Contacts of the helix formed by residues 138 - 155 (chain A) in PDB entry 3PM0
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 SER 138 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A HIS* 3.5 6.9 + - - +
137A TYR* 1.3 82.4 - - - +
139A GLU* 1.3 59.7 + - - +
140A HIS* 3.9 10.0 + - - +
141A TRP* 3.2 18.8 + - - +
142A LYS* 2.7 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A SER* 1.3 71.9 - - - +
140A HIS* 1.3 73.2 + - + +
142A LYS* 2.9 53.3 + - - +
143A VAL* 3.3 14.6 + - + +
146A ARG* 5.3 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A SER* 3.4 8.5 + - - +
139A GLU* 1.3 81.1 + - + +
141A TRP* 1.3 63.2 + - - +
143A VAL* 3.6 6.0 + - - +
144A GLN* 3.4 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A MET* 2.8 28.1 + - + +
135A GLY* 4.2 8.3 - - - -
136A HIS 2.9 28.3 - - - +
137A TYR* 3.6 33.7 - + - -
138A SER* 3.2 16.7 + - - +
139A GLU 3.1 0.4 - - - -
140A HIS* 1.3 78.0 - - - +
142A LYS* 1.3 73.8 + - + +
144A GLN* 3.1 21.2 + - - +
145A ARG* 3.0 57.2 + - + -
467A LYS* 4.2 7.6 - - + -
468A ARG* 3.3 43.0 - - - +
900A HEM 3.7 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TYR* 3.2 47.4 + - + +
138A SER* 2.7 15.7 + - - +
139A GLU* 2.9 47.0 + - - +
141A TRP* 1.3 86.2 - - + +
143A VAL* 1.3 55.9 + - + +
145A ARG* 4.2 1.7 - - - +
146A ARG* 3.2 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLU* 3.3 14.6 + - + +
140A HIS* 4.3 6.1 - - - +
142A LYS* 1.3 75.4 - - - +
144A GLN* 1.3 61.5 + - - +
145A ARG 3.2 0.4 - - - -
146A ARG* 4.1 19.3 - - - +
147A ALA* 2.7 34.5 + - - +
303A LYS* 4.9 5.8 - - - +
313A ALA* 3.5 30.1 - - + -
314A ARG 3.7 17.3 - - - +
315A LEU* 4.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG 2.8 29.0 + - - +
131A SER 4.0 2.8 - - - +
132A MET* 3.5 30.8 - - + +
140A HIS 3.4 10.6 + - - +
141A TRP* 3.1 20.3 + - - +
143A VAL* 1.3 81.0 - - - +
145A ARG* 1.3 56.1 + - - +
148A ALA* 3.0 27.9 + - - +
315A LEU* 3.6 24.2 - - + +
319A ASN* 4.5 16.7 + - + +
323A THR* 3.7 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A MET* 3.4 29.4 - - + -
141A TRP* 3.0 41.0 + - + +
142A LYS 4.2 3.1 - - - +
144A GLN* 1.3 75.9 - - - +
146A ARG* 1.3 56.6 + - - +
148A ALA* 3.1 1.0 + - - +
149A HIS* 2.7 56.5 + - - +
466A GLY 4.8 0.2 + - - -
467A LYS 3.0 20.9 + - - -
468A ARG* 3.7 1.0 - - - +
469A ARG* 2.6 37.2 + - - +
471A ILE* 3.4 16.1 - - + +
900A HEM 2.4 38.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
139A GLU* 5.3 3.4 + - - -
142A LYS* 3.2 43.0 + - - +
143A VAL* 3.8 15.8 - - - +
145A ARG* 1.3 78.9 - - - +
147A ALA* 1.3 51.3 + - - +
149A HIS* 3.4 6.1 + - - +
150A SER* 2.4 41.8 + - - +
153A ARG* 4.9 4.1 + - - +
312A GLY 5.7 0.4 - - - -
313A ALA* 3.4 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A VAL 2.7 24.0 + - - +
146A ARG* 1.3 72.2 - - - +
148A ALA* 1.3 63.5 + - - +
150A SER* 3.4 8.4 + - - -
151A MET* 3.2 22.5 + - - +
296A PHE* 4.0 6.9 - - + -
313A ALA* 3.8 19.4 - - - +
314A ARG* 4.0 2.2 - - - -
315A LEU* 3.7 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A MET* 3.3 27.6 - - + -
144A GLN 3.0 20.6 + - - +
145A ARG 3.5 0.4 - - - +
147A ALA* 1.3 75.2 - - - +
149A HIS* 1.3 63.8 + - - +
151A MET* 3.5 3.8 + - - +
152A MET* 3.3 26.5 + - - +
296A PHE* 4.5 10.7 - - - -
315A LEU* 5.0 0.2 - - - +
323A THR* 4.5 14.4 - - - +
327A ILE* 4.6 5.1 - - + +
471A ILE* 3.8 9.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
145A ARG* 2.7 46.6 + - - +
146A ARG* 3.7 6.3 - - - +
148A ALA* 1.3 71.1 - - - +
150A SER* 1.3 66.3 + - - +
152A MET* 3.3 3.6 + - + +
153A ARG* 3.0 62.8 + - - +
469A ARG* 5.5 5.4 - - + -
470A CYS 4.6 3.6 + - - -
471A ILE* 3.8 37.5 + - + +
----------------------------------------------------------
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 ARG* 2.4 30.9 + - - +
147A ALA* 3.5 9.5 - - - -
148A ALA 3.3 0.2 - - - -
149A HIS* 1.3 77.4 - - - +
151A MET* 1.3 58.3 + - - +
153A ARG* 3.2 11.7 + - - +
154A ASN* 2.9 45.7 + - - +
313A ALA* 4.4 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ALA 3.2 3.4 + - - +
148A ALA 3.8 4.3 - - - +
150A SER* 1.3 78.1 - - - +
152A MET* 1.3 57.0 + - + +
154A ASN* 4.9 2.0 - - - -
155A PHE* 2.6 54.2 + - + +
292A MET* 3.8 20.4 - - + -
295A ALA* 3.8 23.8 - - + +
296A PHE* 3.3 72.2 - - + +
299A SER* 5.0 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ALA 3.3 14.5 + - - +
149A HIS* 3.6 9.0 - - + +
150A SER 3.3 0.2 - - - -
151A MET* 1.3 77.1 - - - +
153A ARG* 1.3 58.5 + - - +
156A PHE* 3.3 51.3 - - + +
205A MET* 6.1 0.9 - - - -
292A MET* 4.6 12.1 - - - +
327A ILE* 4.4 12.8 - - + -
471A ILE* 3.5 35.9 - - + +
472A GLY* 4.1 10.3 - - - -
475A LEU* 4.0 13.2 - - + -
900A HEM 3.5 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ARG* 4.9 4.4 + - - +
149A HIS* 3.0 64.8 + - - +
150A SER* 3.8 11.1 + - - +
152A MET* 1.3 75.7 - - - +
154A ASN* 1.3 66.3 + - - +
156A PHE* 2.7 26.7 - - - +
157A THR* 4.0 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A SER* 2.9 24.0 + - - +
151A MET* 4.9 2.2 - - - -
153A ARG* 1.3 80.2 + - - +
155A PHE* 1.3 67.3 + - - +
156A PHE 2.6 6.4 + - - +
157A THR* 5.2 2.0 - - - -
158A ARG* 2.8 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A MET* 2.6 51.0 + - + +
154A ASN* 1.3 72.9 - - - +
156A PHE* 1.3 88.9 + + + +
157A THR 3.8 0.5 + - - -
158A ARG* 2.6 61.3 + - - +
162A SER* 4.6 3.1 + - - -
208A VAL* 3.5 41.1 - - + -
291A ASP* 3.4 23.6 - - - -
292A MET* 3.6 19.7 - - + -
295A ALA* 4.4 3.4 - - + -
----------------------------------------------------------
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