Contacts of the helix formed by residues 117 - 133 (chain B) in PDB entry 1D8L
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 GLY 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B VAL* 4.8 0.9 - - - -
115B GLY 4.0 0.2 - - - -
116B ILE* 1.3 84.9 - - - +
118B LYS* 1.3 62.8 + - - +
119B LYS 3.3 2.7 - - - -
120B THR* 3.3 15.0 + - - -
121B ALA* 2.6 35.0 + - - +
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Residues in contact with LYS 118 (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 VAL* 4.6 2.1 - - - +
111B VAL* 3.9 32.6 + - + +
117B GLY* 1.3 76.7 - - - +
119B LYS* 1.3 65.3 + - + +
121B ALA* 3.6 4.5 - - - +
122B GLU* 3.1 27.5 + - - +
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Residues in contact with LYS 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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118B LYS* 1.3 80.7 - - + +
120B THR* 1.3 57.6 + - + +
121B ALA 3.2 0.7 - - - -
122B GLU* 3.2 12.9 + - + +
123B ARG* 2.7 40.8 + - + +
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Residues in contact with THR 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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79B ASN 5.7 2.9 - - - +
80B GLY* 5.9 6.5 - - - +
81B VAL* 5.6 7.2 - - - +
85B LEU* 5.6 1.2 - - - +
116B ILE* 3.1 35.5 + - - +
117B GLY* 3.3 16.4 + - - -
119B LYS* 1.3 79.2 - - + +
121B ALA* 1.3 55.0 + - - +
123B ARG* 3.3 20.2 - - - +
124B LEU* 2.6 39.2 + - - +
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Residues in contact with ALA 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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107B VAL* 3.9 20.9 - - + +
110B LEU* 4.5 8.5 - - + +
111B VAL* 4.2 13.5 - - + -
116B ILE* 3.6 18.8 - - + -
117B GLY 2.6 21.8 + - - +
118B LYS 3.6 9.0 - - - +
120B THR* 1.3 74.7 - - - +
122B GLU* 1.3 61.6 + - - +
124B LEU* 3.3 3.5 + - - +
125B ILE* 3.2 27.0 + - - +
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Residues in contact with GLU 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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107B VAL* 3.4 27.3 - - - +
118B LYS 3.1 18.6 - - - +
119B LYS* 3.3 13.2 - - + +
121B ALA* 1.3 78.9 - - - +
123B ARG* 1.3 62.1 + - - +
125B ILE* 3.4 6.2 + - - +
126B VAL* 3.0 33.4 + - + +
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Residues in contact with ARG 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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78B THR* 3.9 5.1 + - - -
79B ASN* 2.9 52.4 + - - +
81B VAL* 5.7 0.2 - - - +
119B LYS* 2.7 26.2 + - + +
120B THR* 3.3 26.6 - - - +
122B GLU* 1.3 74.3 - - - +
124B LEU* 1.3 58.2 + - + +
126B VAL* 3.8 4.8 - - - +
127B GLU* 2.8 69.4 + - - +
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Residues in contact with LEU 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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75B LEU* 5.1 4.5 - - + +
78B THR* 4.0 19.1 - - + +
81B VAL* 3.8 28.7 - - + -
85B LEU* 5.5 0.4 - - + -
89B ILE* 3.7 31.4 - - + -
98B PHE* 4.8 5.6 - - + -
102B VAL* 5.3 0.4 - - - -
110B LEU* 4.7 13.9 - - + -
116B ILE* 3.7 28.3 - - + -
120B THR* 2.6 19.6 + - - +
121B ALA 3.3 4.9 + - - +
123B ARG* 1.3 72.0 - - + +
125B ILE* 1.3 56.2 + - - +
127B GLU* 4.7 1.3 - - - -
128B MET* 2.6 52.1 + - + +
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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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101B ALA 4.8 1.3 - - - +
102B VAL* 3.2 53.8 - - - +
105B GLU* 3.7 31.2 - - + +
106B GLU 4.0 4.5 - - - +
107B VAL* 3.6 43.3 - - + +
110B LEU* 4.0 15.2 - - + +
121B ALA 3.2 16.3 + - - +
122B GLU* 3.8 7.0 - - - +
124B LEU* 1.3 76.7 - - - +
126B VAL* 1.3 66.2 + - + +
129B LYS* 3.3 8.2 + - - +
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Residues in contact with VAL 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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105B GLU* 6.0 1.8 - - - +
122B GLU* 3.0 24.2 + - + +
123B ARG* 3.8 4.9 - - - +
125B ILE* 1.3 79.9 - - + +
127B GLU* 1.3 63.7 + - + +
129B LYS* 3.2 26.8 - - + +
130B ASP* 3.6 9.3 - - - +
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Residues in contact with GLU 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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78B THR* 3.2 30.5 - - + -
79B ASN* 3.9 6.8 + - - +
123B ARG* 2.8 59.5 + - - +
124B LEU 3.8 0.9 - - - +
126B VAL* 1.3 77.1 - - + +
128B MET* 1.3 62.0 + - - +
129B LYS 3.5 0.3 + - - -
130B ASP* 3.6 17.4 + - - +
131B ARG* 3.7 32.8 + - - +
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Residues in contact with MET 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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71B LEU* 3.8 4.3 - - + -
74B GLU* 3.8 21.3 - - + +
75B LEU* 3.3 32.5 - - + -
78B THR* 4.5 5.6 - - - -
98B PHE* 3.5 20.9 - - + -
102B VAL* 3.5 19.5 - - + -
124B LEU* 2.6 31.9 + - + +
127B GLU* 1.3 72.7 - - - +
129B LYS* 1.3 63.7 + - - +
131B ARG* 3.2 27.0 + - - +
132B PHE* 3.0 52.7 + - + -
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Residues in contact with LYS 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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102B VAL* 2.6 41.4 + - + +
103B GLU* 4.6 15.4 + - - +
105B GLU* 3.3 32.8 - - - +
125B ILE* 3.3 12.6 + - - +
126B VAL* 3.2 25.8 - - + +
128B MET* 1.3 77.0 - - - +
130B ASP* 1.3 75.1 + - - +
132B PHE* 3.3 18.1 + - - +
133B LYS* 3.8 9.2 + - - +
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Residues in contact with ASP 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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126B VAL* 3.6 14.7 - - - +
127B GLU* 3.6 9.3 + - - +
128B MET 3.3 0.6 - - - -
129B LYS* 1.3 82.3 - - - +
131B ARG* 1.3 55.1 + - + +
133B LYS* 2.8 43.3 + - - +
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Residues in contact with ARG 131 (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 GLU* 3.2 41.9 + - + +
77B LYS* 3.8 18.9 + - - +
78B THR* 3.1 48.1 - - - +
127B GLU* 3.7 29.4 + - - +
128B MET* 3.2 25.8 + - - +
130B ASP* 1.3 78.1 - - + +
132B PHE* 1.3 67.8 + - + +
133B LYS* 3.3 2.4 + - - +
134B GLY* 3.2 19.5 + - - +
135B LEU* 4.9 6.1 - - - +
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Residues in contact with PHE 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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71B LEU* 3.6 15.0 - - + -
74B GLU* 5.5 4.7 - - + -
98B PHE* 3.5 25.6 - + - -
99B VAL* 3.5 43.5 - - + -
102B VAL* 4.0 20.9 - - + -
103B GLU* 4.2 19.5 - - - +
128B MET* 3.0 43.6 + - + +
129B LYS* 3.3 8.2 + - - +
131B ARG* 1.3 78.7 - - + +
133B LYS* 1.3 57.8 + - - +
134B GLY 3.2 2.0 + - - -
135B LEU* 4.3 11.3 + - - +
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Residues in contact with LYS 133 (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* 5.6 1.3 + - - +
129B LYS 3.8 7.9 + - - +
130B ASP* 2.8 32.2 + - - +
131B ARG* 3.3 3.6 + - - +
132B PHE* 1.3 76.6 - - - +
134B GLY* 1.3 86.8 + - - +
135B LEU 3.7 3.7 + - - +
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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
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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