Contacts of the helix formed by residues 140 - 156 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASP* 3.2 22.7 - - + +
71A ARG* 3.8 14.8 - - + +
138A GLY 3.7 4.7 + - - +
139A CYS* 1.3 77.3 - - - +
141A GLY* 1.3 69.9 + - - +
142A ASP 3.2 2.8 + - - -
143A GLU* 3.2 14.5 + - - +
144A LEU* 3.3 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASP* 2.9 24.6 + - - +
140A ALA* 1.3 70.4 - - - +
142A ASP* 1.3 63.6 + - - -
144A LEU* 3.7 1.6 - - - +
145A ASP* 3.0 23.7 + - - +
170A CYS* 3.7 11.3 - - - -
171A ARG* 3.3 23.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ALA 3.2 1.4 + - - -
141A GLY* 1.3 69.9 - - - -
143A GLU* 1.3 58.1 + - - +
145A ASP* 3.3 3.4 + - - +
146A ARG* 2.9 27.8 + - - +
171A ARG* 2.8 39.5 + - - +
283A ARG* 5.3 2.5 + - - +
338A LYS* 3.0 21.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A CYS* 3.6 28.3 - - + -
140A ALA 3.2 7.8 + - - +
142A ASP* 1.3 79.1 - - - +
144A LEU* 1.3 62.6 + - - +
146A ARG* 3.0 46.6 + - - +
147A ARG* 3.1 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASP 3.6 20.9 - - - +
71A ARG* 3.6 25.1 - - - +
72A LEU 4.2 0.2 - - - +
73A GLY* 4.2 5.2 - - - +
102A LEU* 3.9 32.5 - - + -
133A VAL* 5.1 2.9 - - + -
134A THR 5.1 1.8 - - - -
135A CYS* 4.6 9.9 - - + +
139A CYS* 4.3 9.4 - - + +
140A ALA* 3.3 22.9 + - - +
141A GLY 3.3 2.8 + - - +
143A GLU* 1.3 79.4 - - - +
145A ASP* 1.3 56.5 + - - +
147A ARG* 3.2 5.1 + - + +
148A LEU* 3.0 48.0 + - + +
170A CYS* 3.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLY 3.0 13.5 + - - +
142A ASP 3.9 2.7 - - - +
144A LEU* 1.3 75.7 - - - +
146A ARG* 1.3 57.5 + - - +
148A LEU* 3.7 6.5 - - - +
149A TYR* 2.9 30.0 + - - +
152A ARG* 4.7 2.4 + - - +
168A PHE 4.9 0.6 - - - +
169A SER* 2.7 28.7 + - - -
170A CYS* 2.6 38.3 + - - +
171A ARG* 4.1 18.3 - - - +
172A THR* 5.2 0.2 - - - +
283A ARG* 3.6 32.7 + - - +
336A ASP 4.7 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASP 2.9 15.3 + - - +
143A GLU* 3.0 42.7 + - - +
145A ASP* 1.3 78.2 - - - +
147A ARG* 1.3 59.9 + - - +
149A TYR* 3.4 8.3 + - - +
150A ILE* 3.1 37.9 + - - +
251A GLY 3.4 16.2 + - - -
252A TRP* 3.2 52.1 - - + +
256A GLU* 2.3 49.3 + - - -
283A ARG* 4.6 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLU* 3.5 44.5 + - + +
101A LYS* 4.1 20.3 - - - +
102A LEU* 4.2 18.5 - - + +
135A CYS* 3.6 22.8 - - - -
137A GLU* 5.3 4.6 - - - +
139A CYS* 3.3 27.4 - - - -
143A GLU* 3.1 36.7 + - - +
144A LEU* 3.7 7.0 - - - +
146A ARG* 1.3 79.4 - - - +
148A LEU* 1.3 62.1 + - - +
150A ILE* 3.4 6.9 + - + +
151A ALA* 3.0 26.5 + - - +
256A GLU* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLY* 4.1 8.5 - - - -
97A VAL* 5.9 0.2 - - + -
102A LEU* 3.4 30.7 - - + -
133A VAL* 4.4 4.7 - - + -
144A LEU* 3.0 35.8 + - + +
145A ASP* 3.7 21.3 - - - +
147A ARG* 1.3 76.2 - - - +
149A TYR* 1.3 54.8 + - - +
151A ALA* 3.5 5.0 - - + +
152A ARG* 2.8 37.2 + - - +
168A PHE* 3.4 52.4 - - + +
169A SER* 3.9 15.3 - - - -
170A CYS 4.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASP 2.9 18.1 + - - +
146A ARG 3.4 4.3 - - - +
148A LEU* 1.3 76.4 - - - +
150A ILE* 1.3 55.7 + - - +
152A ARG* 3.3 22.3 + - - +
153A SER* 3.0 42.6 + - - -
252A TRP* 3.8 14.4 - + - -
260A LEU* 3.5 36.4 - - + +
263A ILE* 4.3 6.2 - - - +
276A SER* 4.6 3.6 + - - -
279A GLU* 3.5 34.1 - - + -
280A LEU* 3.3 30.5 + - + +
283A ARG* 3.5 35.7 - - + -
284A THR* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLU* 3.6 29.6 - - - +
146A ARG* 3.1 23.1 + - - +
147A ARG* 3.6 10.3 - - + +
148A LEU 3.3 0.2 - - - -
149A TYR* 1.3 75.3 - - - +
151A ALA* 1.3 62.3 + - - +
153A SER* 3.1 4.0 + - - -
154A ILE* 3.0 25.6 + - + +
252A TRP* 3.8 33.0 - - + -
256A GLU* 3.8 32.1 - - + +
259A ALA* 4.0 23.3 - - + +
260A LEU* 4.1 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A VAL* 3.6 24.7 - - + +
97A VAL* 5.0 6.3 - - + -
100A GLU* 4.2 11.4 - - + +
102A LEU* 5.8 0.4 - - + -
147A ARG 3.0 17.6 + - - +
148A LEU* 3.5 11.4 - - + +
150A ILE* 1.3 73.8 - - - +
152A ARG* 1.3 58.8 + - - +
154A ILE* 3.2 2.6 + - - -
155A ILE* 2.9 36.2 + - + +
168A PHE* 4.6 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASP* 4.7 1.6 + - - -
148A LEU 2.8 14.1 + - - +
149A TYR* 3.5 30.8 - - - +
151A ALA* 1.3 71.7 - - - +
153A SER* 1.3 57.7 + - - +
155A ILE* 3.8 8.1 - - - +
156A GLY* 2.9 27.0 + - - -
165A VAL* 3.9 19.9 - - + +
168A PHE* 3.4 55.2 + - + +
169A SER* 5.8 1.4 - - - -
222A ARG* 3.5 54.0 + - - +
279A GLU* 2.7 43.4 + - - -
283A ARG* 4.4 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A TYR* 3.0 26.8 + - - -
150A ILE 3.1 8.2 + - - -
152A ARG* 1.3 76.4 + - - +
154A ILE* 1.3 61.5 + - - +
156A GLY* 3.4 9.6 + - - -
157A LYS* 3.6 18.5 + - - -
259A ALA 3.9 2.9 - - - -
260A LEU* 3.6 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TYR* 3.8 21.8 + - - +
96A VAL* 4.1 24.2 - - + -
99A LEU* 6.0 3.4 - - + -
100A GLU* 4.1 11.0 - - + +
150A ILE* 3.0 35.6 + - + +
151A ALA 3.7 4.3 - - - +
153A SER* 1.3 71.9 - - - +
155A ILE* 1.3 65.9 + - - +
156A GLY 3.1 1.6 - - - -
157A LYS* 3.1 30.8 + - + +
259A ALA* 4.0 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TYR* 4.1 8.5 - - + -
93A VAL* 4.1 32.1 - - + +
96A VAL* 3.8 24.7 - - + -
97A VAL* 5.1 0.2 - - + -
151A ALA* 2.9 26.2 + - + +
152A ARG* 3.9 4.9 - - - +
154A ILE* 1.3 75.3 - - - +
156A GLY* 1.3 57.2 + - - +
158A LYS* 3.2 26.3 + - - +
159A LEU 4.2 0.3 + - - -
163A PHE* 3.8 30.6 - - + +
164A TYR* 6.0 0.9 - - - -
165A VAL* 3.7 29.8 - - + +
168A PHE* 4.6 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ARG 2.9 17.3 + - - -
153A SER* 3.7 6.1 - - - -
154A ILE 3.1 0.8 - - - -
155A ILE* 1.3 73.4 - - - +
157A LYS* 1.3 58.0 + - - +
158A LYS 3.1 5.8 - - - -
159A LEU* 3.3 25.0 + - - +
222A ARG* 5.7 5.2 - - - -
272A TYR* 5.0 8.6 + - - -
----------------------------------------------------------
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