Contacts of the helix formed by residues 131 - 151 (chain B) in PDB entry 2PO5
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 PRO 131 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ILE* 4.9 0.9 - - + -
129B GLY 3.9 5.6 - - - +
130B SER* 1.3 87.9 - - - +
132B ILE* 1.3 64.0 + - - +
133B LYS 3.3 2.7 - - - -
134B ILE* 3.0 23.0 + - + +
135B TRP* 3.0 42.1 + - + +
340B ASP* 3.6 27.6 - - + +
341B HIS* 4.6 4.0 - - - -
345B LEU* 4.2 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASN* 5.1 9.4 - - - +
77B GLY* 4.1 3.4 - - - -
78B GLY* 3.4 33.2 - - - +
80B GLU* 5.5 1.8 - - + -
130B SER* 2.9 27.6 - - - +
131B PRO* 1.3 78.1 - - - +
133B LYS* 1.3 74.0 + - + +
135B TRP* 3.9 1.3 - - - +
136B THR* 2.6 39.9 + - - +
163B PHE* 3.3 32.5 - - + -
339B SER* 4.4 11.4 + - - +
340B ASP 3.4 20.0 - - - +
341B HIS* 3.8 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLU* 3.5 42.3 + - + +
130B SER 4.8 1.5 + - - +
131B PRO 3.3 1.0 - - - -
132B ILE* 1.3 87.8 - - + +
134B ILE* 1.3 59.8 + - + +
136B THR* 3.8 1.6 - - - -
137B SER* 2.8 44.7 + - - +
161B ILE* 4.3 9.0 - - + -
163B PHE* 3.8 20.4 - - + -
167B HIS 5.0 0.2 - - - +
168B PRO* 4.1 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLU* 5.6 3.8 - - - +
130B SER 5.2 2.9 - - - +
131B PRO* 3.0 23.3 + - + +
133B LYS* 1.3 80.5 - - + +
135B TRP* 1.3 67.9 + - + +
137B SER* 3.6 4.8 - - - -
138B LYS* 3.1 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PRO* 3.0 44.4 + - + +
132B ILE 4.1 0.9 - - - +
134B ILE* 1.3 79.1 - - + +
136B THR* 1.3 65.2 + - - +
138B LYS* 3.4 37.9 + - + +
139B GLN* 3.0 32.5 + - - +
339B SER* 3.8 23.8 - - - +
340B ASP* 4.3 5.4 + - - +
372B ASN* 3.4 45.3 + - + +
373B GLY* 3.4 31.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B MET* 4.0 26.1 - - + +
75B ASN* 5.3 5.8 + - + +
132B ILE* 2.6 28.9 + - - +
133B LYS* 3.8 4.5 - - - -
135B TRP* 1.3 75.8 - - - +
137B SER* 1.3 58.3 + - - +
139B GLN* 3.4 11.8 + - - +
140B GLY* 2.9 27.4 + - - -
159B TYR* 4.8 0.3 - - - -
161B ILE* 3.8 30.7 - - + -
163B PHE* 4.0 12.5 - - + -
190B GLN* 5.3 5.2 - - + +
339B SER* 5.3 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LYS* 2.8 29.7 + - - +
134B ILE* 3.6 7.2 - - - -
135B TRP 3.3 0.2 - - - -
136B THR* 1.3 77.3 - - - +
138B LYS* 1.3 58.1 + - - +
140B GLY 3.3 0.5 + - - -
141B GLU* 2.9 43.1 + - - +
159B TYR* 3.6 22.7 + - - -
161B ILE* 3.5 13.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ILE* 3.1 35.4 + - - +
135B TRP* 3.8 41.0 - - + +
137B SER* 1.3 74.9 - - - +
139B GLN* 1.3 61.7 + - + +
141B GLU* 3.8 11.0 - - - +
142B GLY* 3.0 24.6 + - - -
373B GLY* 5.6 4.0 - - - -
378B SER* 4.2 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B MET* 4.5 2.0 - - + +
135B TRP* 3.0 25.1 + - - +
136B THR* 3.8 12.3 + - - +
138B LYS* 1.3 74.3 - - + +
140B GLY* 1.3 61.1 + - - +
142B GLY 3.3 0.5 + - - -
143B MET* 2.8 28.8 + - - +
190B GLN* 4.4 8.0 - - - +
338B THR* 3.4 22.1 + - - -
339B SER* 4.3 6.5 - - - -
372B ASN* 2.8 31.7 + - - +
373B GLY* 5.4 1.1 - - - -
377B PHE* 3.1 32.6 - - + -
378B SER* 3.4 15.3 + - - +
381B LEU* 3.8 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B MET* 3.6 26.9 - - - +
136B THR 2.9 13.6 + - - -
137B SER 3.8 1.1 - - - -
138B LYS 3.3 0.2 - - - -
139B GLN* 1.3 77.0 - - - +
141B GLU* 1.3 56.6 + - - +
143B MET* 3.2 6.3 + - - +
144B VAL* 2.9 32.7 + - - +
159B TYR* 3.6 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B SER* 2.9 32.1 + - - +
138B LYS* 3.8 10.6 + - - +
140B GLY* 1.3 74.1 - - - +
142B GLY* 1.3 64.4 + - - +
144B VAL* 3.4 4.6 + - - +
145B LYS* 3.0 25.5 + - - +
159B TYR* 3.4 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LYS 3.0 16.0 + - - -
139B GLN 3.7 2.5 - - - -
141B GLU* 1.3 77.5 - - - +
143B MET* 1.3 61.8 + - - +
145B LYS* 3.4 9.5 + - - +
146B LEU* 3.2 27.7 + - - +
378B SER* 3.8 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 3.4 46.4 - - + -
73B MET* 4.4 10.8 - - - -
139B GLN 2.8 17.9 + - - +
140B GLY 3.3 5.8 - - - +
142B GLY* 1.3 76.5 - - - +
144B VAL* 1.3 61.1 + - + +
146B LEU* 3.1 5.5 + - - +
147B LEU* 2.9 38.1 + - + +
159B TYR* 4.0 21.1 - - + -
188B PHE* 4.1 6.5 - - - -
378B SER* 4.0 10.4 - - - -
381B LEU* 3.9 26.0 - - + -
382B ALA* 3.9 14.8 - - - +
385B VAL* 4.1 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 5.0 0.7 - - + -
140B GLY 2.9 22.4 + - - +
141B GLU* 3.8 5.8 - - - +
143B MET* 1.3 78.7 - - + +
145B LYS* 1.3 64.7 + - - +
147B LEU* 3.1 7.1 + - - +
148B ASP* 3.0 35.0 + - - +
157B HIS* 3.2 29.6 - - + +
158B LYS* 4.1 3.4 - - - -
159B TYR* 3.7 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLU 3.0 18.5 + - - +
142B GLY* 3.6 8.5 + - - +
144B VAL* 1.3 79.2 - - - +
146B LEU* 1.3 83.1 + - - +
148B ASP* 3.9 9.1 + - - +
149B GLU* 3.7 18.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
142B GLY 3.2 13.2 + - - +
143B MET 3.1 6.8 + - - +
145B LYS* 1.3 97.0 - - - +
147B LEU* 1.3 61.0 + - - +
149B GLU* 3.0 8.8 + - + +
150B LEU* 2.9 34.9 + - + +
375B PRO 5.1 1.6 - - - +
378B SER* 3.7 13.0 - - - +
379B LYS* 3.5 38.4 - - + +
382B ALA* 3.7 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 4.0 20.4 - - + -
143B MET* 2.9 35.6 + - + +
144B VAL* 3.1 4.0 + - - +
146B LEU* 1.3 76.0 - - - +
148B ASP* 1.3 58.9 + - - +
150B LEU* 4.1 9.9 - - + -
151B SER* 2.8 31.5 + - - -
157B HIS* 3.4 30.1 - - + +
382B ALA* 3.4 31.9 - - + +
385B VAL* 3.6 30.5 - - + -
386B HIS* 4.1 8.1 - - + +
389B ILE* 5.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B VAL* 3.0 29.8 + - - +
145B LYS* 4.1 8.1 - - - +
146B LEU 3.3 0.4 - - - -
147B LEU* 1.3 76.3 - - - +
149B GLU* 1.3 70.6 + - - +
152B PRO* 4.2 17.7 - - - +
155B ALA* 4.3 10.5 - - + +
156B PRO* 3.7 7.2 - - - +
157B HIS* 2.8 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LYS* 3.7 15.7 - - + +
146B LEU* 3.0 7.3 + - + +
147B LEU 3.0 0.4 - - - -
148B ASP* 1.3 89.7 - - - +
150B LEU* 1.3 63.4 + - + +
151B SER 3.5 0.7 - - - -
152B PRO* 3.8 13.1 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
146B LEU* 2.9 22.5 + - + +
147B LEU* 3.9 5.8 - - + +
149B GLU* 1.3 79.4 - - + +
151B SER* 1.3 57.7 + - - +
152B PRO* 3.5 6.8 - - - +
379B LYS* 6.2 2.0 - - - +
382B ALA* 3.6 38.6 - - + +
383B ASP* 3.9 17.9 - - - +
386B HIS* 3.4 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 2.8 22.7 + - - -
148B ASP 4.5 0.2 - - - -
150B LEU* 1.3 76.5 - - - +
152B PRO* 1.3 64.2 - - - +
153B ASN* 3.1 6.8 + - - +
154B THR* 2.7 40.3 + - - +
155B ALA* 3.3 0.7 + - - +
157B HIS* 3.2 18.7 - - - -
386B HIS* 3.9 19.8 - - - -
389B ILE* 4.5 8.6 - - - +
390B GLN* 5.5 1.4 + - - -
----------------------------------------------------------
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