Contacts of the helix formed by residues 137 - 153 (chain B) in PDB entry 2J3R
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 LEU 137 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLN* 3.6 25.3 + - - +
136B THR* 1.3 74.5 - - - +
138B ASN* 1.3 60.3 + - - +
140B ALA* 3.4 9.4 + - + -
141B ALA* 2.8 30.1 + - - +
162B VAL* 4.1 15.0 - - + +
163B HIS* 3.8 34.3 - - - +
164B TRP* 3.3 53.1 - - + +
168B THR* 4.2 14.4 - - + -
169B THR 5.7 0.2 - - - +
1177B NO3 3.4 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PHE* 3.4 12.5 - - + -
37B VAL* 4.1 29.9 - - + +
47B VAL* 5.0 3.8 - - - +
50B LEU* 4.0 11.7 - - - +
51B GLN* 3.8 15.6 - - - +
54B LEU* 3.5 30.0 - - + +
136B THR* 3.1 32.0 + - - +
137B LEU* 1.3 74.5 - - - +
139B CYS* 1.3 65.6 + - - +
141B ALA* 3.4 2.7 + - - +
142B PHE* 3.1 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PHE* 4.2 28.9 - - - -
33B PHE* 3.5 20.0 - - + -
98B PHE* 4.9 5.6 - - - -
123B LEU* 3.8 23.1 - - + -
124B ILE* 4.1 14.1 - - + +
127B TYR* 6.1 0.4 - - - -
138B ASN* 1.3 77.8 - - - +
140B ALA* 1.3 53.6 + - - +
142B PHE* 3.7 3.5 - - - +
143B THR* 2.7 43.8 + - - -
1177B NO3 2.9 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 4.2 11.7 - - + -
137B LEU* 3.6 15.9 - - + +
138B ASN 3.2 0.2 - - - -
139B CYS* 1.3 68.3 - - - +
141B ALA* 1.3 60.0 + - - +
143B THR* 3.7 0.7 - - - -
144B GLY 2.8 24.4 + - - -
162B VAL* 3.2 27.4 - - + +
168B THR* 5.0 5.8 - - - +
169B THR 5.6 1.8 - - - +
170B LEU* 3.7 6.9 - - + +
1177B NO3 2.4 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLN* 3.4 41.5 - - + +
54B LEU* 4.4 1.1 - - + -
55B ALA* 3.4 14.6 - - + +
137B LEU 2.8 19.5 + - - +
138B ASN 3.7 4.7 - - - +
140B ALA* 1.3 76.2 - - - +
142B PHE* 1.3 62.9 + - - +
144B GLY* 3.1 2.6 + - - -
145B GLY 3.0 18.5 + - - -
162B VAL* 3.8 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.9 5.2 - - + -
21A LEU* 4.7 2.9 - - + -
22A THR* 3.6 35.2 - - + -
25A ALA* 3.8 25.1 - - + -
29B PHE* 5.1 4.7 - + - -
33B PHE* 3.9 23.1 - + + -
36B MET* 4.7 6.1 - - + -
54B LEU* 3.3 31.2 - - + +
57B MET* 3.9 6.7 - - + -
58B GLY* 3.5 28.8 - - - -
61B VAL* 5.1 0.2 - - + -
138B ASN 3.1 13.8 + - - +
139B CYS* 3.7 6.1 - - - +
141B ALA* 1.3 76.9 - - - +
143B THR* 1.3 68.4 + - - +
145B GLY* 3.1 10.7 + - - -
146B ILE* 3.2 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TRP* 3.9 33.9 - - + -
97B LEU* 5.0 7.6 - - + -
98B PHE* 3.7 19.0 - - + -
123B LEU* 3.4 14.9 - - + +
139B CYS* 2.7 24.8 + - - -
140B ALA 3.7 4.3 - - - -
142B PHE* 1.3 78.6 - - - +
144B GLY* 1.3 60.0 + - - +
146B ILE* 3.1 13.0 + - - +
147B VAL* 2.9 30.1 + - + +
170B LEU* 4.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ALA* 5.3 0.4 - - - -
140B ALA 2.8 16.4 + - - -
141B ALA 3.1 4.5 + - - -
143B THR* 1.3 73.4 - - - +
145B GLY* 1.3 60.4 + - - +
147B VAL* 3.5 0.8 + - - -
148B GLU* 2.9 29.0 + - - +
160B VAL* 3.6 18.9 - - - +
162B VAL* 4.8 2.0 - - - -
170B LEU* 3.6 21.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ALA* 3.3 28.2 - - - +
59B GLN* 2.9 33.6 - - - +
141B ALA 3.0 11.6 + - - -
142B PHE 3.1 2.6 + - - -
144B GLY* 1.3 72.8 - - - +
146B ILE* 1.3 60.3 + - - +
148B GLU* 3.2 3.0 + - - -
149B ALA 3.0 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 5.4 0.9 - - + -
21A LEU* 3.7 27.6 - - + -
58B GLY* 3.5 22.2 - - - +
61B VAL* 4.6 2.9 - - + -
62B GLY* 3.8 15.0 - - - -
65B LEU* 4.1 14.6 - - + -
93B VAL* 5.1 0.9 - - + -
97B LEU* 4.4 18.4 - - + -
142B PHE* 3.2 31.3 + - + +
143B THR* 3.1 12.7 + - - +
145B GLY* 1.3 77.0 - - - +
147B VAL* 1.3 63.8 + - + +
148B GLU 3.2 0.2 + - - -
149B ALA* 3.2 3.3 + - - +
150B ILE* 3.0 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 3.9 35.4 - - + -
93B VAL* 5.3 6.3 - - + -
94B TRP* 4.6 4.0 - - + -
97B LEU* 6.1 0.2 - - + -
143B THR* 2.9 27.7 + - + +
144B GLY* 3.8 6.5 - - - +
146B ILE* 1.3 77.7 - - + +
148B GLU* 1.3 57.8 + - - +
150B ILE* 3.5 8.2 + - - +
151B LEU* 3.0 41.4 + - + +
160B VAL* 4.6 3.8 - - + -
170B LEU* 3.9 21.3 - - + -
172B ILE* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLN* 2.9 33.0 + - - +
144B GLY 2.9 17.2 + - - +
145B GLY* 3.5 7.1 - - - +
146B ILE 3.1 0.4 - - - -
147B VAL* 1.3 75.2 - - - +
149B ALA* 1.3 65.4 + - - +
151B LEU* 3.3 2.8 + - - +
152B THR* 3.0 33.1 + - + +
158B ALA* 4.0 17.6 - - + +
159B LYS* 3.8 1.7 - - - -
160B VAL* 2.9 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLN* 3.3 33.6 - - + +
62B GLY* 3.6 19.5 - - - -
63B ALA 3.9 5.6 - - - +
145B GLY 3.0 13.1 + - - +
146B ILE 3.2 0.2 + - - -
148B GLU* 1.3 75.9 - - - +
150B ILE* 1.3 57.9 + - - +
152B THR* 3.8 6.1 - - - -
153B HIS* 2.9 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLY 3.5 18.2 - - - +
65B LEU* 4.1 11.4 - - + -
66B LEU* 4.0 25.6 - - + +
85B ILE* 4.8 3.8 - - + -
88B PHE* 4.5 11.2 - - + -
89B ILE* 3.4 24.5 - - + -
93B VAL* 3.7 36.3 - - + -
146B ILE* 3.0 31.4 + - + +
147B VAL* 3.6 5.2 - - - +
148B GLU 3.2 0.2 - - - -
149B ALA* 1.3 77.9 - - - +
151B LEU* 1.3 59.6 + - - +
154B SER* 2.7 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 3.7 35.4 - - + -
86B LEU* 4.8 3.4 - - + -
89B ILE* 4.6 11.4 - - + -
147B VAL* 3.0 35.3 + - + +
148B GLU 3.8 3.1 - - - +
150B ILE* 1.3 74.0 - - - +
152B THR* 1.3 64.2 + - - +
154B SER* 3.2 8.1 + - - -
155B GLY 3.4 0.2 + - - -
156B PHE* 2.9 37.4 + - + +
158B ALA* 4.3 9.0 - - + -
160B VAL* 4.2 10.3 - - + -
172B ILE* 3.5 32.1 - - + -
174B PHE* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLN* 5.5 2.1 + - - +
148B GLU* 3.0 30.6 + - + +
149B ALA* 3.4 6.4 + - - -
151B LEU* 1.3 75.1 - - + +
153B HIS* 1.3 76.9 + - - +
155B GLY* 2.9 21.0 + - - -
156B PHE 3.7 7.4 + - - +
157B PRO* 4.4 5.3 - - + -
158B ALA* 4.0 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLN 5.5 1.8 + - - -
63B ALA* 3.9 25.1 - - + +
66B LEU* 4.3 11.2 - - + -
78B ARG* 2.5 36.3 + - - +
149B ALA* 2.9 37.0 + - + +
150B ILE 4.3 2.0 - - - +
152B THR* 1.3 91.2 + - - +
154B SER* 1.3 51.4 + - - +
155B GLY 3.3 1.8 - - - -
----------------------------------------------------------
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