Contacts of the helix formed by residues 142 - 156 (chain B) in PDB entry 5E1M
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 THR 142 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B THR* 3.7 12.1 - - - +
6B ILE* 4.2 19.3 - - + -
9B GLU* 3.6 32.3 - - + +
12B PHE* 4.2 2.4 - - + -
13B TYR* 3.2 15.7 + - + +
141B LEU* 1.3 75.9 - - - +
143B ASP* 1.3 59.5 + - - +
144B GLN 4.2 1.3 - - - -
145B HIS* 3.0 18.7 + - - +
146B LEU* 2.8 27.2 + - - +
185B ARG* 3.4 0.7 - - - +
309B UNX 2.7 20.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B SER* 3.4 16.5 - - - -
2B THR* 2.9 43.3 + - - +
3B SER 4.6 0.3 + - - -
142B THR* 1.3 70.6 - - - +
144B GLN* 1.3 58.4 + - - +
146B LEU* 3.7 1.7 - - - +
147B ALA* 2.9 30.7 + - - +
174B VAL* 5.4 0.3 - - - +
185B ARG* 2.9 34.4 + - - +
189B VAL* 4.6 5.0 - - - +
193B ILE* 3.4 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B THR* 3.3 1.4 + - - -
143B ASP* 1.3 78.7 - - - +
145B HIS* 1.3 60.8 + - - +
147B ALA* 3.4 5.7 + - + +
148B GLU* 2.8 63.2 + - + +
309B UNX 3.9 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLU* 3.4 24.9 + - - -
13B TYR* 2.6 34.2 + + - +
120B GLN* 3.9 25.5 + - + +
141B LEU* 3.7 10.8 - - + +
142B THR* 3.0 17.1 + - - +
144B GLN* 1.3 79.4 - - + +
146B LEU* 1.3 57.8 + - - +
148B GLU* 3.7 20.4 - - + +
149B PHE* 2.8 31.2 + - - +
152B ARG* 5.1 1.6 + - - -
309B UNX 3.7 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 6.5 0.4 - - + -
134B ILE* 5.8 1.6 - - + -
138B ILE* 3.9 40.2 - - + +
141B LEU* 3.8 20.1 - - + +
142B THR 2.8 18.0 + - - +
143B ASP 3.7 4.3 - - - +
145B HIS* 1.3 73.7 - - - +
147B ALA* 1.3 60.0 + - - +
149B PHE* 3.7 6.2 - - + +
150B LEU* 2.9 54.1 + - + +
165B ILE* 5.4 1.3 - - + -
185B ARG* 3.8 29.6 - - - +
190B VAL* 6.1 2.9 - - + -
193B ILE* 4.0 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASP 2.9 16.7 + - - +
144B GLN* 3.8 6.3 - - + +
146B LEU* 1.3 77.7 - - - +
148B GLU* 1.3 58.2 + - + +
150B LEU 3.4 0.2 + - - -
151B ARG* 3.1 26.1 + - - +
193B ILE* 3.9 12.3 - - + +
196B SER* 3.7 26.5 - - - +
197B ALA* 3.5 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLN* 2.8 48.7 + - + +
145B HIS* 3.7 24.7 - - - +
147B ALA* 1.3 72.8 - - + +
149B PHE* 1.3 66.8 + - - +
151B ARG* 3.3 8.5 + - - +
152B ARG* 3.0 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 5.4 0.2 - - + -
68B CYS* 3.9 18.6 - - - -
119B LEU* 3.4 51.8 - - + -
122B PHE* 3.8 25.8 - + - -
124B PRO* 4.3 4.0 - - + -
134B ILE* 3.9 21.5 - - + -
141B LEU* 4.1 11.7 - - + -
145B HIS 2.8 22.4 + - - +
146B LEU* 3.7 8.3 - - + +
148B GLU* 1.3 70.3 - - - +
150B LEU* 1.3 64.0 + - + +
152B ARG* 3.1 20.1 + - - +
153B CYS* 2.8 54.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ILE* 3.8 28.9 - - + -
146B LEU* 2.9 39.8 + - + +
149B PHE* 1.3 78.4 - - + +
151B ARG* 1.3 57.3 + - - +
153B CYS* 3.2 5.5 + - - +
154B LYS* 3.0 26.7 + - - +
163B ILE* 4.1 16.3 - - + +
165B ILE* 4.0 27.8 - - + -
193B ILE* 4.4 13.5 - - + -
194B ILE* 4.6 11.4 - - + -
197B ALA* 3.7 20.2 - - + -
199B LEU* 3.9 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA 3.1 14.5 + - - +
148B GLU* 3.7 9.4 - - - +
149B PHE 3.2 0.4 - - - -
150B LEU* 1.3 75.2 - - - +
152B ARG* 1.3 64.5 - - + +
154B LYS* 3.2 20.0 + - + +
155B GLY* 3.4 9.2 + - - -
196B SER 2.8 28.7 + - - -
197B ALA* 3.3 29.6 + - - +
198B GLY* 3.4 8.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
119B LEU 2.9 28.1 + - - -
120B GLN* 3.6 18.2 + - - +
121B ASP 5.3 0.7 - - - -
122B PHE 2.8 21.5 + - - +
123B THR* 3.6 26.5 + - + +
124B PRO* 4.0 20.2 - - + +
145B HIS 5.1 0.8 + - - -
148B GLU* 3.0 40.3 + - - +
149B PHE* 3.1 22.2 + - - +
151B ARG* 1.3 77.7 - - + +
153B CYS* 1.3 61.7 + - - +
155B GLY* 3.2 11.7 + - - +
156B SER* 3.4 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 5.5 0.2 - - - -
124B PRO* 4.0 6.3 - - - -
132B ILE* 3.5 28.6 - - + +
134B ILE* 4.4 5.2 - - - -
149B PHE* 2.8 54.0 + - - -
150B LEU* 3.2 10.9 + - + +
152B ARG* 1.3 77.2 - - - +
154B LYS* 1.3 62.5 + - - +
156B SER* 2.9 24.6 + - - -
157B LEU* 3.3 6.8 + - - +
163B ILE* 3.6 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU 3.0 12.3 + - - +
151B ARG* 3.4 17.5 - - + +
153B CYS* 1.3 75.3 - - - +
155B GLY* 1.3 61.7 + - - +
156B SER 3.3 1.0 + - - -
157B LEU* 3.3 23.5 + - + +
163B ILE* 3.8 7.8 - - - +
197B ALA 4.3 9.0 - - - +
198B GLY* 3.8 22.2 - - - +
199B LEU* 3.9 20.0 - - + -
223B ARG* 4.0 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PRO 5.7 0.4 - - - -
126B PRO* 3.4 21.9 - - - +
127B ASP 3.5 4.5 + - - -
151B ARG 3.4 5.5 + - - -
152B ARG 3.2 9.4 + - - -
153B CYS 3.2 1.0 - - - -
154B LYS* 1.3 79.3 - - - +
156B SER* 1.3 55.2 + - - +
157B LEU 3.4 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PRO* 3.5 32.5 - - - +
125B GLU 2.9 25.8 - - - -
126B PRO* 3.8 0.4 - - - -
127B ASP 3.6 2.9 - - - +
128B SER 2.8 23.4 + - - -
129B TYR* 3.0 13.0 + - - -
132B ILE* 3.2 16.6 - - - +
152B ARG 3.4 1.6 + - - -
153B CYS 2.9 14.4 + - - -
155B GLY* 1.3 75.2 - - - +
157B LEU* 1.3 61.2 + - - +
----------------------------------------------------------
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