Contacts of the helix formed by residues 119 - 145 (chain A) in PDB entry 1JI5
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 ASP 119 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 4.1 15.5 - - + +
59A ARG* 3.2 13.7 + - - -
63A ILE* 4.5 10.5 - - - +
114A ALA* 2.8 30.6 + - - +
115A GLN* 4.2 1.2 + - - +
117A SER* 4.1 5.2 - - - +
118A ASP* 1.3 76.3 - - - +
120A GLU* 1.3 61.1 + - - +
121A MET* 3.3 8.4 - - - +
122A THR* 2.6 37.4 + - - -
123A SER 3.3 11.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ALA 4.9 0.2 - - - -
115A GLN* 4.9 13.0 - - + +
118A ASP* 4.0 2.2 - - - +
119A ASP* 1.3 72.4 - - - +
121A MET* 1.3 76.1 + - + +
123A SER* 3.2 12.5 - - - -
124A ASP* 2.7 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 2.9 27.8 - - - +
118A ASP 5.9 0.4 - - - +
119A ASP* 3.0 6.2 - - - +
120A GLU* 1.3 103.5 - - + +
122A THR* 1.3 64.0 + - - +
124A ASP* 2.9 18.4 + - - +
125A LEU* 3.1 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 3.7 15.8 - - + +
9A LEU* 3.5 37.4 - - + +
59A ARG* 3.1 25.8 + - + +
63A ILE* 4.5 2.3 - - - +
114A ALA* 4.5 2.2 - - + -
119A ASP* 2.6 30.9 + - - -
121A MET* 1.3 77.9 - - - +
123A SER* 1.3 62.9 + - - +
125A LEU* 3.1 6.1 + - - +
126A LEU* 2.9 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A MET* 3.5 27.9 - - - +
114A ALA* 4.0 14.5 - - - +
115A GLN* 3.8 16.9 + - - +
119A ASP 3.3 5.5 + - - -
120A GLU* 3.2 22.2 - - - -
121A MET 3.1 0.4 - - - -
122A THR* 1.3 79.6 - - - +
124A ASP* 1.3 52.1 + - - +
126A LEU* 3.1 4.4 + - - +
127A LEU* 2.7 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU 2.7 16.3 + - - +
121A MET* 2.9 11.4 + - - +
123A SER* 1.3 74.2 - - - +
125A LEU* 1.3 64.0 + - - +
127A LEU* 3.1 23.1 + - - +
128A GLY* 3.1 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 5.6 0.2 - - + -
55A GLU* 4.2 27.8 - - + +
56A ILE* 4.3 18.2 - - + +
59A ARG* 3.7 38.1 - - + -
121A MET 3.1 10.5 + - - +
122A THR* 3.1 9.8 + - - +
124A ASP* 1.3 76.9 + - - +
126A LEU* 1.3 74.5 + - + +
128A GLY* 3.2 10.7 + - - -
129A ILE* 3.4 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 6.1 0.4 - - + -
8A VAL* 4.3 13.0 - - + -
9A LEU* 3.8 22.4 - - + -
12A GLN* 5.4 4.7 - - + -
56A ILE* 5.8 1.8 - - + -
107A LEU* 3.7 27.1 - - + +
110A GLY* 3.8 34.8 - - - +
111A MET* 3.9 13.5 - - + +
122A THR* 2.9 28.6 + - + +
123A SER 3.5 7.2 - - - +
125A LEU* 1.3 84.5 - - + +
127A LEU* 1.3 65.2 + - - +
129A ILE* 3.2 14.1 + - + +
130A TYR* 3.0 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A MET* 3.9 19.0 - - + -
123A SER* 2.7 18.5 + - - +
124A ASP* 3.1 26.6 + - - +
126A LEU* 1.3 71.7 - - - +
128A GLY* 1.3 65.5 + - - +
130A TYR* 3.1 9.2 - - + +
131A THR* 3.0 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASP 3.1 12.3 + - - -
125A LEU 3.2 4.2 + - - -
126A LEU 3.1 0.6 - - - -
127A LEU* 1.3 79.5 - - - +
129A ILE* 1.3 61.3 + - - +
131A THR* 3.1 10.3 + - - -
132A GLU* 2.9 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLN* 3.8 17.0 - - - +
16A TRP* 3.6 29.6 - - + +
52A HIS* 3.9 24.9 - - + +
55A GLU* 5.5 0.9 - - - +
56A ILE* 4.1 22.9 - - + -
103A MET* 4.4 0.7 - - + -
107A LEU* 4.4 11.2 - - + -
125A LEU* 3.4 24.9 - - + +
126A LEU* 3.2 15.0 + - + +
128A GLY* 1.3 73.8 - - - +
130A TYR* 1.3 57.0 + - - +
132A GLU* 3.1 6.5 + - - +
133A LEU* 2.8 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 3.4 42.5 - - + +
107A LEU* 3.9 10.4 - - + +
108A LYS* 3.2 45.1 + - + +
111A MET* 3.7 18.6 - - + -
126A LEU 3.0 11.7 + - - +
127A LEU* 3.1 19.1 - - + +
129A ILE* 1.3 77.9 - - - +
131A THR* 1.3 65.2 + - - +
133A LEU 3.4 0.2 + - - -
134A GLU* 2.9 65.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 3.0 24.9 + - - +
128A GLY* 3.4 9.6 - - - -
130A TYR* 1.3 84.4 - - - +
132A GLU* 1.3 66.6 + - - +
134A GLU* 3.3 8.3 + - - +
135A LYS* 3.3 19.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 4.7 0.7 - - - -
48A GLU* 3.4 30.8 - - - +
52A HIS* 2.7 38.8 + - - -
128A GLY 2.9 12.9 + - - +
129A ILE* 3.1 9.4 + - - +
131A THR* 1.3 79.5 - - - +
133A LEU* 1.3 77.0 + - - +
135A LYS* 3.3 6.6 + - - +
136A HIS* 3.2 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 3.6 21.8 - - + -
100A TYR* 4.1 48.0 - - + +
103A MET* 4.0 30.5 - - + -
104A LEU* 4.0 10.5 - - + -
107A LEU* 4.3 8.7 - - + -
129A ILE* 2.8 24.1 + - + +
130A TYR 3.9 2.7 - - - +
132A GLU* 1.3 94.0 - - + +
134A GLU* 1.3 58.8 + - - +
136A HIS* 3.0 9.2 + - + +
137A ALA* 2.8 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 3.8 16.9 - - + +
130A TYR* 2.9 55.4 + - + +
131A THR* 3.6 8.5 - - - +
133A LEU* 1.3 75.5 - - - +
135A LYS* 1.3 61.8 + - - +
137A ALA* 3.5 8.1 + - - +
138A TRP* 3.2 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A THR* 3.3 8.7 + - + +
132A GLU* 3.3 11.1 + - - +
133A LEU 3.1 0.6 - - - -
134A GLU* 1.3 76.2 - - - +
136A HIS* 1.3 68.4 + - + +
138A TRP* 3.0 43.0 + - + +
139A MET* 3.1 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 4.3 7.0 + - - -
44A GLU* 4.2 12.3 - - - -
45A LEU* 3.5 23.2 - - + +
48A GLU* 2.7 34.0 + - - -
100A TYR* 3.8 29.4 - + + -
132A GLU* 3.2 29.4 + - + +
133A LEU* 3.0 9.8 + - + +
135A LYS* 1.3 79.6 - - + +
137A ALA* 1.3 55.7 + - - +
139A MET* 2.9 22.3 + - + +
140A LEU* 2.6 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A MET* 4.2 9.1 - - + +
100A TYR* 4.7 6.7 - - + -
101A GLU* 4.5 14.1 - - + +
104A LEU* 5.5 5.2 - - + -
133A LEU 2.8 19.1 + - - +
134A GLU* 3.6 9.2 - - - +
136A HIS* 1.3 71.8 - - - +
138A TRP* 1.3 52.9 + - - +
140A LEU* 3.8 7.4 - - - +
141A ARG* 2.7 58.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLU 3.2 9.0 + - - +
135A LYS* 3.0 46.5 + - + +
137A ALA* 1.3 80.3 - - - +
139A MET* 1.3 75.9 + - + +
141A ARG* 3.3 14.7 + - + +
142A ALA* 2.7 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 3.3 32.8 - - - +
135A LYS* 3.1 22.8 + - + +
136A HIS* 2.9 27.3 + - + +
138A TRP* 1.3 104.2 - - + +
140A LEU* 1.3 69.5 + - + +
142A ALA* 3.3 5.4 + - - +
143A PHE* 2.9 23.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
38A LEU* 6.0 3.1 - - + -
41A LYS* 5.1 21.5 - - + -
42A PHE* 6.3 1.3 - - + -
45A LEU* 5.1 7.2 - - + -
93A VAL* 3.6 29.1 - - + +
96A ILE* 4.1 24.9 - - + -
97A MET* 4.2 15.9 - - + -
100A TYR* 4.3 17.7 - - + -
136A HIS* 2.6 30.6 + - + +
137A ALA 3.8 3.4 - - - +
139A MET* 1.3 74.6 - - + +
141A ARG* 1.3 63.8 + - - +
143A PHE* 3.0 22.2 - - + +
144A LEU* 3.2 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A MET* 3.8 18.6 - - + +
101A GLU* 2.3 35.0 + - - +
137A ALA* 2.7 48.4 + - - +
138A TRP* 3.5 12.2 - - - +
140A LEU* 1.3 73.5 - - - +
142A ALA* 1.3 57.9 + - - +
144A LEU* 2.9 8.2 + - - +
145A ASN* 2.9 57.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
138A TRP* 2.7 36.9 + - + +
139A MET* 3.8 5.8 - - - +
141A ARG* 1.3 73.5 - - - +
143A PHE* 1.3 62.5 + - - +
145A ASN* 3.5 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLN* 3.6 28.5 - - + -
37A THR* 5.1 2.7 - - - -
38A LEU* 3.4 30.5 - - + -
89A ALA* 5.9 1.1 - - + -
90A GLU* 5.0 9.6 - - - -
93A VAL* 3.7 29.4 - - + -
139A MET 2.9 13.3 + - - +
140A LEU* 3.0 17.0 + - + +
142A ALA* 1.3 79.2 - - - +
144A LEU* 1.3 76.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLU* 4.4 22.4 - - + +
93A VAL* 3.6 23.1 - - + -
94A GLU* 4.2 21.1 - - + +
97A MET* 4.2 17.5 - - + -
140A LEU 3.2 22.4 + - - +
141A ARG* 2.9 5.1 + - - +
143A PHE* 1.3 102.3 - - + +
145A ASN* 1.3 79.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 2.9 41.7 + - + +
142A ALA* 3.5 15.9 - - - +
143A PHE 4.7 0.2 - - - +
144A LEU* 1.3 87.8 - - - +
----------------------------------------------------------
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