Contacts of the helix formed by residues 117 - 136 (chain D) in PDB entry 1JT0
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 ASN 117 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B GLU* 5.1 5.9 - - - +
103D TYR* 4.9 6.3 - - + +
113D ASN* 3.2 23.0 + - - +
114D GLU* 2.8 18.4 + - - +
116D MET* 1.3 77.7 - - - +
118D LYS* 1.3 70.4 + - - +
119D LEU 3.2 2.0 - - - -
120D GLU* 2.6 41.0 - - - +
121D ASN* 2.8 17.8 + - - +
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Residues in contact with LYS 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D GLU* 3.2 13.0 + - + +
117D ASN* 1.3 82.6 - - - +
119D LEU* 1.3 65.3 + - - +
120D GLU 3.0 2.9 + - - -
121D ASN* 3.4 36.1 + - + +
122D LYS* 3.2 30.0 + - + +
125D ASP* 4.2 14.5 + - - -
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Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D LEU* 5.5 0.4 - - + -
54D LEU* 3.7 38.1 - - + -
55D ASN* 4.2 22.2 - - - +
58D GLU* 3.4 58.7 - - + +
92D TYR* 3.4 15.6 + - + +
114D GLU 4.6 0.4 + - - -
115D LYS* 3.6 22.2 - - - +
116D MET* 3.6 11.8 - - - +
117D ASN 3.2 0.4 - - - -
118D LYS* 1.3 81.1 - - - +
120D GLU* 1.3 58.4 + - - +
122D LYS* 3.8 10.1 - - - +
123D TYR* 3.5 11.3 - - - -
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Residues in contact with GLU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLU* 6.1 1.1 - - - -
92D TYR* 4.4 8.1 - - + +
96D GLN* 6.1 2.5 - - - +
116D MET 4.0 7.9 - - - +
117D ASN* 2.6 24.7 - - - +
118D LYS 3.0 0.2 - - - -
119D LEU* 1.3 78.9 - - - +
121D ASN* 1.3 94.5 + - - +
122D LYS 2.7 5.6 + - - -
123D TYR* 2.5 43.5 + - + +
124D ILE* 3.4 23.8 - - + +
154D ASN* 5.7 1.6 + - - -
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Residues in contact with ASN 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ASN* 2.8 28.6 + - - +
118D LYS* 3.4 33.6 + - + +
120D GLU* 1.3 101.0 + - - +
122D LYS* 1.3 55.2 - - - +
123D TYR 3.0 0.4 - - - -
124D ILE* 3.3 19.1 + - - +
125D ASP* 2.9 34.4 + - - +
150D LYS* 5.7 4.6 - - - +
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Residues in contact with LYS 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLU* 3.0 50.5 + - - +
62D GLN* 4.3 21.6 + - + +
82D TYR* 4.5 1.2 + - - -
118D LYS* 3.2 25.1 - - + +
119D LEU* 3.8 12.6 - - - +
120D GLU 2.7 0.8 + - - -
121D ASN* 1.3 79.5 - - + +
123D TYR* 1.3 61.0 + - + +
125D ASP* 3.4 24.7 - - - +
126D ALA* 3.4 10.0 + - - +
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Residues in contact with TYR 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLU* 3.8 11.2 + - - -
61D TRP* 3.0 44.4 - + - +
62D GLN* 6.2 0.2 - - - -
82D TYR* 3.2 19.9 + + + -
91D TYR 4.8 0.2 + - - -
92D TYR* 3.2 41.6 - + - +
93D TYR* 3.7 41.7 + + - +
96D GLN* 6.2 0.7 - - - -
119D LEU 3.5 20.2 - - - -
120D GLU* 2.5 28.5 + - + +
122D LYS* 1.3 72.8 - - + +
124D ILE* 1.3 63.3 + - + +
125D ASP 2.9 5.7 + - - -
126D ALA* 3.5 9.4 + - - +
127D TYR* 3.2 24.3 + - + -
153D ALA* 5.2 4.0 - - + -
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Residues in contact with ILE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D GLU* 3.4 28.7 - - + +
121D ASN* 3.4 31.2 - - - +
123D TYR* 1.3 77.6 - - + +
125D ASP* 1.3 64.5 + - - +
127D TYR* 3.7 5.0 + - - +
128D HIS* 3.2 17.0 + - - +
149D SER* 3.8 7.3 - - - +
150D LYS* 3.4 48.9 - - + +
153D ALA* 4.0 16.4 - - + -
154D ASN* 5.3 7.2 - - - +
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Residues in contact with ASP 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D LYS* 4.2 13.9 + - - -
121D ASN* 2.9 22.8 + - - +
122D LYS* 3.4 20.4 - - - +
123D TYR 2.9 1.0 - - - -
124D ILE* 1.3 77.3 - - - +
126D ALA* 1.3 58.0 + - - +
128D HIS* 2.5 39.3 + - - +
129D VAL* 3.0 10.3 + - + +
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Residues in contact with ALA 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D GLN* 6.0 2.5 - - - +
65D TRP* 4.3 16.4 - - + +
82D TYR* 3.5 41.3 - - + +
122D LYS 3.4 6.4 + - - +
123D TYR 3.9 1.6 - - - +
125D ASP* 1.3 77.7 - - - +
127D TYR* 1.3 63.8 + - - +
129D VAL* 3.1 10.7 + - - +
130D ILE* 2.9 29.8 + - + +
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Residues in contact with TYR 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D PHE* 3.4 37.9 - + - -
82D TYR* 3.5 31.3 - + + -
83D ASN* 2.3 26.7 + - - -
86D SER* 5.3 1.0 + - - -
93D TYR* 5.4 4.2 + - - -
123D TYR* 3.2 21.8 + - + -
124D ILE 3.9 4.0 - - - +
125D ASP 2.9 1.2 + - - -
126D ALA* 1.3 78.6 - - - +
128D HIS* 1.3 58.5 + - - +
130D ILE* 3.8 6.5 - - + +
131D PHE* 2.9 39.9 + + + -
149D SER* 3.2 24.0 - - - +
152D ALA* 3.9 9.0 - - + -
153D ALA* 3.5 34.3 - - + -
156D VAL* 3.5 19.0 - - + +
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Residues in contact with HIS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ILE 3.2 8.6 + - - +
125D ASP* 2.5 23.7 + - - +
127D TYR* 1.3 72.8 - - - +
129D VAL* 1.3 61.4 + - + +
131D PHE* 4.0 0.6 - - - +
132D LYS* 2.8 44.1 + - + +
145D VAL* 3.1 36.7 - - + +
146D ASN* 3.7 27.6 + - - -
149D SER* 2.9 18.1 + - - +
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Residues in contact with VAL 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D ASN* 5.5 0.7 - - - +
78D LYS* 6.5 0.7 - - + -
125D ASP* 3.0 15.3 + - + +
126D ALA* 3.5 11.9 - - - +
128D HIS* 1.3 78.5 + - + +
130D ILE* 1.3 63.0 + - + +
132D LYS* 3.4 3.8 - - - +
133D GLU* 2.8 52.2 + - + +
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Residues in contact with ILE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D TRP* 4.0 28.3 - - + +
75D ASN* 3.3 51.3 - - + +
78D LYS* 4.0 15.9 - - + -
79D PHE* 4.0 21.3 - - + +
82D TYR* 4.2 15.0 - - + -
126D ALA* 2.9 21.0 + - + +
127D TYR* 3.8 9.0 - - + +
129D VAL* 1.3 83.5 - - + +
131D PHE* 1.3 64.6 + - + +
134D GLY 3.1 14.9 + - - -
140D TRP* 3.5 5.5 - - + -
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Residues in contact with PHE 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D PHE* 3.7 26.9 - + - -
127D TYR* 2.9 34.0 + + + +
128D HIS 4.0 0.4 - - - +
130D ILE* 1.3 74.2 - - + +
132D LYS* 1.3 62.3 + - - +
134D GLY 3.0 4.9 + - - -
135D ASN* 3.1 6.8 + - - -
140D TRP* 2.9 31.6 + + - +
142D ILE* 3.1 30.3 - - + -
145D VAL* 3.9 14.1 - - + -
148D VAL* 3.6 26.5 - - + -
149D SER* 3.3 19.5 - - - +
152D ALA* 3.8 6.7 - - + -
182D PHE* 3.6 24.2 - + - -
183D LEU* 4.6 5.4 - - + -
186D LEU* 4.2 13.0 - - + -
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Residues in contact with LYS 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D HIS* 2.8 41.6 + - + +
129D VAL* 3.4 3.6 - - - +
131D PHE* 1.3 68.3 - - - +
133D GLU* 1.3 57.3 + - - +
134D GLY 2.8 4.6 + - - -
135D ASN* 2.5 47.8 + - - +
136D LEU* 3.3 15.0 + - + +
145D VAL* 3.6 28.0 - - + +
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Residues in contact with GLU 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D ASN* 2.9 29.2 + - - +
78D LYS* 4.6 10.6 - - - -
129D VAL* 2.8 32.2 + - + +
132D LYS* 1.3 74.7 - - - +
134D GLY* 1.3 56.3 + - - +
135D ASN 3.2 0.2 - - - -
136D LEU* 3.9 19.7 + - + +
137D ASN* 3.3 29.9 + - - +
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Residues in contact with GLY 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D ASN* 2.8 17.5 - - - +
130D ILE 3.1 5.8 + - - -
131D PHE 3.0 9.6 + - - -
132D LYS 2.8 1.8 + - - -
133D GLU* 1.3 76.4 - - - +
135D ASN* 1.3 61.6 + - - +
137D ASN 3.6 0.8 + - - -
138D GLY 3.5 0.9 + - - -
139D GLU* 3.0 39.6 + - - +
140D TRP* 3.5 14.5 + - - -
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Residues in contact with ASN 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D PHE 3.1 7.2 + - - -
132D LYS* 2.5 31.4 + - - +
134D GLY* 1.3 68.3 - - - +
136D LEU* 1.3 51.0 + - - +
137D ASN 2.7 15.8 + - - -
138D GLY* 2.9 13.9 + - - -
140D TRP* 2.7 28.3 - - - +
141D SER* 3.0 4.2 - - - -
142D ILE* 2.7 47.9 + - - +
145D VAL* 3.9 15.8 - - - +
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Residues in contact with LEU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LYS* 3.3 14.2 + - + +
133D GLU* 3.9 26.2 - - + +
134D GLY 3.5 0.2 - - - -
135D ASN* 1.3 75.5 - - - +
137D ASN* 1.3 78.0 + - - +
138D GLY 3.7 0.4 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
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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