Contacts of the helix formed by residues 112 - 135 (chain B) in PDB entry 4PKN
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 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B GLY 3.8 1.4 + - - -
111B MET* 1.3 70.2 - - - +
113B PRO* 1.3 75.1 - - - +
114B MET* 3.6 14.1 + - - +
115B ASP* 3.1 44.4 + - + +
116B LEU* 3.2 13.8 + - - +
118B ARG* 4.9 2.6 - - - +
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Residues in contact with PRO 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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13B ARG* 5.8 2.7 - - - +
107B VAL* 4.1 25.8 - - + -
111B MET 3.3 8.5 - - - +
112B ASN* 1.3 93.9 - - - +
114B MET* 1.3 56.8 + - - +
116B LEU* 2.7 32.3 + - + +
117B LYS* 3.0 12.1 + - - +
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Residues in contact with MET 114 (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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112B ASN* 3.4 12.4 + - - +
113B PRO* 1.3 79.7 - - - +
115B ASP* 1.3 58.3 + - - +
117B LYS* 3.7 31.1 + - + +
118B ARG* 3.1 59.9 + - + +
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Residues in contact with ASP 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASN* 3.1 35.7 + - + +
113B PRO 3.0 0.8 - - - -
114B MET* 1.3 77.2 - - - +
116B LEU* 1.3 60.2 + - - +
118B ARG* 3.2 26.5 + - - +
119B GLY* 3.0 24.3 + - - -
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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
----------------------------------------------------------
103B GLY* 4.1 7.0 - - - +
106B ALA* 4.0 26.2 - - + -
107B VAL* 3.7 31.2 - - + +
111B MET* 4.4 23.1 - - + -
112B ASN 3.2 9.1 + - - +
113B PRO* 2.7 18.4 + - + +
115B ASP* 1.3 75.5 - - + +
117B LYS* 1.3 63.0 + - - +
119B GLY* 3.2 2.5 + - - -
120B ILE* 3.0 34.5 + - + +
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Residues in contact with LYS 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 PRO 3.0 10.4 + - - +
114B MET* 3.9 36.6 - - + +
115B ASP 3.3 0.2 - - - -
116B LEU* 1.3 77.4 - - - +
118B ARG* 1.3 58.3 + - + +
120B ILE* 3.3 10.1 + - + +
121B ASP* 2.4 74.0 + - - +
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASN* 4.9 2.2 - - - +
114B MET* 3.1 58.7 + - + +
115B ASP* 3.2 27.9 + - - +
116B LEU 3.2 0.2 - - - -
117B LYS* 1.3 79.5 - - + +
119B GLY* 1.3 62.8 + - - +
121B ASP* 3.4 6.8 + - - +
122B LYS* 3.0 25.2 + - - +
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Residues in contact with GLY 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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115B ASP 3.0 14.6 + - - -
116B LEU* 3.2 2.9 + - - -
118B ARG* 1.3 75.3 - - - +
120B ILE* 1.3 64.4 + - - +
122B LYS* 3.2 8.5 + - - +
123B ALA* 3.0 23.4 + - - +
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Residues in contact with ILE 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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99B ILE* 3.7 38.8 - - + +
103B GLY* 5.9 5.6 - - - -
116B LEU* 3.0 26.0 + - + +
117B LYS* 3.5 10.1 - - - +
119B GLY* 1.3 74.8 - - - +
121B ASP* 1.3 70.4 + - - +
123B ALA* 3.0 8.8 + - - +
124B VAL* 2.9 33.1 + - + +
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Residues in contact with ASP 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 LYS* 2.4 56.5 + - - +
118B ARG* 3.8 6.5 - - - +
120B ILE* 1.3 83.5 - - - +
122B LYS* 1.3 54.0 + - - +
124B VAL* 3.4 6.7 + - - +
125B THR* 2.6 40.0 + - - +
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Residues in contact with LYS 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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118B ARG 3.0 18.1 + - - +
119B GLY* 3.5 7.9 - - - +
120B ILE 3.1 0.2 - - - -
121B ASP* 1.3 76.4 - - - +
123B ALA* 1.3 64.2 + - - +
125B THR* 3.2 7.0 + - - -
126B ALA* 3.0 25.4 + - + +
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Residues in contact with ALA 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 GLY 3.0 13.3 + - - +
120B ILE* 3.5 9.9 - - - +
122B LYS* 1.3 78.0 - - - +
124B VAL* 1.3 58.1 + - + +
126B ALA* 3.4 6.1 + - - +
127B ALA* 2.9 29.0 + - - +
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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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99B ILE* 5.7 7.2 - - + -
120B ILE* 2.9 28.9 + - + +
121B ASP* 3.8 7.9 - - - +
123B ALA* 1.3 75.6 - - + +
125B THR* 1.3 68.9 + - - +
127B ALA* 3.0 7.6 + - + +
128B VAL* 2.9 27.6 + - + +
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Residues in contact with THR 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 ASP* 2.6 25.1 + - - +
122B LYS* 3.6 7.2 - - - -
124B VAL* 1.3 78.2 - - - +
126B ALA* 1.3 58.6 + - - +
128B VAL* 3.0 28.4 - - + +
129B GLU* 3.8 8.3 + - + +
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Residues in contact with ALA 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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122B LYS* 3.0 16.9 + - + +
123B ALA* 3.8 5.8 - - - +
125B THR* 1.3 75.2 - - - +
127B ALA* 1.3 65.9 + - - +
129B GLU* 3.0 18.9 + - - +
130B GLU* 3.0 11.7 + - - +
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Residues in contact with ALA 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 ALA 2.9 19.0 + - - +
124B VAL* 3.0 8.9 + - + +
126B ALA* 1.3 77.7 - - - +
128B VAL* 1.3 57.6 + - - +
130B GLU* 3.2 10.5 + - - +
131B LEU* 2.9 34.2 + - + +
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B VAL* 2.9 14.4 + - + +
125B THR* 3.0 25.8 - - + +
126B ALA 3.2 0.2 - - - -
127B ALA* 1.3 78.2 - - - +
129B GLU* 1.3 76.3 + - - +
131B LEU* 3.3 12.9 + - + +
132B LYS* 2.9 49.2 + - + +
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Residues in contact with GLU 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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125B THR* 3.8 12.8 - - + +
126B ALA* 3.0 10.4 + - - +
128B VAL* 1.3 96.2 - - - +
130B GLU* 1.3 65.8 + - - +
132B LYS* 3.1 29.3 + - - +
133B ALA* 2.9 23.6 + - - +
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Residues in contact with GLU 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 ALA 3.0 12.2 + - - +
127B ALA* 3.2 13.4 + - - +
129B GLU* 1.3 76.9 - - - +
131B LEU* 1.3 56.4 + - + +
133B ALA* 3.3 12.1 + - - +
134B LEU* 3.0 51.3 + - + +
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Residues in contact with LEU 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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127B ALA* 2.9 17.2 + - + +
128B VAL* 3.5 15.5 - - + +
130B GLU* 1.3 74.4 - - + +
132B LYS* 1.3 66.2 + - + +
133B ALA 3.0 1.6 - - - -
134B LEU* 3.0 16.0 + - + +
135B SER* 2.9 24.1 + - - -
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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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128B VAL* 2.9 33.6 + - + +
129B GLU* 3.1 38.3 + - - +
131B LEU* 1.3 74.6 - - + +
133B ALA* 1.3 61.8 + - - +
135B SER* 3.7 17.8 - - - +
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Residues in contact with ALA 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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129B GLU 2.9 12.4 + - - +
130B GLU* 3.3 17.9 - - - +
131B LEU 3.0 0.2 - - - -
132B LYS* 1.3 76.9 - - - +
134B LEU* 1.3 68.3 + - + +
135B SER 3.1 6.6 + - - +
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Residues in contact with LEU 134 (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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130B GLU* 3.0 44.2 + - + +
131B LEU* 3.0 19.9 + - + +
133B ALA* 1.3 76.5 - - + +
135B SER* 1.3 64.7 + - - +
136B VAL* 3.2 16.2 + - - +
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Residues in contact with SER 135 (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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131B LEU 2.9 15.7 + - - -
132B LYS* 3.7 15.7 - - - +
133B ALA 3.1 7.9 - - - +
134B LEU* 1.3 76.7 - - - +
136B VAL* 1.3 67.3 + - - +
137B PRO* 4.5 1.9 - - - +
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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