Contacts of the helix formed by residues 120 - 135 (chain B) in PDB entry 4P9U
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 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116B ALA 3.4 9.0 + - - +
119B LEU* 1.3 87.3 - - - +
121B LYS* 1.3 57.8 + - - +
122B GLU 3.3 3.1 - - - -
123B SER* 3.9 21.1 + - - +
124B ALA* 2.9 29.1 + - - +
195B HIS* 3.5 41.9 + - + +
197B GLY* 5.3 3.2 - - - +
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Residues in contact with LYS 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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116B ALA 3.7 3.3 + - - -
117B PHE 3.5 20.6 + - - +
118B LYS 4.9 3.8 - - - +
119B LEU 3.6 4.6 + - - -
120B ASN* 1.3 74.3 - - - +
122B GLU* 1.3 69.8 + - + +
125B GLU* 2.7 66.4 + - - +
240B CYS* 3.4 38.3 - - - +
241B GLN* 3.9 14.9 - - - +
243B GLY* 5.7 3.6 - - - +
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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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120B ASN 3.3 0.4 - - - -
121B LYS* 1.3 85.2 + - + +
123B SER* 1.3 62.5 + - - +
125B GLU* 3.3 26.2 - - - +
126B ARG* 2.9 46.7 + - - +
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ASN* 3.3 16.4 + - - +
122B GLU* 1.3 78.7 - - - +
124B ALA* 1.3 57.2 + - - +
126B ARG* 3.2 21.9 + - - +
127B ILE* 2.9 35.2 + - - +
195B HIS* 3.4 31.1 - - - -
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Residues in contact with ALA 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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116B ALA* 4.0 13.9 - - + +
117B PHE* 4.1 14.4 - - + -
120B ASN* 2.9 18.9 + - - +
121B LYS 3.5 4.3 - - - +
123B SER* 1.3 74.5 - - - +
125B GLU* 1.3 66.2 + - - +
126B ARG 3.0 1.3 - - - -
127B ILE* 3.1 13.7 - - - +
128B MET* 2.9 28.0 + - - +
192B LEU* 3.8 18.8 - - + -
195B HIS* 4.7 3.3 - - + -
240B CYS* 4.1 1.1 - - - -
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Residues in contact with GLU 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 LYS* 2.7 55.2 + - - +
122B GLU* 3.3 26.6 - - - +
124B ALA* 1.3 75.6 - - - +
126B ARG* 1.3 56.1 + - - +
128B MET* 3.8 2.6 - - - +
129B ILE* 2.9 42.3 + - + +
237B LEU* 3.7 22.7 - - + -
240B CYS* 4.1 7.9 - - - -
241B GLN* 3.2 27.8 + - - +
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Residues in contact with ARG 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 GLU* 2.9 34.0 + - - +
123B SER* 3.2 40.0 + - - +
124B ALA 3.0 0.2 - - - -
125B GLU* 1.3 79.1 - - - +
127B ILE* 1.3 66.4 + - + +
129B ILE* 3.4 6.9 + - - +
130B ASN* 3.0 28.7 + - + +
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Residues in contact with ILE 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 SER* 2.9 19.7 + - - +
124B ALA* 3.1 18.6 - - - +
126B ARG* 1.3 84.4 - - + +
128B MET* 1.3 57.4 + - + +
130B ASN* 3.4 8.5 - - - +
131B VAL* 2.9 35.7 + - + +
187B MET* 5.7 1.2 - - + +
188B LEU* 5.0 2.5 - - - +
191B ARG* 3.6 59.5 - - + +
192B LEU* 3.8 19.5 - - + +
195B HIS* 4.2 17.9 - - + +
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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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117B PHE* 4.0 29.6 - - - -
124B ALA 2.9 23.7 + - - +
125B GLU* 3.8 5.4 - - - +
127B ILE* 1.3 74.5 - - - +
129B ILE* 1.3 60.3 + - - +
131B VAL* 3.1 6.9 + - - +
132B ILE* 2.9 36.9 + - + +
188B LEU* 4.5 11.7 - - + -
192B LEU* 4.0 20.9 - - + -
233B TYR* 3.2 29.8 - - - +
236B LEU* 3.4 17.0 - - + -
237B LEU* 3.3 30.1 - - + +
240B CYS* 4.8 1.3 - - - -
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Residues in contact with ILE 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 GLU* 2.9 29.2 + - + +
126B ARG* 3.8 6.1 - - - +
128B MET* 1.3 74.7 - - - +
130B ASN* 1.3 66.0 + - - +
132B ILE* 3.2 8.5 + - - +
133B GLU* 3.0 44.0 + - + +
237B LEU* 3.7 19.7 - - + -
241B GLN* 4.4 17.5 - - - +
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Residues in contact with ASN 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 ARG* 3.0 18.4 + - + +
127B ILE* 3.4 10.1 - - - +
129B ILE* 1.3 79.0 - - - +
131B VAL* 1.3 58.7 + - - +
133B GLU* 4.0 7.6 - - - +
134B SER* 2.8 45.2 + - - -
184B TYR* 4.5 3.5 - - - -
187B MET* 4.2 18.6 - - - +
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Residues in contact with VAL 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 ILE* 2.9 20.7 + - + +
128B MET 3.1 6.9 + - - +
130B ASN* 1.3 78.0 - - - +
132B ILE* 1.3 58.6 + - - +
134B SER* 3.3 2.4 + - - -
135B CYS* 2.9 28.8 + - - +
184B TYR* 3.8 37.9 - - + +
187B MET* 4.5 17.7 - - + -
188B LEU* 3.7 39.9 - - + +
191B ARG* 6.0 0.4 - - - -
233B TYR* 4.2 17.9 - - + -
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Residues in contact with ILE 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 MET* 2.9 27.1 + - + +
129B ILE* 3.2 4.7 + - - +
131B VAL* 1.3 75.0 - - + +
133B GLU* 1.3 59.0 + - - +
135B CYS* 3.1 17.3 + - - +
136B GLU* 2.9 20.3 - - - +
230B MET* 4.8 4.2 - - + +
233B TYR* 3.7 46.4 - - + +
234B ARG* 3.8 37.2 - - + +
237B LEU* 3.9 29.4 - - + -
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Residues in contact with GLU 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 ILE* 3.0 37.0 + - - +
130B ASN* 4.0 7.4 - - - +
132B ILE* 1.3 74.2 - - + +
134B SER* 1.3 65.2 + - - +
135B CYS 3.0 4.9 - - - -
136B GLU* 3.2 29.3 + - + +
147B PHE* 4.3 13.6 - - + -
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Residues in contact with SER 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 ASN* 2.8 31.8 + - - -
131B VAL 3.6 2.0 - - - -
133B GLU* 1.3 75.0 - - - +
135B CYS* 1.3 57.3 + - - +
136B GLU 3.0 9.8 + - - -
137B ALA* 4.0 4.7 + - - +
144B TRP* 3.7 23.0 - - - -
147B PHE* 5.0 8.1 - - - -
148B ILE* 4.6 9.6 - - - +
184B TYR* 3.4 41.0 + - - -
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Residues in contact with CYS 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 VAL* 2.9 16.6 + - - +
132B ILE* 3.3 13.5 - - - +
133B GLU 3.0 1.2 - - - -
134B SER* 1.3 75.7 - - - +
136B GLU* 1.3 64.7 + - - +
137B ALA* 3.1 11.0 + - - +
138B LEU* 3.9 8.7 - - - +
181B PHE* 3.7 33.7 - - + -
184B TYR* 3.8 26.9 - - - -
230B MET* 3.4 24.3 - - + +
233B TYR* 4.3 13.7 - - - -
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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