Contacts of the helix formed by residues 118 - 132 (chain B) in PDB entry 2J16
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 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B TYR* 3.4 32.5 - - + -
109B TRP* 2.8 32.7 + - + +
114B GLN 4.9 3.5 - - - +
115B ILE* 3.0 11.0 + - - +
117B LEU* 1.3 86.3 - - - +
119B LEU* 1.3 64.2 + - - +
121B SER* 3.2 8.3 + - - -
122B LEU* 3.0 28.4 + - + +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B TRP* 4.1 17.7 - - + -
115B ILE* 3.1 47.8 + - + +
116B ALA* 4.2 5.6 - - - +
118B ASP* 1.3 76.5 - - - +
120B PRO* 1.4 59.2 - - + +
122B LEU* 4.6 1.3 - - - -
123B THR* 2.7 41.9 + - + +
150B LEU* 4.4 10.1 - - + -
153B ALA* 3.7 23.6 - - + -
186B GLN 5.0 2.7 - - - +
187B LEU* 5.0 2.0 - - + -
190B TRP* 3.6 50.0 - - + -
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Residues in contact with PRO 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ALA 3.6 10.1 - - - +
117B LEU* 3.5 16.8 - - - +
119B LEU* 1.4 92.6 - - + +
121B SER* 1.3 55.7 + - - +
123B THR* 3.3 7.0 + - - +
124B SER* 2.7 34.0 + - - -
157B LYS* 4.8 9.7 + - - +
190B TRP* 3.9 18.6 - - + -
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Residues in contact with SER 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B TYR* 3.7 19.2 - - - -
117B LEU 3.8 11.1 + - - -
118B ASP* 3.2 8.2 + - - -
120B PRO* 1.3 77.6 - - - +
122B LEU* 1.3 58.2 - - - +
124B SER* 3.5 5.9 + - - -
125B ILE* 3.2 33.3 + - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ILE* 3.6 29.8 - - + -
88B VAL* 4.7 1.3 - - + -
105B HIS* 5.4 0.2 - - + -
107B TYR* 3.6 50.0 - - + -
109B TRP* 3.5 36.8 - - + -
118B ASP* 3.0 17.4 + - + +
119B LEU 3.9 1.6 - - - +
121B SER* 1.3 73.7 - - - +
123B THR* 1.3 64.6 + - - +
124B SER 3.0 1.8 - - - -
125B ILE* 3.1 20.2 + - + +
126B ILE* 3.2 18.6 + - - +
150B LEU* 3.6 19.7 - - + -
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Residues in contact with THR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU 2.7 31.6 + - - +
120B PRO* 3.3 12.3 + - - +
122B LEU* 1.3 71.9 - - - +
124B SER* 1.3 55.9 + - - +
126B ILE* 3.7 9.3 + - - +
127B HIS* 3.0 19.9 + - - +
150B LEU* 4.4 7.4 - - + -
153B ALA* 3.9 15.5 - - + +
154B TYR* 3.7 32.2 - - + +
157B LYS* 4.1 9.0 + - - +
158B TYR* 3.1 33.0 - - - -
190B TRP* 4.1 6.3 - - + -
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Residues in contact with SER 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B PRO 2.7 22.4 + - - -
121B SER* 3.6 7.0 - - - -
122B LEU 3.0 0.8 - - - -
123B THR* 1.3 76.4 - - - +
125B ILE* 1.3 59.4 + - - +
126B ILE 3.2 1.3 - - - -
127B HIS* 4.0 2.3 - - - +
128B ALA* 2.8 33.8 + - - +
157B LYS* 4.6 3.3 + - - -
158B TYR* 3.3 17.8 + - - -
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B VAL* 4.2 8.5 - - + +
86B ILE* 3.8 18.8 - - + -
105B HIS* 3.5 48.5 - - + +
107B TYR* 4.3 13.9 - - + +
121B SER* 3.2 21.5 + - - +
122B LEU* 3.1 17.8 + - + +
124B SER* 1.3 75.6 - - - +
126B ILE* 1.3 62.8 + - - +
128B ALA* 3.9 4.8 - - - +
129B ALA* 3.2 22.9 + - - +
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ILE* 3.6 32.5 - - + -
86B ILE* 3.6 16.8 - - + -
122B LEU 3.2 14.9 + - - +
123B THR* 3.8 6.1 - - - +
124B SER 3.2 0.4 - - - -
125B ILE* 1.3 74.1 - - - +
127B HIS* 1.3 64.5 + - - +
129B ALA* 3.1 8.8 + - - +
130B THR* 3.0 21.7 + - + +
136B ILE* 4.3 10.8 - - + -
138B ILE* 3.8 21.1 - - + -
150B LEU* 3.8 27.6 - - + -
151B ILE* 5.5 2.0 - - + -
154B TYR* 3.6 27.8 - - + -
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Residues in contact with HIS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B THR 3.0 19.9 + - - +
124B SER* 3.4 3.5 + - - +
126B ILE* 1.3 75.1 - - - +
128B ALA* 1.3 62.9 + - - +
130B THR* 2.7 26.7 + - - -
131B THR* 3.0 31.6 + - - -
154B TYR* 4.0 7.0 + - + -
158B TYR* 3.4 49.4 - + + +
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Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B SER 2.8 21.9 + - - +
125B ILE* 3.9 5.4 - - - +
127B HIS* 1.3 76.4 - - - +
129B ALA* 1.3 62.8 + - - +
131B THR* 3.3 10.1 + - - -
132B LYS* 3.2 30.6 + - + +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B VAL* 3.9 22.0 - - + -
125B ILE 3.2 15.9 + - - +
126B ILE* 3.1 7.0 + - - +
128B ALA* 1.3 80.2 - - - +
130B THR* 1.3 58.6 + - - +
132B LYS* 3.2 2.6 + - - -
133B ARG 3.1 4.7 + - - -
134B GLU* 2.9 39.0 + - + +
136B ILE* 3.6 23.8 - - + -
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Residues in contact with THR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B GLU* 3.8 40.2 - - + +
68B ILE* 4.3 3.8 - - + -
126B ILE 3.0 16.0 + - - +
127B HIS* 2.7 33.1 + - - -
129B ALA* 1.3 73.0 - - - +
131B THR* 1.3 60.5 + - - +
133B ARG* 3.1 21.2 + - - +
134B GLU 4.7 2.7 - - - +
136B ILE* 3.6 17.5 - - + -
154B TYR* 3.9 11.7 + - - +
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B HIS* 3.0 33.8 + - - -
128B ALA* 3.4 12.2 - - - -
130B THR* 1.3 78.0 + - - +
132B LYS* 1.3 58.8 - - + +
133B ARG* 3.1 10.7 + - - +
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Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B GLU* 4.6 14.1 + - - -
128B ALA* 3.2 18.8 + - + +
129B ALA* 3.2 3.1 + - - +
130B THR 3.2 0.4 - - - -
131B THR* 1.3 78.4 - - + +
133B ARG* 1.3 70.5 + - - +
134B GLU* 3.2 35.6 + - - +
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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