Contacts of the helix formed by residues 119 - 140 (chain A) in PDB entry 2J6U
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 ARG 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A HIS* 3.6 11.0 + - - +
2A HIS* 2.9 43.5 + - + +
118A VAL* 1.3 75.6 - - - +
120A ASP* 1.3 86.3 + - + +
123A GLU* 2.7 19.6 + - - +
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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
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1A HIS* 4.0 9.9 + - - -
2A HIS* 5.5 0.6 - - - -
5A ILE* 5.3 5.2 - - - +
118A VAL* 3.0 17.8 - - - +
119A ARG* 1.3 97.7 - - + +
121A TYR* 1.3 66.1 + - - +
122A ARG* 2.9 40.9 + - - +
123A GLU* 3.4 8.1 + - - +
124A ALA* 4.1 0.3 - - - +
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Residues in contact with TYR 121 (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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3A HIS* 3.5 11.4 - + - -
5A ILE* 3.9 32.3 - - + +
120A ASP* 1.3 74.6 + - - +
122A ARG* 1.3 57.1 + - - +
124A ALA* 2.8 3.9 + - + +
125A TYR* 2.7 36.4 + - - +
147A ILE* 3.9 24.9 - - + -
148A SER* 3.5 10.3 - - - -
149A LYS 3.4 18.7 + - - -
168A VAL* 3.6 23.5 - - + +
169A ILE 4.4 0.6 + - - -
170A ASP* 3.6 31.0 - - + -
171A ASP* 3.0 24.4 + - - -
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Residues in contact with ARG 122 (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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120A ASP* 2.9 25.2 + - - +
121A TYR* 1.3 71.4 - - - +
123A GLU* 1.3 87.7 + - - +
125A TYR* 3.3 6.7 + - - +
126A ASN* 2.8 64.1 + - - +
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Residues in contact with GLU 123 (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 LYS 4.5 0.5 - - - +
118A VAL* 3.1 29.7 - - + +
119A ARG* 2.7 42.0 + - - +
120A ASP* 3.4 3.4 + - - +
121A TYR 3.2 0.4 - - - -
122A ARG* 1.3 99.6 + - - +
124A ALA* 1.3 55.9 + - - +
126A ASN* 3.6 8.6 + - - +
127A LEU* 3.0 27.7 + - - +
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Residues in contact with ALA 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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5A ILE* 4.4 2.5 - - + -
7A LEU* 4.5 0.7 - - - +
114A ILE* 4.3 11.4 - - + -
118A VAL* 3.4 11.4 - - + +
120A ASP 4.1 2.9 - - - +
121A TYR* 2.8 24.6 + - + +
123A GLU* 1.3 76.8 - - - +
125A TYR* 1.3 66.5 + - - +
127A LEU* 2.8 18.5 + - - +
128A GLY 2.9 10.0 + - - -
147A ILE* 3.7 32.9 - - + +
168A VAL* 5.6 0.2 - - + -
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Residues in contact with TYR 125 (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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121A TYR 2.7 18.2 + - - +
122A ARG* 3.6 7.4 - - + +
124A ALA* 1.3 71.5 - - - +
126A ASN* 1.3 70.6 + - - +
128A GLY* 3.0 10.7 + - - -
129A LEU* 3.1 34.1 + - + +
147A ILE* 3.9 8.6 - - - +
166A ILE* 3.5 54.0 + - + +
167A LYS* 5.0 1.3 - - - -
168A VAL* 3.8 22.7 - - + -
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Residues in contact with ASN 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 ARG* 2.8 54.1 + - - +
123A GLU* 3.9 6.0 - - - +
125A TYR* 1.3 86.3 - - - +
127A LEU* 1.3 57.2 + - - +
129A LEU* 3.3 15.6 + - - +
130A GLU* 3.0 31.9 + - - +
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Residues in contact with LEU 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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7A LEU* 4.3 3.4 - - + -
98A TYR* 3.3 39.3 - - + +
114A ILE* 4.0 36.6 - - + -
117A LYS* 4.8 7.9 - - + +
118A VAL* 4.3 14.1 - - + -
123A GLU 3.0 15.1 + - - +
124A ALA 2.8 10.6 + - - +
126A ASN* 1.3 76.5 - - - +
128A GLY* 1.3 56.3 + - - +
130A GLU* 3.3 17.2 - - - +
131A ILE* 3.0 29.2 + - + +
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Residues in contact with GLY 128 (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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7A LEU* 4.2 14.6 - - - +
124A ALA 2.9 11.1 + - - -
125A TYR 3.0 5.1 + - - -
127A LEU* 1.3 74.7 - - - +
129A LEU* 1.3 55.0 + - - +
130A GLU 3.0 1.3 - - - -
131A ILE* 3.1 3.6 + - - +
132A LYS* 2.7 39.8 + - - +
145A VAL* 4.2 7.2 - - - +
147A ILE* 5.1 0.2 - - - -
166A ILE* 3.8 16.2 - - - -
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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 TYR* 3.1 41.0 + - + +
126A ASN* 3.7 15.9 - - - +
128A GLY* 1.3 76.5 - - - +
130A GLU* 1.3 56.8 + - - +
132A LYS* 3.9 14.7 - - + +
133A ASN* 2.9 34.5 + - - +
166A ILE* 4.0 20.6 - - + +
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A TYR* 4.0 22.1 + - + +
126A ASN* 3.0 18.0 + - - +
127A LEU* 3.3 25.5 - - + +
129A LEU* 1.3 78.7 - - - +
131A ILE* 1.3 56.7 + - - +
133A ASN* 3.7 8.3 + - - +
134A LYS* 2.8 32.8 + - - +
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Residues in contact with ILE 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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7A LEU* 4.0 25.6 - - + -
9A VAL* 4.6 6.7 - - + -
95A LEU* 3.3 28.5 - - + -
98A TYR* 3.4 43.5 - - + -
112A LEU* 4.2 12.3 - - + -
127A LEU* 3.0 22.6 + - + +
128A GLY* 3.7 4.3 - - - +
130A GLU* 1.3 73.7 - - - +
132A LYS* 1.3 69.9 + - - +
134A LYS* 3.1 6.2 + - + +
135A ILE* 3.0 31.3 + - + +
145A VAL* 5.4 3.1 - - + -
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Residues in contact with LYS 132 (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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128A GLY 2.7 20.3 + - - +
129A LEU* 3.9 16.8 - - - +
131A ILE* 1.3 74.2 - - - +
133A ASN* 1.3 65.2 + - - +
135A ILE* 3.2 2.9 + - - +
136A LEU* 3.0 23.9 + - - +
141A ILE 4.8 1.2 - - - +
143A VAL* 3.0 37.8 + - + +
145A VAL* 3.5 25.4 - - + -
164A ASN* 2.8 34.5 + - - -
165A GLY* 3.4 24.5 + - - +
166A ILE* 4.0 14.6 - - + -
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Residues in contact with ASN 133 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A LEU 2.9 20.7 + - - +
130A GLU* 3.7 7.5 + - - +
132A LYS* 1.3 77.3 - - - +
134A LYS* 1.3 67.7 + - - +
136A LEU* 3.6 12.3 + - - +
137A GLU* 3.0 37.2 + - - +
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Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A LEU* 4.7 14.6 - - + -
98A TYR* 3.2 32.3 - - + +
130A GLU* 2.8 21.0 + - - +
131A ILE* 3.1 6.7 + - + +
133A ASN* 1.3 82.6 - - - +
135A ILE* 1.3 65.4 + - + +
137A GLU* 3.0 18.1 + - - +
138A LYS* 2.9 44.9 + - + +
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A VAL* 4.5 3.6 - - + -
91A ILE* 3.9 37.5 - - + -
94A LEU* 3.9 19.3 - - + -
95A LEU* 4.0 10.3 - - + -
131A ILE* 3.0 34.4 + - + +
132A LYS 3.6 4.7 - - - +
134A LYS* 1.3 73.7 - - + +
136A LEU* 1.3 64.8 + - - +
139A GLU* 2.8 23.9 + - + -
140A LYS 3.3 2.6 + - - -
141A ILE* 3.5 27.6 - - + +
143A VAL* 4.2 25.4 - - + -
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A LYS 3.0 16.8 + - - +
133A ASN* 3.8 12.8 - - - +
135A ILE* 1.3 75.3 - - - +
137A GLU* 1.3 58.9 + - - +
140A LYS* 2.6 50.0 + - + +
141A ILE 3.5 12.0 + - - +
142A THR* 4.1 24.0 - - + -
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Residues in contact with GLU 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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133A ASN* 3.0 31.6 + - - +
134A LYS* 3.2 21.3 + - - +
136A LEU* 1.3 81.6 - - - +
138A LYS* 1.3 74.8 + - + +
140A LYS* 4.3 8.5 + - - +
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Residues in contact with LYS 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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94A LEU* 4.1 34.3 - - + -
134A LYS* 2.9 37.7 + - + +
137A GLU* 1.3 86.3 - - + +
139A GLU* 1.3 71.2 + - + +
140A LYS* 5.4 0.6 - - - +
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Residues in contact with GLU 139 (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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21A VAL* 3.9 14.7 - - - +
87A VAL* 4.7 6.1 - - + +
90A ARG* 2.9 53.5 + - + +
91A ILE* 4.1 22.4 - - + -
94A LEU* 4.7 7.0 - - + -
135A ILE* 2.8 12.8 + - + +
138A LYS* 1.3 89.1 - - + +
140A LYS* 1.3 73.6 - - - +
141A ILE* 3.2 21.3 + - + +
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Residues in contact with LYS 140 (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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17A GLN* 3.8 5.2 - - - +
21A VAL* 3.6 24.3 - - + +
27A LYS* 6.0 6.9 - - - +
135A ILE 3.3 0.2 + - - -
136A LEU* 2.6 41.3 + - + +
137A GLU 4.5 7.2 - - - +
138A LYS 5.4 0.7 - - - +
139A GLU* 1.3 75.5 - - - +
141A ILE* 1.3 58.3 + - - +
142A THR* 4.1 0.9 + - - +
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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
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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