Contacts of the helix formed by residues 136 - 151 (chain A) in PDB entry 4U2M
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 ARG 136 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE* 3.2 1.0 + - - +
135A THR* 1.3 77.7 + - - +
137A HIS* 1.3 64.7 + - - +
138A ALA 3.4 2.7 - - - -
139A SER* 3.4 13.7 + - - +
140A ASP* 3.0 52.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.1 5.8 - - + -
45A CYS* 3.9 13.2 - - + -
76A PHE* 3.4 44.4 + + + -
77A MET 2.8 26.9 + - - -
80A ALA* 3.7 17.5 - - + -
103A ASP* 5.3 4.8 + - - +
134A PHE* 3.2 27.8 + - + +
135A THR 3.4 0.4 - - - -
136A ARG* 1.3 78.6 - - - +
138A ALA* 1.3 65.4 + - - +
140A ASP* 3.0 13.5 + - + +
141A VAL* 2.8 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A SER* 3.6 30.5 - - - +
8A GLN* 3.6 25.8 - - + +
11A LEU* 3.9 20.9 - - + +
80A ALA* 5.0 1.0 - - - +
134A PHE 4.8 0.4 + - - -
135A THR 4.9 4.1 + - - +
136A ARG 3.4 0.2 - - - -
137A HIS* 1.3 79.6 - - - +
139A SER* 1.3 62.6 + - - +
141A VAL* 3.3 5.6 + - - +
142A LEU* 3.1 23.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
7A SER* 3.0 21.8 + - - -
136A ARG* 3.4 19.9 + - - +
137A HIS 3.3 0.2 - - - -
138A ALA* 1.3 78.2 - - - +
140A ASP* 1.3 60.9 + - - +
142A LEU* 3.4 2.1 + - - +
143A LEU* 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASP* 4.8 9.0 - - - +
136A ARG* 3.0 60.2 + - - +
137A HIS* 3.0 14.7 + - - +
139A SER* 1.3 76.2 - - - +
141A VAL* 1.3 59.2 + - + +
143A LEU* 3.3 12.6 + - - +
144A ASN* 2.9 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 6.3 0.4 - - + -
11A LEU* 4.4 13.7 - - + -
14A LEU* 4.6 8.1 - - + -
41A VAL* 5.0 5.8 - - + -
44A ALA* 4.0 11.5 - - + +
45A CYS* 3.7 16.8 - - - -
77A MET 4.3 2.9 - - - +
137A HIS* 2.8 52.4 + - + +
138A ALA* 3.6 8.7 - - - +
139A SER 3.3 0.2 - - - -
140A ASP* 1.3 73.6 - - - +
142A LEU* 1.3 59.2 + - - +
144A ASN* 3.2 5.3 + - - +
145A LEU* 2.8 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A HIS* 3.9 11.4 - - + -
7A SER* 3.8 19.3 - - - +
10A VAL* 4.1 24.5 - - + -
138A ALA 3.1 14.5 + - - +
139A SER* 3.9 3.4 - - - +
141A VAL* 1.3 79.9 - - - +
143A LEU* 1.3 63.1 + - - +
145A LEU* 3.2 15.5 + - + +
146A ASN* 2.9 23.6 + - - +
172A VAL* 5.2 3.6 - - + -
213A MET 3.6 15.5 - - - +
214A TYR* 3.4 29.3 - - + +
215A THR* 4.2 2.7 - - - +
216A SER* 3.7 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A SER 3.0 18.8 + - - +
140A ASP* 3.6 11.7 - - - +
142A LEU* 1.3 76.1 - - - +
144A ASN* 1.3 60.0 + - - +
146A ASN* 3.2 12.1 + - + +
147A ARG* 2.9 66.5 + - + +
214A TYR 5.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA* 3.0 35.5 + - + +
140A ASP* 2.9 28.3 + - - +
141A VAL 3.8 2.0 - - - +
143A LEU* 1.3 77.6 - - - +
145A LEU* 1.3 60.3 + - - +
147A ARG* 3.2 35.3 + - + +
148A LEU* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 5.2 0.9 - - + -
14A LEU* 4.3 15.5 - - + -
40A ALA* 3.7 40.6 - - + +
41A VAL* 4.5 5.2 - - + +
44A ALA* 4.0 7.0 - - + -
141A VAL* 2.8 37.1 + - + +
142A LEU* 3.2 15.9 + - + +
144A ASN* 1.3 73.3 - - - +
146A ASN* 1.3 58.6 + - - +
148A LEU* 3.3 9.9 + - + +
149A ARG* 2.9 23.4 + - - +
169A HIS* 3.6 11.5 - - - +
171A THR* 5.7 0.9 - - + -
172A VAL* 3.9 24.7 - - + -
214A TYR* 3.7 13.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU 2.9 12.7 + - - +
143A LEU* 3.5 14.0 - - + +
145A LEU* 1.3 76.4 - - - +
147A ARG* 1.3 60.9 + - - +
149A ARG* 2.9 38.0 + - - +
150A SER* 2.8 33.8 + - - -
214A TYR* 3.3 24.3 - - + +
215A THR* 3.6 21.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
50A LYS* 6.3 1.1 - - - +
143A LEU* 2.9 46.1 + - + +
144A ASN* 3.2 32.7 + - - +
146A ASN* 1.3 75.9 - - - +
148A LEU* 1.3 64.4 + - + +
150A SER* 3.3 17.1 + - - -
151A ARG* 3.3 18.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
40A ALA* 3.6 29.2 - - - +
43A ALA* 4.0 14.8 - - + +
44A ALA* 4.2 5.6 - - + +
50A LYS* 4.0 30.7 - - + +
144A ASN* 2.9 21.2 + - + +
145A LEU* 3.4 17.3 - - + +
147A ARG* 1.3 77.1 - - + +
149A ARG* 1.3 64.0 + - - +
151A ARG 3.3 0.9 + - - -
152A ASP 3.1 3.8 + - - -
153A ILE* 2.8 66.6 + - + +
154A LEU* 4.8 1.6 - - + -
169A HIS* 3.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU 2.9 14.1 + - - +
146A ASN* 2.9 36.2 + - - +
148A LEU* 1.3 77.9 - - - +
150A SER* 1.3 62.6 + - - +
152A ASP* 3.0 14.2 + - - +
155A THR* 4.4 5.4 - - + +
166A PHE* 6.0 0.2 - - - -
167A ARG* 3.8 26.0 + - + +
168A ALA* 4.9 0.2 - - - -
169A HIS* 3.7 15.4 - - + -
207A CYS* 6.3 0.2 - - - -
210A LEU* 3.5 24.6 - - - +
211A ASP* 3.0 37.0 + - - +
214A TYR* 3.5 35.1 - - + +
215A THR* 5.2 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ASN* 2.8 23.6 + - - -
147A ARG* 3.4 13.8 - - - -
149A ARG* 1.3 74.0 - - - +
151A ARG* 1.3 66.0 + - - +
152A ASP* 3.3 0.9 + - - +
1B SER 3.7 8.7 - - - +
2B ASP* 5.3 3.6 - - - +
4B PRO* 5.9 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ARG* 3.3 14.1 + - + +
149A ARG 3.2 0.4 - - - -
150A SER* 1.3 84.0 + - - +
152A ASP* 1.3 69.4 + - - +
153A ILE* 3.3 22.4 + - + -
-1B LEU 3.1 21.5 + - - +
0B GLY* 3.2 27.7 + - - -
1B SER* 3.1 31.1 + - - +
2B ASP* 2.9 45.1 + - - +
----------------------------------------------------------
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