Contacts of the helix formed by residues 148 - 155 (chain A) in PDB entry 4TMU
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 148 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A VAL* 3.6 19.7 - - - +
146A ASP 2.9 4.0 + - - -
147A GLU* 1.3 67.8 - - - +
149A HIS* 1.3 64.0 + - - +
150A CYS 3.0 2.5 - - - -
151A ILE* 3.0 30.2 + - + +
179A ALA* 3.7 16.6 - - + -
180A LEU 2.7 30.5 + - - +
181A THR* 3.9 1.5 - - + -
192A ILE* 3.5 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLU* 3.4 39.8 - - + -
148A ALA* 1.3 77.3 - - - +
150A CYS* 1.3 64.9 + - - +
152A SER* 3.1 7.3 + - - -
153A GLN* 2.9 56.7 + - + +
181A THR* 3.1 21.6 + - - +
182A ALA* 5.4 3.4 - - + -
183A THR* 3.5 24.8 + - - +
188A THR* 4.2 11.3 - - + +
192A ILE* 4.1 10.1 - - - -
298A MET* 4.0 5.9 - - - -
318A GLU* 5.8 0.2 - - - +
322A GLN* 3.2 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PRO* 4.1 9.0 - - - -
147A GLU* 3.0 18.9 + - - +
149A HIS* 1.3 92.5 - - - +
151A ILE* 1.3 66.4 + - - +
153A GLN* 4.2 8.5 - - - +
154A TRP* 2.9 58.4 + - + +
155A GLY 3.3 1.4 + - - -
162A TYR* 3.9 23.6 - - + -
298A MET* 4.0 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A VAL* 3.9 23.6 - - + -
148A ALA* 3.0 18.6 + - + +
150A CYS* 1.3 75.2 - - - +
152A SER* 1.3 58.7 + - - +
155A GLY* 2.9 27.5 + - - -
156A HIS 4.3 0.2 + - - -
162A TYR* 3.8 36.8 - - + +
165A LEU* 4.5 0.9 - - + -
192A ILE* 4.2 20.2 - - + -
195A LEU* 3.7 38.6 - - + +
196A LEU* 4.0 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ALA 4.2 0.2 + - - -
149A HIS 3.1 7.8 + - - -
151A ILE* 1.3 81.5 - - - +
153A GLN* 1.3 60.3 + - - +
154A TRP 3.4 0.4 + - - -
155A GLY 4.4 0.2 + - - -
156A HIS* 3.3 21.8 - - - +
187A THR* 5.4 0.9 - - - +
188A THR* 3.9 30.0 + - - -
191A ASP* 3.0 37.1 + - - +
192A ILE* 4.8 3.1 - - - -
195A LEU* 4.7 0.2 - - - -
367A LYS* 5.4 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A HIS* 2.9 43.6 + - + +
150A CYS* 4.2 2.8 - - - -
152A SER* 1.3 78.6 - - - +
154A TRP* 1.3 94.9 + - + +
156A HIS* 5.3 0.4 - - - -
157A ASP* 3.9 9.9 - - - +
298A MET* 6.3 0.4 - - - -
316A ASN* 6.2 2.0 - - - +
318A GLU* 5.9 2.9 - - - +
319A SER* 5.5 4.8 + - - -
322A GLN* 4.9 9.4 + - - +
26B T 4.5 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PRO* 3.8 8.5 - - + -
74A LEU* 4.8 0.2 - - + -
150A CYS* 2.9 34.8 + - - +
153A GLN* 1.3 110.1 - - - +
155A GLY* 1.3 64.1 + - - +
156A HIS 3.2 3.1 + - - -
157A ASP* 4.0 4.7 - - - -
158A PHE* 3.2 24.9 + + + -
159A ARG* 2.9 67.7 + - + +
162A TYR* 4.0 11.2 - + + -
298A MET* 3.6 25.6 - - + -
26B T 2.9 45.1 + + + -
27B G 4.1 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A CYS 3.3 0.8 + - - -
151A ILE 2.9 21.0 + - - -
154A TRP* 1.3 79.9 - - - +
156A HIS* 1.3 61.4 + - - +
159A ARG 3.4 12.3 - - - -
160A PRO* 3.3 19.9 - - - +
162A TYR* 3.7 2.0 - - - -
163A ALA* 3.5 28.8 - - - +
----------------------------------------------------------
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