5 + - - +
141B GLY 3.8 1.3 - - - +
143B GLU* 1.3 77.4 - - - +
145B ASP* 1.3 57.3 + - - +
147B ARG* 3.2 4.6 + - - +
148B LEU* 3.0 50.8 + - + +
170B CYS* 3.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLY 2.9 14.3 + - - +
142B ASP 3.8 2.9 - - - +
144B LEU* 1.3 74.4 - - - +
146B ARG* 1.3 56.0 + - - +
148B LEU* 3.3 6.5 + - - +
149B TYR* 2.9 29.9 + - - +
152B ARG* 4.9 1.6 + - - -
168B PHE 5.0 0.8 - - - +
169B SER* 2.7 28.9 + - - -
170B CYS* 2.7 37.5 + - - +
171B ARG* 4.2 16.5 + - - +
283B ARG* 3.7 33.6 + - - +
336B ASP 4.9 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ASP 2.9 14.8 + - - +
143B GLU* 3.0 46.2 + - - +
145B ASP* 1.3 76.4 - - - +
147B ARG* 1.3 63.9 + - - +
149B TYR* 3.3 9.5 + - - +
150B ILE* 3.1 34.3 + - - +
251B GLY 3.7 14.6 + - - -
252B TRP* 3.4 49.6 - - + +
256B GLU* 2.5 45.2 + - - -
283B ARG* 4.3 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B GLU* 2.6 70.7 + - + +
101B LYS* 4.1 16.9 + - - +
102B LEU* 4.4 16.1 - - + +
135B CYS* 3.6 23.8 - - - -
137B GLU* 5.1 11.3 + - - +
139B CYS* 3.7 22.6 - - - -
143B GLU* 3.0 40.2 + - - +
144B LEU* 3.6 8.3 - - - +
146B ARG* 1.3 77.9 - - - +
148B LEU* 1.3 57.3 + - - +
150B ILE* 3.4 8.4 + - + +
151B ALA 3.0 4.2 + - - -
256B GLU* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLY* 4.1 11.9 - - - -
100B GLU* 4.9 1.1 - - - +
102B LEU* 3.4 30.5 - - + -
133B VAL* 4.2 4.0 - - + -
144B LEU* 3.0 42.3 + - + +
145B ASP* 3.7 17.0 - - - +
147B ARG* 1.3 73.8 - - - +
149B TYR* 1.3 60.5 + - - +
151B ALA* 3.3 4.8 + - + +
152B ARG* 2.8 35.7 + - - +
168B PHE* 3.4 49.4 - - + +
169B SER* 4.0 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ASP 2.9 17.7 + - - +
146B ARG 3.4 4.7 - - - +
147B ARG 3.3 0.2 - - - -
148B LEU* 1.3 76.6 - - - +
150B ILE* 1.3 55.3 + - - +
152B ARG* 3.4 21.5 + - - +
153B SER* 2.9 41.5 + - - -
252B TRP* 3.8 16.4 - + - -
260B LEU* 3.6 35.5 - - + +
263B ILE* 4.7 2.9 - - - +
276B SER* 4.5 3.1 + - - -
279B GLU* 3.5 34.1 - - + -
280B LEU* 3.3 31.0 + - + +
283B ARG* 3.4 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B GLU* 2.9 22.7 - - + +
146B ARG* 3.1 27.0 + - - +
147B ARG* 3.7 8.1 - - + +
148B LEU 3.3 0.2 - - - -
149B TYR* 1.3 71.9 - - - +
151B ALA* 1.3 63.3 + - - +
153B SER* 3.2 2.4 + - - -
154B ILE* 3.1 30.3 + - + +
252B TRP* 3.8 28.9 - - + -
256B GLU* 3.8 32.5 - - + +
259B ALA* 3.9 24.7 - - + -
260B LEU* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL* 3.6 19.0 - - + +
97B VAL* 4.9 4.3 - - + -
100B GLU* 2.4 36.6 + - - +
147B ARG 3.0 2.1 + - - +
148B LEU* 3.3 13.0 + - + +
150B ILE* 1.3 70.8 - - - +
152B ARG* 1.3 59.9 + - - +
154B ILE* 3.2 1.8 + - - -
155B ILE* 2.9 36.3 + - + +
168B PHE* 4.5 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ASP 4.9 1.2 + - - -
148B LEU 2.8 13.2 + - - +
149B TYR* 3.6 26.1 - - - +
151B ALA* 1.3 72.9 - - - +
153B SER* 1.3 59.7 + - - +
155B ILE* 4.0 6.9 - - - +
156B GLY* 2.8 28.2 + - - -
165B VAL* 3.9 20.1 - - + +
167B SER 4.1 1.1 - - - -
168B PHE* 3.3 59.1 + - + +
169B SER* 5.9 0.6 - - - -
222B ARG* 3.5 45.4 + - - +
279B GLU* 2.6 44.2 + - - -
283B ARG* 4.5 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TYR* 2.9 28.6 + - - -
150B ILE 3.7 5.2 - - - -
151B ALA 3.2 0.4 - - - -
152B ARG* 1.3 79.4 - - - +
154B ILE* 1.3 62.3 + - - +
156B GLY* 3.4 7.4 + - - -
157B LYS* 3.5 18.4 + - - +
259B ALA 3.8 16.8 - - - -
260B LEU* 3.6 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TYR* 3.8 22.7 + - - +
96B VAL* 4.2 22.4 - - + +
99B LEU* 6.3 2.9 - - + -
100B GLU* 4.8 4.0 - - + +
150B ILE* 3.1 27.6 + - + +
151B ALA 3.8 3.4 - - - +
153B SER* 1.3 72.5 - - - +
155B ILE* 1.3 64.9 + - - +
157B LYS* 3.1 29.4 + - + +
259B ALA* 4.0 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TYR* 4.1 8.7 - - + -
93B VAL* 4.1 32.5 - - + +
96B VAL* 3.7 28.5 - - + -
151B ALA* 2.9 28.8 + - + +
152B ARG* 4.0 5.8 - - - +
154B ILE* 1.3 74.8 - - - +
156B GLY* 1.3 57.7 + - - +
158B LYS* 3.1 28.8 + - - +
159B LEU* 5.1 0.2 - - - -
163B PHE* 3.7 29.1 - - + +
164B TYR* 5.9 0.9 - - - -
165B VAL* 3.7 29.4 - - + +
168B PHE* 4.8 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ARG 2.8 18.3 + - - -
153B SER* 3.7 5.4 - - - -
154B ILE 3.2 0.2 - - - -
155B ILE* 1.3 73.1 - - - +
157B LYS* 1.3 58.0 + - - +
158B LYS 3.1 5.7 + - - -
159B LEU* 3.4 25.7 + - - +
222B ARG* 5.6 5.8 - - - -
272B TYR* 5.2 5.9 + - - -
----------------------------------------------------------
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