Contacts of the helix formed by residues 117 - 138 (chain A) in PDB entry 2JC6
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 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PHE* 3.4 33.0 - - + -
116A TYR* 1.3 83.6 - - - +
118A GLU* 1.3 65.4 + - - +
119A LYS* 3.3 11.1 + - - +
120A ASP* 3.2 21.6 + - - +
121A ALA* 3.3 18.0 + - - +
285A LEU 3.9 6.7 - - - -
286A ASN* 3.5 24.3 + - - +
287A LYS 3.2 23.8 - - - +
289A ILE* 4.3 8.7 - - - -
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A THR* 1.3 75.4 - - - +
119A LYS* 1.3 57.0 + - - +
121A ALA* 3.3 0.7 + - - +
122A SER* 2.9 29.5 + - - -
215A LEU* 3.7 26.2 - - + -
247A ASP 4.1 0.7 - - - +
248A ILE* 3.4 16.8 - - + +
249A SER* 2.6 48.0 + - - -
252A ALA* 4.2 4.3 - - - -
278A TRP* 3.1 20.4 + - - +
284A ALA* 4.1 2.2 - - - -
285A LEU* 3.1 42.6 + - + +
287A LYS 4.3 2.4 + - - -
289A ILE* 4.6 3.1 - - + +
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Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A THR* 3.3 8.4 - - - +
118A GLU* 1.3 72.5 - - - +
120A ASP* 1.3 58.7 + - - +
122A SER* 3.8 1.8 - - - -
123A THR* 2.7 38.8 + - - +
281A GLY 5.4 0.4 + - - -
282A ASP* 2.7 32.7 + - - +
284A ALA* 2.6 45.8 + - + +
285A LEU 3.1 7.2 + - - +
286A ASN* 3.4 30.1 - - + +
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Residues in contact with ASP 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LYS* 4.9 11.7 - - - +
115A PHE* 4.1 6.2 - - - +
116A TYR* 3.6 25.5 - - + -
117A THR* 3.2 33.6 + - - +
118A GLU 3.3 0.2 - - - -
119A LYS* 1.3 75.5 - - - +
121A ALA* 1.3 65.6 + - - +
123A THR* 3.5 7.6 + - - -
124A LEU* 3.2 29.0 + - - +
286A ASN* 6.0 0.2 - - - -
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TYR* 3.5 21.2 + - + +
117A THR 3.3 5.2 + - - +
118A GLU 3.3 4.8 + - - +
120A ASP* 1.3 78.1 - - - +
122A SER* 1.3 56.6 + - - +
124A LEU* 3.2 4.6 + - - +
125A ILE* 2.9 31.6 + - + +
214A LEU* 4.1 16.1 - - + +
215A LEU* 3.5 32.5 - - + -
278A TRP* 4.0 7.9 - - + -
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Residues in contact with SER 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLU 2.9 17.5 + - - -
119A LYS* 3.9 3.8 - - - -
121A ALA* 1.3 76.2 - - - +
123A THR* 1.3 56.9 + - - +
125A ILE 4.4 0.2 - - - +
126A ARG* 2.9 30.8 + - - +
278A TRP* 2.6 53.5 + - - -
279A ILE* 3.7 11.9 + - - +
284A ALA* 4.1 7.1 - - - +
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Residues in contact with THR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LYS* 2.7 23.1 + - - +
120A ASP* 3.6 8.5 + - - +
121A ALA 3.4 0.2 - - - -
122A SER* 1.3 76.7 + - - +
124A LEU* 1.3 60.8 + - + +
126A ARG* 3.7 22.2 + - - +
127A GLN* 2.9 41.1 + - - +
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 3.8 22.7 - - + -
110A ILE* 4.9 0.4 - - + -
113A LYS* 4.9 3.8 - - - +
116A TYR* 4.6 13.5 - - + +
120A ASP* 3.2 19.2 + - + +
121A ALA* 3.2 7.9 + - - +
123A THR* 1.3 76.6 - - + +
125A ILE* 1.3 66.9 + - - +
127A GLN* 3.3 11.4 + - - +
128A VAL* 3.2 28.3 + - + +
150A LEU* 6.4 1.1 - - + -
152A TYR* 3.6 23.6 - - + +
159A SER 5.9 0.2 - - - +
161A ILE* 3.7 35.0 - - + +
214A LEU* 4.0 20.4 - - + -
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Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ALA 2.9 19.7 + - - +
122A SER 3.5 3.8 + - - +
124A LEU* 1.3 74.4 - - - +
126A ARG* 1.3 58.9 + - - +
128A VAL* 3.3 7.4 + - + +
129A LEU* 2.9 45.2 + - + +
207A ILE* 3.9 20.9 - - + +
210A ILE* 3.7 18.8 - - + -
211A ALA* 3.7 37.5 - - + +
214A LEU* 4.1 9.0 - - + -
255A PHE* 3.9 20.2 - - + -
278A TRP* 4.4 6.7 - - + -
279A ILE* 3.9 5.2 - - + -
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Residues in contact with ARG 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A SER 2.9 18.9 + - - +
123A THR* 3.8 32.3 + - - +
125A ILE* 1.3 75.3 - - - +
127A GLN* 1.3 80.9 + - - +
129A LEU* 3.7 5.3 + - - +
130A ASP* 3.2 24.9 + - - +
274A ALA* 6.3 1.3 - - + -
279A ILE* 3.9 35.8 - - + +
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Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ASN* 3.0 34.2 + - - +
123A THR* 2.9 38.5 + - - +
124A LEU* 3.3 11.2 + - - +
125A ILE 3.3 0.6 - - - -
126A ARG* 1.3 93.9 - - - +
128A VAL* 1.3 60.9 + - - +
130A ASP* 3.4 5.8 + - - +
131A ALA* 3.0 27.2 + - - +
159A SER 5.2 2.0 + - - -
160A LYS* 3.2 12.4 - - - +
161A ILE* 2.9 41.5 + - + +
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASN* 5.8 0.2 - - - -
124A LEU* 3.2 17.4 + - + +
125A ILE* 3.3 14.6 + - + +
127A GLN* 1.3 73.8 - - - +
129A LEU* 1.3 54.7 + - - +
131A ALA* 3.1 7.5 + - - +
132A VAL* 2.8 45.0 + - + +
145A LEU* 5.2 3.6 - - + -
150A LEU* 4.2 30.7 - - + -
161A ILE* 4.4 9.4 - - + -
163A ILE* 4.7 10.3 - - + -
207A ILE* 3.9 29.6 - - + -
210A ILE* 4.8 11.7 - - + -
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ILE* 2.9 37.1 + - + +
126A ARG* 3.8 4.9 - - - +
128A VAL* 1.3 74.4 - - - +
130A ASP* 1.3 54.5 + - - +
133A TYR* 2.8 36.9 + - - +
207A ILE* 3.8 32.3 - - + -
255A PHE* 4.0 5.4 - - + -
259A LEU* 5.1 2.5 - - + -
270A CYS* 3.9 22.9 - - - +
273A ALA* 3.9 18.2 - - + -
274A ALA* 4.0 28.7 - - + +
279A ILE* 4.0 21.8 - - + -
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Residues in contact with ASP 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A HIS* 2.7 29.5 + - + +
80A ASN* 4.7 1.7 - - - +
126A ARG* 3.2 16.2 + - - +
127A GLN* 3.4 11.9 - - - +
128A VAL 3.2 0.2 - - - -
129A LEU* 1.3 75.7 - - - +
131A ALA* 1.3 66.0 + - - +
133A TYR* 3.9 7.5 - - - +
134A TYR* 3.0 23.9 + - - +
137A ARG* 5.1 1.4 + - - -
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Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A HIS* 3.6 17.6 - - - +
80A ASN* 4.0 6.7 - - + -
81A ILE* 3.6 20.7 - - + +
127A GLN 3.0 11.1 + - - +
128A VAL 3.5 4.0 - - - +
130A ASP* 1.3 78.0 - - - +
132A VAL* 1.3 58.2 + - - +
134A TYR* 3.2 6.8 + - - +
135A LEU* 3.1 27.4 + - - +
163A ILE* 3.4 28.0 - - + -
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 2.8 23.7 + - + +
131A ALA* 1.3 70.0 - - - +
133A TYR* 1.3 59.7 + - - +
135A LEU* 3.2 12.4 + - + +
136A HIS* 3.0 57.3 + - + +
145A LEU* 3.4 32.8 - - + -
163A ILE* 4.2 7.9 - - + -
203A ASP* 3.8 15.7 - - + +
207A ILE* 3.9 13.5 - - + -
270A CYS* 3.6 9.0 - - - -
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Residues in contact with TYR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU 2.8 25.0 + - - +
130A ASP* 3.9 7.0 - - - +
132A VAL* 1.3 73.0 - - - +
134A TYR* 1.3 60.6 + - - +
136A HIS* 3.4 8.4 + - + -
137A ARG* 3.0 60.5 + - + +
270A CYS* 3.6 21.5 - - + -
271A GLU* 3.6 43.1 + - + +
274A ALA* 6.1 2.7 - - + -
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Residues in contact with TYR 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS 3.6 9.5 + - - -
76A ILE* 3.7 23.7 - - + -
77A LYS* 2.8 42.2 + - - +
78A HIS* 3.6 27.4 - + + -
81A ILE* 4.4 0.2 - - + -
130A ASP 3.0 14.2 + - - +
131A ALA 3.3 9.6 - - - +
133A TYR* 1.3 76.2 - - - +
135A LEU* 1.3 71.5 + - + +
137A ARG* 3.3 26.1 + - - +
138A MET* 3.1 65.2 + - + +
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ILE* 3.7 34.3 - - + -
81A ILE* 3.6 27.8 - - + -
131A ALA 3.1 17.1 + - - +
132A VAL* 3.2 19.0 + - + +
134A TYR* 1.3 79.0 - - + +
136A HIS* 1.3 57.8 + - + +
138A MET* 3.3 5.2 + - - +
139A GLY 3.1 4.9 + - - -
140A ILE* 2.7 56.5 + - + +
142A HIS* 4.4 33.7 - - + +
163A ILE* 5.4 1.8 - - + -
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Residues in contact with HIS 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A VAL* 3.0 36.2 + - + +
133A TYR* 3.7 11.6 - - + +
134A TYR 3.2 0.2 - - - -
135A LEU* 1.3 77.5 - - + +
137A ARG* 1.3 56.4 + - - +
139A GLY* 2.9 15.2 + - - -
140A ILE 3.4 17.0 - - - -
141A VAL* 4.7 0.2 - - - -
200A LYS* 3.2 68.2 + - + +
203A ASP* 2.8 27.6 + - + +
204A CYS* 4.0 6.6 - - - -
269A THR* 6.3 0.6 - - - -
270A CYS* 3.9 18.6 + - - +
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Residues in contact with ARG 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A HIS* 5.7 1.0 - - - -
130A ASP 5.1 1.0 + - - -
133A TYR* 3.0 80.1 + - + +
134A TYR* 3.3 35.8 + - - +
136A HIS* 1.3 76.3 - - - +
138A MET* 1.3 68.5 + - + +
139A GLY* 3.1 1.4 + - - -
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Residues in contact with MET 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS* 5.5 11.4 - - + +
76A ILE* 5.9 0.2 - - - -
134A TYR* 3.1 69.0 + - + +
135A LEU* 3.5 6.7 - - - +
136A HIS 3.2 0.2 - - - -
137A ARG* 1.3 85.5 - - + +
139A GLY* 1.3 59.5 + - - +
140A ILE* 3.5 20.7 - - + +
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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
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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) + - + + + + + -
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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