Contacts of the helix formed by residues 133 - 149 (chain A) in PDB entry 1M2V
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 GLU 133 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A SER* 1.3 80.1 - - - +
134A THR* 1.3 56.0 + - - +
135A GLU* 4.5 6.1 - - + +
136A ASN* 3.0 20.9 + - + +
137A LEU* 2.7 33.1 + - - +
247A PRO* 4.9 0.4 - - - -
289A SER* 5.5 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A SER 3.8 1.2 + - - -
133A GLU* 1.3 71.9 - - - +
135A GLU* 1.3 59.2 + - + +
137A LEU* 3.1 1.5 + - - +
138A ASP* 2.6 63.6 + - - +
247A PRO* 3.8 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU* 3.4 4.3 - - + +
134A THR* 1.3 79.1 - - + +
136A ASN* 1.3 62.4 + - - +
138A ASP* 3.7 6.5 - - - +
139A SER* 3.1 25.7 + - - -
376A SER* 4.4 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A SER* 3.3 24.5 + - - -
133A GLU* 3.0 24.4 + - + +
135A GLU* 1.3 78.6 - - - +
137A LEU* 1.3 62.0 + - - +
139A SER* 3.2 17.1 + - - -
140A LEU* 3.2 12.7 + - - +
289A SER* 3.5 10.7 + - - -
348A GLY 3.5 14.7 + - - -
374A ALA* 3.7 11.3 - - + +
375A PHE* 2.8 41.1 + - - +
376A SER* 4.5 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 4.3 17.7 - - + -
129A ASP 4.5 2.7 - - - +
130A LEU* 3.8 24.7 - - + +
132A SER* 3.5 21.7 + - - +
133A GLU 2.7 18.9 + - - +
134A THR* 3.8 3.6 - - - +
136A ASN* 1.3 73.7 - - - +
138A ASP* 1.3 58.6 + - - +
140A LEU* 3.8 12.6 - - + -
141A LYS* 2.9 36.5 + - + +
245A LEU* 4.4 4.9 - - + +
246A SER* 3.6 13.0 - - - +
247A PRO* 3.5 35.2 - - + -
375A PHE* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A THR* 2.6 49.9 + - - +
135A GLU* 3.7 6.7 + - - +
137A LEU* 1.3 70.7 - - - +
139A SER* 1.3 58.4 + - - +
140A LEU 3.1 4.5 - - - -
141A LYS* 3.1 33.4 + - - +
142A GLU* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLU 3.1 14.8 + - - -
136A ASN 3.2 7.1 + - - -
138A ASP* 1.3 75.7 - - - +
140A LEU* 1.3 61.4 + - - +
142A GLU* 3.6 13.3 - - - +
143A SER* 3.3 12.1 + - - -
375A PHE 3.2 14.4 + - - +
376A SER* 3.3 17.3 + - - -
381A LYS* 2.8 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 4.2 17.5 - - + -
129A ASP 5.6 1.1 - - - +
136A ASN 3.2 14.8 + - - +
137A LEU* 3.8 13.0 - - + +
138A ASP 3.1 0.6 - - - -
139A SER* 1.3 75.3 + - - +
141A LYS* 1.3 66.9 + - + +
142A GLU 3.1 1.6 - - - -
143A SER* 3.1 3.4 + - - +
144A ILE* 3.0 34.9 + - + +
287A PHE* 3.3 56.3 - - + +
375A PHE* 3.6 26.9 - - + -
380A PHE* 3.7 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 2.9 35.2 - - + +
138A ASP* 3.1 27.9 + - - +
140A LEU* 1.3 78.7 - - + +
142A GLU* 1.3 62.3 + - - +
144A ILE* 4.2 6.9 - - - +
145A ILE* 3.2 33.9 + - + +
242A LEU* 3.2 31.3 - - - +
243A GLU* 3.5 18.0 + - - +
245A LEU* 3.0 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASP 3.0 11.8 + - - +
139A SER* 3.6 16.3 - - - +
141A LYS* 1.3 79.6 - - - +
143A SER* 1.3 61.4 + - - +
145A ILE* 3.4 7.0 + - - +
146A THR* 3.0 33.5 + - - +
381A LYS* 4.1 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A SER 3.3 11.3 + - - -
140A LEU 3.1 7.6 + - - -
142A GLU* 1.3 75.8 - - - +
144A ILE* 1.3 67.0 + - - +
146A THR* 3.0 8.6 + - - -
147A SER* 2.8 24.1 + - - -
380A PHE* 3.7 14.4 - - - -
381A LYS* 3.4 28.1 + - - +
384A TYR* 3.7 22.7 - - - -
385A LEU* 4.1 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PHE* 4.0 26.5 - - + -
128A VAL* 3.7 22.9 - - + -
140A LEU* 3.0 35.3 + - + +
141A LYS* 4.2 6.3 - - - +
143A SER* 1.3 75.1 - - - +
145A ILE* 1.3 62.0 + - - +
147A SER* 2.5 23.6 + - - -
148A LEU* 3.2 11.0 + - + +
242A LEU* 3.7 29.6 - - + -
287A PHE* 3.6 35.2 - - + -
384A TYR* 3.9 2.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LYS* 3.2 21.4 + - + +
142A GLU* 3.6 6.5 - - - +
143A SER 3.1 0.4 - - - -
144A ILE* 1.3 77.6 - - - +
146A THR* 1.3 66.4 + - - +
148A LEU* 3.0 27.7 + - + +
149A SER* 3.6 5.2 + - - -
239A ASN* 3.6 25.1 - - - +
242A LEU* 4.0 26.7 - - + +
243A GLU* 3.7 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLU* 3.0 20.9 + - - +
143A SER* 3.0 10.3 + - - -
145A ILE* 1.3 79.3 - - - +
147A SER* 1.3 59.8 + - - +
149A SER* 2.9 25.3 + - - +
150A LEU* 3.5 10.6 - - + +
385A LEU* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PHE* 4.5 4.0 - - - -
143A SER 2.8 5.8 + - - -
144A ILE* 2.5 23.2 + - - +
146A THR* 1.3 73.9 - - - +
148A LEU* 1.3 55.7 + - - +
149A SER 3.0 2.0 - - - -
150A LEU* 2.6 43.2 + - - +
151A LEU* 3.4 8.3 + - - +
384A TYR* 2.9 40.9 + - - -
385A LEU* 4.0 4.7 - - - +
388A PHE* 4.0 17.6 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
126A PHE* 4.3 18.8 - - + -
144A ILE* 3.2 12.8 - - + +
145A ILE* 3.0 16.3 + - + +
147A SER* 1.3 82.7 + - - +
149A SER* 1.3 56.2 + - - +
150A LEU 3.3 2.9 + - - -
151A LEU* 3.4 26.0 + - + +
157A ILE* 4.6 5.4 - - + -
231A LEU* 3.1 44.2 - - + +
235A GLU* 4.4 6.9 - - - +
238A LEU* 3.3 34.3 - - + -
239A ASN* 4.5 15.0 - - - +
242A LEU* 3.6 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE 3.6 3.4 + - - -
146A THR* 2.9 24.8 + - - +
147A SER 2.9 0.2 + - - -
148A LEU* 1.3 77.0 - - - +
150A LEU* 1.3 63.7 + - - +
151A LEU 3.5 3.0 - - - +
235A GLU* 4.8 8.7 - - - -
----------------------------------------------------------
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