Contacts of the helix formed by residues 108 - 126 (chain B) in PDB entry 1JWG
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 SER 108 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLU* 2.2 39.8 + - - +
106B ARG 4.2 1.0 + - - -
107B THR* 1.3 82.0 - - - +
109B GLU* 1.3 64.1 + - - +
110B LYS* 3.7 1.8 - - - +
111B VAL* 3.4 13.9 + - - +
112B LYS* 3.2 21.7 + - - +
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Residues in contact with GLU 109 (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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107B THR 3.9 0.4 + - - -
108B SER* 1.3 72.5 - - - +
110B LYS* 1.3 67.0 + - - +
112B LYS* 3.3 19.4 + - - +
113B ASN* 3.0 61.1 + - - +
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Residues in contact with LYS 110 (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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60B GLU* 3.7 30.1 - - - +
64B ILE* 4.3 25.4 - - + -
108B SER* 4.3 0.6 - - - -
109B GLU* 1.3 79.2 - - - +
111B VAL* 1.3 62.5 + - - +
113B ASN* 3.5 5.5 + - - +
114B LYS* 3.2 25.1 + - + +
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ILE 4.7 2.9 - - - +
60B GLU* 3.8 16.6 - - + -
63B ALA* 4.1 18.4 - - + -
64B ILE* 3.7 27.1 - - + +
67B LEU* 3.9 13.6 - - + +
97B VAL* 3.9 13.2 - - + -
107B THR* 3.6 27.4 - - + -
108B SER* 3.4 14.8 + - - +
109B GLU 3.3 0.4 - - - -
110B LYS* 1.3 80.0 - - - +
112B LYS* 1.3 63.6 + - - +
114B LYS* 3.4 4.6 - - - +
115B ILE* 3.2 22.4 + - + +
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Residues in contact with LYS 112 (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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97B VAL* 3.5 26.7 - - + +
98B VAL* 3.7 25.5 + - + +
100B PRO* 6.4 0.8 - - - +
104B GLY* 2.8 28.2 + - - +
105B SER* 5.0 0.6 - - - +
107B THR* 3.4 24.1 + - + +
108B SER 3.2 11.9 + - - +
109B GLU* 3.3 21.1 + - - +
111B VAL* 1.3 78.4 - - - +
113B ASN* 1.3 65.1 + - - +
115B ILE* 3.3 6.1 + - - +
116B LEU* 3.1 29.4 + - + +
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Residues in contact with ASN 113 (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 GLU* 3.0 51.4 + - - +
110B LYS* 4.1 4.7 - - - +
112B LYS* 1.3 75.4 - - - +
114B LYS* 1.3 61.5 + - - +
116B LEU* 3.2 15.7 + - - +
117B GLU* 2.8 46.0 + - + +
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 4.5 16.4 - - + -
67B LEU* 4.1 20.9 - - + +
68B THR* 5.3 7.6 - - - -
71B GLU* 3.0 34.4 + - - +
110B LYS* 3.2 12.7 + - + +
111B VAL* 3.4 11.9 - - - +
113B ASN* 1.3 80.1 - - - +
115B ILE* 1.3 63.5 + - - +
117B GLU* 3.1 22.5 + - - +
118B LEU* 2.9 40.8 + - + +
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Residues in contact with ILE 115 (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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55B ILE* 4.1 15.7 - - + -
67B LEU* 3.5 22.4 - - + -
94B LEU* 4.0 25.8 - - + +
97B VAL* 3.6 38.8 - - + -
98B VAL* 3.9 15.5 - - + -
111B VAL* 3.2 14.3 + - + +
112B LYS 3.6 6.1 - - - +
113B ASN 3.3 0.2 - - - -
114B LYS* 1.3 79.1 - - - +
116B LEU* 1.3 58.1 + - - +
118B LEU* 3.2 8.5 + - - +
119B LEU* 2.9 53.1 + - + +
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Residues in contact with LEU 116 (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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98B VAL* 4.0 17.5 - - + -
112B LYS* 3.1 18.3 + - + +
113B ASN* 3.6 19.7 - - - +
115B ILE* 1.3 74.8 - - - +
117B GLU* 1.3 63.1 + - - +
119B LEU* 3.2 8.1 + - + +
120B TYR* 3.0 23.6 + - - +
136B TYR* 3.9 5.1 + - + -
139B LEU* 4.1 25.4 - - + -
144B ILE* 4.2 29.4 - - + +
145B VAL* 4.2 21.1 - - + +
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Residues in contact with GLU 117 (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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113B ASN* 2.8 35.8 + - + +
114B LYS* 3.4 24.5 + - + +
116B LEU* 1.3 70.9 - - + +
118B LEU* 1.3 65.8 + - + +
120B TYR* 3.2 8.1 + - - +
121B SER* 3.0 24.4 + - - -
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.9 44.4 - - + +
70B LEU* 4.3 6.3 - - + -
71B GLU* 3.7 37.2 - - + +
94B LEU* 6.2 1.1 - - + -
114B LYS* 2.9 27.4 + - + +
115B ILE* 3.5 8.5 - - - +
117B GLU* 1.3 76.8 - - + +
119B LEU* 1.3 63.4 + - - +
121B SER* 2.7 25.5 + - - +
122B TRP* 3.1 43.5 + - + +
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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
----------------------------------------------------------
91B LEU* 4.0 15.5 - - + +
94B LEU* 3.8 18.2 - - + -
95B ILE* 5.5 5.4 - - + +
98B VAL* 5.7 0.7 - - + -
115B ILE* 2.9 39.6 + - + +
116B LEU* 3.5 9.2 - - + +
117B GLU 3.2 0.2 - - - -
118B LEU* 1.3 78.7 - - - +
120B TYR* 1.3 62.4 + - - +
122B TRP* 3.3 29.2 + - + +
123B THR* 3.0 24.7 + - - +
132B ILE* 3.8 9.2 - - + +
135B ALA* 6.0 3.8 - - + -
136B TYR* 3.8 14.6 - - + +
139B LEU* 3.8 28.7 - - + -
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Residues in contact with TYR 120 (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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116B LEU 3.0 10.6 + - - +
117B GLU* 3.7 9.0 - - - +
119B LEU* 1.3 76.3 - - - +
121B SER* 1.3 58.9 + - - +
123B THR* 2.3 47.2 + - - -
124B VAL* 3.1 32.6 + - + +
136B TYR* 3.5 39.4 - + + +
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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
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117B GLU 3.0 13.3 + - - -
118B LEU* 2.7 26.1 + - - +
120B TYR* 1.3 82.6 - - - +
122B TRP* 1.3 62.2 + - - +
124B VAL* 3.0 13.2 - - - +
125B GLY* 2.7 32.7 + - - -
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Residues in contact with TRP 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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70B LEU* 3.6 37.9 - - + -
71B GLU* 5.0 2.2 + - - +
74B MET* 3.8 43.1 - - + +
85B VAL* 3.9 14.8 - - + -
91B LEU* 4.9 0.9 - - + -
94B LEU* 4.0 8.5 - - + -
118B LEU* 3.1 37.5 + - + +
119B LEU* 3.6 32.8 - - + +
120B TYR 3.1 0.8 - - - -
121B SER* 1.3 89.0 + - - +
123B THR* 1.3 59.6 + - - +
125B GLY* 4.7 0.7 - - - -
126B LEU* 2.6 45.5 + - + +
132B ILE* 3.8 31.9 - - + +
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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
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119B LEU 3.0 18.2 - - - +
120B TYR* 2.3 44.0 + - - -
122B TRP* 1.3 77.9 - - - +
124B VAL* 1.3 59.8 + - - +
126B LEU 5.0 0.7 - - - -
127B PRO* 3.5 23.0 - - - +
129B GLU 5.9 0.9 - - - -
132B ILE* 3.8 26.9 - - + +
133B ALA* 4.2 15.9 - - - +
136B TYR* 4.0 16.0 - - + -
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Residues in contact with VAL 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 TYR* 3.1 49.4 + - + +
121B SER* 3.0 20.4 - - - +
123B THR* 1.3 79.1 - - - +
125B GLY* 1.3 62.9 + - - +
126B LEU 3.5 0.2 - - - -
127B PRO* 3.4 12.6 - - - +
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Residues in contact with GLY 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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121B SER 2.7 20.4 + - - -
122B TRP* 4.5 0.4 - - - -
124B VAL* 1.3 73.3 - - - +
126B LEU* 1.3 72.5 + - - +
127B PRO* 3.2 8.0 - - - +
128B GLU* 3.9 4.9 - - - +
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Residues in contact with LEU 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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74B MET* 3.3 35.2 - - + +
82B HIS* 3.7 36.6 - - + +
122B TRP* 2.6 39.8 + - + +
123B THR* 5.2 0.2 - - - -
125B GLY* 1.3 80.9 - - - +
127B PRO* 1.3 49.7 - - - +
128B GLU* 2.5 38.3 + - + +
129B GLU* 2.7 31.7 + - + +
132B ILE* 5.2 0.7 - - + -
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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