Contacts of the helix formed by residues 128 - 141 (chain A) in PDB entry 2J3T
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 128 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 3.7 4.7 - - - -
110A ASN* 2.9 36.2 + - - -
112A LEU* 3.6 23.2 - - - +
126A ILE* 3.0 3.6 + - - +
127A TYR* 1.3 80.4 - - - +
129A ASN* 1.3 57.5 + - - +
130A LEU 2.9 11.8 + - - -
131A LEU* 3.0 13.7 + - - +
150A PHE* 3.0 33.2 - - - -
153A ASP* 5.2 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASN* 2.7 44.9 + - - +
44A LEU* 4.3 9.9 - - + -
45A ASP* 3.8 16.1 + - - +
126A ILE* 2.7 44.0 + - + +
127A TYR 3.2 1.8 + - - -
128A SER* 1.3 69.2 - - - +
130A LEU* 1.3 62.3 + - - +
131A LEU 3.2 0.4 - - - -
132A CYS* 3.3 29.3 + - - +
133A GLY 3.7 2.8 + - - -
150A PHE* 4.0 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 4.6 13.5 - - + -
23A TYR* 3.4 40.7 + - + +
26A LEU* 4.8 3.8 - - + -
44A LEU* 3.3 31.2 - - + +
47A MET* 4.0 12.3 - - + -
48A GLY* 3.5 19.1 - - - +
51A ILE* 4.4 17.0 - - + -
112A LEU* 4.1 8.5 - - + -
128A SER 2.9 1.0 + - - -
129A ASN* 1.3 78.4 - - - +
131A LEU* 1.3 65.7 + - - +
133A GLY 3.0 12.0 + - - -
134A VAL* 3.1 21.8 + - + +
1068A PLM 4.9 4.7 - - + -
10B LEU* 4.6 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 3.9 26.0 - - + -
87A LEU* 5.2 0.2 - - + -
107A LEU* 5.3 0.4 - - + -
110A ASN* 5.3 0.2 - - - +
111A PRO* 4.1 26.2 - - + -
112A LEU* 4.1 18.5 - - + +
128A SER* 3.0 13.5 + - - +
130A LEU* 1.3 80.0 - - - +
132A CYS* 1.3 57.6 + - - +
134A VAL* 2.8 26.4 + - + +
135A LEU* 3.0 23.3 + - + +
150A PHE* 4.2 14.1 - - + -
163A ILE* 3.9 21.5 - - + -
1068A PLM 4.0 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASP* 3.9 11.0 - - - +
129A ASN* 3.3 19.6 + - - +
130A LEU 3.3 0.4 - - - -
131A LEU* 1.3 78.4 - - - +
133A GLY* 1.3 61.3 - - - +
135A LEU* 3.4 2.1 + - - -
136A ARG* 3.0 26.4 + - - +
148A ALA* 3.4 45.0 - - - +
149A LYS* 4.0 6.3 - - - -
150A PHE* 3.5 33.4 - - - -
163A ILE* 4.8 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASP* 3.1 35.5 + - - -
49A TYR* 3.2 19.9 - - - +
129A ASN 3.7 2.0 + - - -
130A LEU 3.0 7.0 + - - -
132A CYS* 1.3 78.5 - - - +
134A VAL* 1.3 58.3 + - - +
136A ARG* 4.1 5.5 - - - +
137A GLY 2.8 23.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
48A GLY* 3.5 21.5 - - - +
51A ILE* 4.3 10.1 - - + -
52A GLY* 3.6 8.0 - - - -
55A LEU* 3.9 27.6 - - + -
130A LEU* 3.1 28.2 + - + +
131A LEU* 2.8 12.1 + - + +
133A GLY* 1.3 78.1 - - - +
135A LEU* 1.3 56.2 + - - +
138A ALA* 2.8 30.8 + - - +
1068A PLM 3.9 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 4.1 24.5 - - + -
83A PHE* 4.2 4.0 - - + -
105A LEU* 4.6 3.8 - - + -
131A LEU* 3.0 34.1 + - + +
132A CYS* 3.7 5.4 - - - +
133A GLY 3.4 0.2 - - - -
134A VAL* 1.3 77.0 - - - +
136A ARG* 1.3 57.2 + - - +
138A ALA* 4.0 3.0 - - - +
139A LEU* 3.0 38.0 + - + +
146A VAL* 4.8 0.4 - - - -
148A ALA* 4.0 14.4 - - + -
163A ILE* 4.3 17.9 - - + -
165A MET* 4.0 34.3 - - + -
1068A PLM 4.1 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASP* 2.6 49.9 + - - -
46A ARG* 5.4 0.4 - - - +
49A TYR* 4.1 23.1 - - + +
132A CYS* 3.0 17.4 + - - +
133A GLY* 4.3 1.5 - - - -
135A LEU* 1.3 74.0 - - - +
137A GLY* 1.3 65.0 + - - +
139A LEU* 4.3 0.5 - - - +
140A GLU* 3.1 33.0 + - + +
144A MET 4.9 0.7 - - - +
145A ALA* 6.0 0.4 - - - -
146A VAL* 3.1 37.7 - - + +
147A GLU* 5.1 2.5 - - - +
148A ALA* 4.7 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 3.4 32.0 - - - -
52A GLY 3.9 6.3 - - - -
53A VAL* 3.6 15.2 - - - +
133A GLY 2.8 18.7 + - - -
134A VAL 3.8 0.2 - - - -
136A ARG* 1.3 76.2 - - - +
138A ALA* 1.3 64.4 + - - +
140A GLU* 3.3 8.5 + - - +
141A MET* 3.4 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLY* 3.4 20.8 + - - +
55A LEU* 5.8 0.4 - - + -
56A ILE* 3.7 18.9 - - + +
134A VAL 2.8 23.4 + - - +
135A LEU 4.0 1.1 - - - +
137A GLY* 1.3 71.5 - - - +
139A LEU* 1.3 61.8 + - - +
141A MET* 3.1 19.8 + - - +
142A VAL* 3.7 7.1 - - - +
1068A PLM 3.7 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 5.1 1.6 - - + -
74A THR* 3.8 27.6 - - + -
78A ILE* 4.1 9.0 - - + -
135A LEU* 3.0 19.0 + - + +
136A ARG 4.3 0.2 - - - +
138A ALA* 1.3 76.1 - - - +
140A GLU* 1.3 61.2 + - - +
142A VAL* 2.9 23.3 + - + +
144A MET* 3.1 39.0 + - + +
146A VAL* 3.3 36.1 - - + -
165A MET* 3.7 20.4 - - + -
1068A PLM 3.9 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 2.6 35.0 + - - -
136A ARG* 3.1 27.4 + - + +
137A GLY 3.6 6.1 - - - +
138A ALA 3.2 0.2 - - - -
139A LEU* 1.3 75.9 - - - +
141A MET* 1.3 74.4 + - + +
142A VAL 3.0 1.3 + - - -
143A GLN* 3.2 12.5 + - - +
144A MET 3.3 12.9 + - - +
145A ALA* 5.6 4.3 - - - +
171A ILE* 3.8 24.0 - - + +
11C ARG* 5.8 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 4.3 1.8 - - - +
53A VAL* 3.7 39.3 - - + +
56A ILE* 3.6 18.8 - - + -
57A GLU* 5.6 1.1 - - - +
137A GLY 3.6 9.9 - - - +
138A ALA 3.1 11.4 + - - +
140A GLU* 1.3 107.2 - - + +
142A VAL* 1.3 57.4 + - - +
143A GLN* 3.5 5.4 - - - +
11C ARG* 3.0 53.2 + - - +
78C THR* 3.5 17.0 - - + -
117C LEU* 6.6 0.2 - - - -
----------------------------------------------------------
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