Contacts of the helix formed by residues 140 - 154 (chain B) in PDB entry 1JPM
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 140 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ASN* 1.3 76.5 + - - +
141B PRO* 1.3 77.1 - - - +
142B GLU* 4.1 6.9 + - - +
143B GLU* 2.8 37.8 + - - +
144B MET* 3.0 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ASN 3.5 3.7 - - - +
140B SER* 1.3 83.5 - - - +
142B GLU* 1.3 57.4 + - + +
144B MET* 3.6 3.4 + - + +
145B ALA 3.1 20.8 + - - -
170B THR* 5.8 2.0 - - + +
173B ALA* 3.6 14.1 - - + +
174B ARG* 3.6 35.9 - - + +
177B GLU* 3.0 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B SER* 2.9 6.9 + - - +
141B PRO* 1.3 80.6 - - + +
143B GLU* 1.3 68.6 + - - +
145B ALA* 3.6 2.3 + - - +
146B ALA* 3.2 24.0 + - - +
177B GLU* 3.6 12.5 - - + +
181B ARG* 3.3 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ASN* 3.2 39.4 + - + +
140B SER* 2.8 25.1 + - - +
142B GLU* 1.3 77.7 - - - +
144B MET* 1.3 66.5 + - - +
146B ALA* 3.3 8.1 + - + +
147B ASP* 3.1 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B VAL* 3.5 32.9 - - + +
137B SER 3.3 26.0 - - - +
138B VAL* 3.7 9.0 - - + -
139B ASN* 3.3 33.2 - - + +
140B SER 3.0 9.3 + - - +
141B PRO* 3.9 4.0 - - + +
143B GLU* 1.3 72.7 - - - +
145B ALA* 1.3 55.1 + - - +
147B ASP* 3.2 5.9 + - - +
148B ALA* 2.7 36.0 + - - +
161B ILE* 4.0 22.9 - - + -
174B ARG* 3.6 26.5 - - + +
178B ILE* 4.1 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PRO 3.1 18.2 + - - +
142B GLU 3.8 4.0 - - - +
144B MET* 1.3 77.5 - - - +
146B ALA* 1.3 61.3 + - - +
148B ALA* 3.6 2.1 - - - +
149B GLU* 3.0 19.4 + - - +
177B GLU* 3.1 32.1 - - + +
178B ILE* 4.0 12.1 - - - +
181B ARG* 3.3 31.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B GLU* 3.2 22.0 + - - +
143B GLU* 3.4 12.3 - - + +
144B MET 3.1 0.2 - - - -
145B ALA* 1.3 74.4 - - - +
147B ASP* 1.3 67.2 + - - +
149B GLU* 3.3 7.5 + - - +
150B ASN* 2.9 33.0 + - - +
181B ARG* 5.2 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B VAL* 4.6 4.3 - - + +
137B SER* 4.9 9.5 + - - +
139B ASN* 4.7 5.9 + - - -
143B GLU* 3.1 28.8 + - - +
144B MET* 3.6 8.6 - - - +
146B ALA* 1.3 77.9 - - - +
148B ALA* 1.3 58.4 + - - +
150B ASN* 3.1 11.0 + - - +
151B TYR* 2.8 62.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B VAL* 4.3 6.5 - - + +
144B MET 2.7 20.9 + - - +
145B ALA* 3.6 5.6 - - - +
147B ASP* 1.3 73.1 - - - +
149B GLU* 1.3 56.5 + - - +
151B TYR* 3.1 13.5 + - - +
152B LEU* 2.9 27.4 + - - +
159B LEU* 3.8 23.4 - - + +
178B ILE* 3.9 22.0 - - + -
182B VAL* 4.0 7.9 - - + +
----------------------------------------------------------
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 ALA 3.0 17.9 + - - +
146B ALA* 3.3 5.8 + - - +
148B ALA* 1.3 74.8 - - - +
150B ASN* 1.3 60.6 + - - +
152B LEU* 3.2 8.6 + - + +
153B LYS* 3.0 57.9 + - + +
181B ARG* 3.8 37.1 - - + +
182B VAL* 3.6 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ALA* 2.9 26.2 + - - +
147B ASP* 3.1 11.5 + - - +
149B GLU* 1.3 76.8 - - - +
151B TYR* 1.3 68.7 + - + +
153B LYS* 3.4 22.3 + - - +
154B GLN* 3.2 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LYS* 4.2 12.8 + - - -
134B TYR* 3.4 43.7 - + + -
135B THR 3.8 9.6 + - - -
136B VAL* 3.9 21.1 - - + -
137B SER* 5.2 4.2 + - - -
147B ASP* 2.8 49.2 + - + +
148B ALA* 3.5 5.2 - - - +
150B ASN* 1.3 76.4 - - + +
152B LEU* 1.3 66.4 + - - +
154B GLN* 3.1 25.0 + - - +
156B PHE* 3.1 37.2 + + + -
159B LEU* 3.9 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ALA 2.9 12.3 + - - +
149B GLU* 3.2 15.9 - - + +
151B TYR* 1.3 78.4 - - - +
153B LYS* 1.3 63.8 + - + +
155B GLY* 3.1 14.0 + - - -
156B PHE 3.5 19.6 + - - +
157B GLN* 4.9 2.9 - - + -
159B LEU* 5.3 1.1 - - + +
181B ARG 4.8 2.9 - - - +
182B VAL* 4.0 26.5 - - + -
185B ALA* 3.9 39.5 - - + +
186B VAL* 4.3 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLU* 3.0 47.0 + - + +
150B ASN* 3.7 22.7 + - - +
151B TYR 3.2 0.2 - - - -
152B LEU* 1.3 80.5 - - + +
154B GLN* 1.3 61.6 + - + +
155B GLY 3.1 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ASN* 3.2 20.3 + - - +
151B TYR* 3.1 28.8 + - - +
153B LYS* 1.3 77.8 - - + +
155B GLY* 1.3 58.2 + - - +
156B PHE* 3.6 17.6 - - + -
341B GLY* 3.9 20.4 - - - -
----------------------------------------------------------
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