Contacts of the helix formed by residues 128 - 149 (chain A) in PDB entry 2J51
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 THR 128 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ARG* 6.0 4.7 - - - +
126A PRO 5.5 0.9 - - - +
127A LEU* 1.3 76.7 - - - +
129A GLU* 1.3 65.8 + - - +
130A SER* 3.3 19.0 + - - -
131A GLN* 2.9 32.8 + - - +
132A ILE* 3.0 21.0 + - - +
261A TRP* 4.3 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR* 1.3 74.9 - - - +
130A SER* 1.3 56.9 + - - +
132A ILE* 3.1 7.0 + - - +
133A GLN* 2.9 36.1 + - - +
260A ARG 4.6 1.5 - - - +
261A TRP* 3.6 30.0 - - + -
262A SER* 2.6 52.9 + - - -
264A ASN* 5.1 0.2 - - - +
265A PHE* 3.8 12.1 - - + -
291A PHE* 3.6 23.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR* 3.3 11.3 + - - -
129A GLU* 1.3 78.0 - - - +
131A GLN* 1.3 62.6 + - - +
133A GLN* 3.5 16.9 + - - +
134A VAL* 3.4 26.2 + - - +
299A PRO* 3.7 23.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ARG* 5.2 4.8 + - - +
126A PRO 4.7 0.5 - - - +
127A LEU* 3.4 20.5 - - + +
128A THR* 2.9 42.7 + - - +
129A GLU 3.2 0.4 - - - -
130A SER* 1.3 75.5 + - - +
132A ILE* 1.3 65.1 + - - +
134A VAL* 3.2 2.4 + - - +
135A VAL* 3.1 25.6 + - - +
299A PRO* 3.5 35.9 + - + +
300A ILE* 3.6 20.2 - - + +
302A GLU* 5.4 3.2 + - - +
303A LEU* 3.9 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 3.7 22.7 - - + +
128A THR 3.0 19.9 + - - +
129A GLU* 3.1 7.2 + - - +
131A GLN* 1.3 76.0 - - - +
133A GLN* 1.3 51.0 + - - +
135A VAL* 3.3 3.7 + - - +
136A CYS* 2.7 32.7 + - - +
225A LEU* 3.8 26.4 - - + +
228A MET* 4.0 13.5 - - + -
229A ALA* 3.8 32.8 - - + +
261A TRP* 4.2 5.4 - - + -
265A PHE* 3.8 24.2 - - + -
291A PHE* 3.9 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 2.9 22.1 + - - +
130A SER* 3.6 22.8 - - - +
131A GLN 3.2 0.2 - - - -
132A ILE* 1.3 77.1 - - - +
134A VAL* 1.3 58.1 + - - +
136A CYS* 3.7 4.8 - - - +
137A LYS* 2.8 32.7 + - - +
264A ASN* 6.1 0.2 - - - +
290A PRO 4.2 3.6 + - - -
291A PHE* 2.8 64.6 + - + +
292A VAL* 4.7 0.3 - - - +
294A VAL* 3.6 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A SER 3.4 14.8 + - - +
131A GLN 3.2 7.2 + - - +
133A GLN* 1.3 76.5 - - + +
135A VAL* 1.3 67.1 + - + +
137A LYS* 3.9 1.3 - - - +
138A GLN* 3.1 36.9 + - - +
167A GLY 4.7 0.9 - - - +
169A ILE* 6.1 1.3 - - + -
294A VAL* 4.3 11.7 - - + -
296A SER 3.3 22.2 - - - +
297A ASN* 4.0 7.9 - - + -
299A PRO* 4.1 15.9 - - + -
300A ILE* 3.8 20.4 - - + -
1310A EDO 3.3 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 4.6 0.4 - - + -
127A LEU* 3.9 15.0 - - + -
131A GLN 3.1 14.1 + - - +
132A ILE 3.8 4.9 - - - +
134A VAL* 1.3 75.3 - - - +
136A CYS* 1.3 56.0 + - - +
138A GLN* 3.8 0.7 - - - +
139A THR* 2.7 49.1 + - - +
161A ILE* 3.9 20.9 - - + -
163A PHE* 4.0 16.2 - - + -
169A ILE* 4.2 11.2 - - + +
228A MET* 3.6 28.9 - - + -
300A ILE* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE 2.7 23.5 + - - +
133A GLN 3.7 3.4 - - - +
135A VAL* 1.3 73.6 - - - +
137A LYS* 1.3 56.5 + - - +
139A THR* 3.8 4.7 - - - -
140A LEU* 2.8 33.1 + - - +
221A LEU* 4.5 8.5 - - - +
225A LEU* 3.6 28.0 - - + +
228A MET* 5.3 0.2 - - - -
268A PHE* 3.5 38.4 - - - -
291A PHE* 4.1 10.1 - - + -
292A VAL* 3.8 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLN 2.8 22.2 + - - +
134A VAL 3.9 1.1 - - - +
136A CYS* 1.3 74.6 - - - +
138A GLN* 1.3 58.4 + - - +
140A LEU* 3.5 3.8 - - - +
141A ASP* 2.8 62.0 + - - +
287A LEU* 4.9 6.3 - - + +
292A VAL* 3.6 39.0 - - + +
294A VAL* 3.8 13.9 - - + +
295A ASP* 6.3 0.2 - - - -
1310A EDO 3.6 38.6 - - - -
1312A EDO 5.1 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ASN* 2.9 30.4 + - - +
134A VAL* 3.1 24.4 + - - +
137A LYS* 1.3 72.8 - - + +
139A THR* 1.3 65.1 + - - +
141A ASP* 3.2 11.1 + - - +
142A ALA 3.1 16.6 + - - -
168A ASP* 2.9 29.0 + - - +
169A ILE* 2.9 43.8 + - + -
297A ASN* 4.2 0.6 - - - +
1310A EDO 3.4 33.5 + - - -
1312A EDO 3.8 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 2.7 38.5 + - - +
136A CYS* 3.8 5.4 - - - -
138A GLN* 1.3 72.2 - - - +
140A LEU* 1.3 57.1 + - - +
142A ALA* 3.2 8.1 + - - +
143A LEU* 3.0 29.9 + - + +
156A LEU* 4.1 27.1 - - + -
161A ILE* 3.7 12.8 - - + +
169A ILE* 3.7 17.6 - - + +
171A LEU* 4.9 6.1 - - + -
221A LEU* 4.1 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A CYS 2.8 17.3 + - - +
137A LYS 3.5 4.3 - - - +
139A THR* 1.3 76.0 - - - +
141A ASP* 1.3 65.0 + - - +
143A LEU* 4.4 4.3 - - + -
144A ASN* 2.9 27.8 + - - +
221A LEU* 4.0 21.3 - - + +
268A PHE* 4.2 4.3 - - + -
283A THR* 3.8 35.0 - - + -
286A LEU* 3.7 38.8 - - + +
287A LEU* 3.7 20.4 - - + +
292A VAL* 3.9 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A HIS* 3.7 22.6 + - + +
90A ASN* 4.0 5.4 - - - +
137A LYS* 2.8 47.3 + - - +
138A GLN* 3.2 12.5 + - - +
140A LEU* 1.3 75.4 - - - +
142A ALA* 1.3 61.8 + - - +
144A ASN* 3.5 6.1 + - - +
145A TYR* 3.2 21.3 + - - +
287A LEU* 3.2 26.6 - - - +
1312A EDO 4.8 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A HIS* 4.0 10.5 - - - -
90A ASN* 3.5 27.4 - - + +
91A ILE* 3.8 7.9 - - + +
138A GLN 3.1 11.6 + - - +
139A THR* 3.3 10.5 - - - +
141A ASP* 1.3 74.7 - - - +
143A LEU* 1.3 59.2 + - - +
145A TYR* 3.3 4.0 + - - +
146A LEU* 2.9 34.0 + - - +
171A LEU* 3.8 18.2 - - + -
----------------------------------------------------------
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 THR* 3.0 21.0 + - + +
140A LEU* 3.4 6.3 + - - +
142A ALA* 1.3 73.2 - - - +
144A ASN* 1.3 60.9 + - - +
146A LEU* 3.3 18.0 + - + -
147A HIS* 2.8 38.5 + - + +
153A HIS* 4.3 5.2 - - + -
156A LEU* 3.7 29.2 - - + -
171A LEU* 4.3 9.2 - - + -
217A ASP* 3.9 42.2 - - + +
218A VAL* 5.1 0.7 - - - +
221A LEU* 4.3 18.8 - - + -
283A THR* 3.9 18.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
140A LEU 2.9 18.0 + - - +
141A ASP* 3.8 5.5 + - - +
143A LEU* 1.3 76.1 - - - +
145A TYR* 1.3 59.5 + - - +
147A HIS* 3.4 1.6 + - - +
148A ASP* 2.9 55.3 + - - +
283A THR* 3.2 24.6 + - - +
284A SER* 3.5 20.4 + - - -
287A LEU* 3.6 25.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER 4.1 3.8 + - - -
86A CYS* 3.6 31.1 - - + -
87A ASP* 2.9 39.5 + - - +
88A HIS* 3.7 31.2 - + + +
91A ILE* 3.6 16.2 - - + -
141A ASP 3.2 4.6 + - - +
142A ALA 3.5 7.0 - - - +
144A ASN* 1.3 77.8 - - - +
146A LEU* 1.3 69.8 + - - +
148A ASP* 3.3 7.3 + - + +
149A ASN* 3.0 54.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE* 4.7 0.2 - - + -
86A CYS* 3.9 17.9 - - - -
91A ILE* 3.8 19.3 - - + -
142A ALA 2.9 16.5 + - - +
143A LEU* 3.4 13.5 - - + +
145A TYR* 1.3 75.9 - - - +
147A HIS* 1.3 62.1 + - + +
149A ASN* 3.0 12.0 + - - +
150A LYS 3.1 0.3 + - - -
151A ILE* 2.9 57.1 + - + +
153A HIS* 4.1 17.3 - - + +
171A LEU* 3.9 22.0 - - + -
174A PHE* 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 2.8 25.6 + - + +
144A ASN 3.9 3.1 - - - +
146A LEU* 1.3 75.3 - - + +
148A ASP* 1.3 62.2 + - - +
150A LYS* 3.0 10.2 + - - -
151A ILE 3.2 18.6 - - - -
214A TYR* 3.3 38.9 + + + +
217A ASP* 2.8 32.2 + - + +
218A VAL* 4.6 1.1 - - + -
283A THR* 3.6 22.6 + - + +
1309A EDO 3.0 37.7 + - - -
1311A EDO 2.9 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ASN* 2.9 44.1 + - - +
145A TYR* 3.5 9.0 - - + +
147A HIS* 1.3 76.8 - - - +
149A ASN* 1.3 64.5 + - - +
150A LYS* 3.3 10.8 + - - +
284A SER* 6.1 0.3 - - - -
1311A EDO 4.4 7.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A CYS* 6.1 0.2 - - - -
145A TYR* 3.0 61.2 + - + +
146A LEU 3.0 7.3 + - - +
148A ASP* 1.3 80.2 - - - +
150A LYS* 1.3 71.4 + - - +
151A ILE* 3.2 18.7 + - + +
179A LYS* 5.0 0.2 - - - -
181A THR* 3.6 16.0 - - + +
----------------------------------------------------------
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