Contacts of the helix formed by residues 120 - 135 (chain B) in PDB entry 1USK
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 LEU 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B THR 3.5 1.6 - - - +
104B PRO* 3.9 18.2 - - + -
116B ARG* 3.5 35.0 - - - +
118B ALA 5.5 0.2 - - - +
119B GLY* 1.3 75.1 - - - +
121B ASP* 1.3 63.0 + - - +
122B SER* 3.2 18.8 - - - +
123B SER* 3.2 14.2 + - - +
124B GLN 3.1 18.5 + - - -
325B ASP* 3.7 35.4 - - + +
326B LEU 4.7 8.3 - - - +
329B PHE* 4.9 2.0 + - - +
331B PHE* 3.7 10.3 - - - -
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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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102B THR* 2.7 45.3 + - - +
103B ASN* 3.4 7.6 + - - +
104B PRO* 4.2 11.0 - - + +
120B LEU* 1.3 69.9 - - - +
122B SER* 1.3 56.6 + - - +
123B SER 3.0 5.2 - - - -
124B GLN* 2.9 32.6 + - - +
125B GLY* 3.2 22.3 + - - -
126B PRO* 3.8 3.1 - - - +
150B TYR* 3.6 14.9 - - - +
153B GLY 5.8 1.1 - - - -
154B LEU* 3.6 27.0 - - + +
157B SER* 4.0 6.8 + - - -
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PRO* 3.9 22.4 - - - +
108B GLN* 5.9 2.0 - - - -
120B LEU* 3.6 24.1 - - - +
121B ASP* 1.3 76.9 - - - +
123B SER* 1.3 55.3 + - - +
126B PRO* 3.2 22.0 - - - +
157B SER* 5.3 1.6 - - - -
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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 LEU* 3.2 15.6 + - - -
121B ASP 3.0 0.2 - - - -
122B SER* 1.3 80.0 + - - +
124B GLN* 1.3 65.1 + - - +
125B GLY 3.3 1.6 - - - -
126B PRO* 3.5 5.1 - - - +
127B THR* 3.1 30.5 + - - -
329B PHE 4.2 17.1 + - - -
330B ASP* 5.2 4.7 + - - -
331B PHE* 4.7 4.9 + - - -
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Residues in contact with GLN 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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102B THR* 4.6 0.4 + - - -
120B LEU 3.1 11.7 + - - +
121B ASP* 2.9 28.4 + - - +
123B SER* 1.3 75.5 - - - +
125B GLY* 1.3 62.9 + - - +
127B THR* 3.5 5.3 + - - -
128B ALA* 3.2 20.8 + - - +
150B TYR* 4.1 2.2 + - - -
154B LEU* 3.8 10.9 - - + +
198B TYR* 5.2 1.1 - - - +
225B PRO* 4.0 5.4 - - + -
226B GLU* 2.7 40.7 + - - +
247B THR* 2.7 36.3 + - - +
331B PHE* 3.5 33.7 - - + -
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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 ASP 3.2 8.3 + - - -
124B GLN* 1.3 74.1 - - - +
126B PRO* 1.3 71.2 - - - +
128B ALA* 3.0 7.7 + - - +
129B ALA* 3.0 20.3 + - - +
154B LEU* 3.6 13.3 - - - +
157B SER* 3.6 14.6 - - - -
158B VAL* 3.7 17.5 - - - +
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Residues in contact with PRO 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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121B ASP 3.8 0.2 - - - +
122B SER* 3.2 30.1 - - - +
123B SER* 3.5 6.3 - - - +
125B GLY* 1.3 88.1 - - - +
127B THR* 1.3 55.5 + - - +
129B ALA* 3.7 8.7 - - + +
130B LYS* 3.0 29.1 + - - +
157B SER* 3.5 15.5 - - - +
161B GLY* 6.1 1.6 - - - -
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Residues in contact with THR 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* 3.1 23.5 + - - -
124B GLN* 3.6 7.6 - - - -
125B GLY 3.1 0.2 - - - -
126B PRO* 1.3 72.7 - - - +
128B ALA* 1.3 66.7 + - - +
130B LYS* 3.6 7.7 + - - +
131B TYR* 3.2 21.7 + - - +
247B THR* 4.3 10.8 - - + -
331B PHE* 3.5 32.3 + - - +
332B GLY* 5.0 0.4 - - - -
333B VAL* 4.4 11.6 - - + +
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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 GLN 3.2 8.9 + - - +
125B GLY 3.0 8.0 + - - +
127B THR* 1.3 80.6 - - - +
129B ALA* 1.3 62.6 + - - +
131B TYR* 3.1 4.3 + - - +
132B ILE* 2.9 28.9 + - + +
158B VAL* 4.1 5.4 - - + -
198B TYR* 3.8 31.0 - - + +
223B MET* 4.0 21.3 - - + +
247B THR* 4.1 8.2 - - + +
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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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125B GLY 3.0 11.1 + - - +
126B PRO* 3.7 12.3 - - + +
127B THR 3.3 0.2 - - - -
128B ALA* 1.3 77.2 - - - +
130B LYS* 1.3 63.1 + - - +
132B ILE* 3.3 11.1 + - - +
133B LEU* 3.1 32.0 + - + +
157B SER 5.3 0.2 - - - +
158B VAL* 4.3 15.0 - - + +
161B GLY* 4.2 28.5 - - - -
162B LEU* 4.1 4.0 - - + +
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Residues in contact with LYS 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 PRO 3.0 18.2 + - - +
127B THR* 3.8 7.4 - - - +
129B ALA* 1.3 77.4 - - - +
131B TYR* 1.3 60.9 + - - +
133B LEU* 4.2 4.7 - - - +
134B GLU* 3.1 54.0 + - - +
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Residues in contact with TYR 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 THR 3.2 10.5 + - - +
128B ALA 3.1 9.4 + - - +
130B LYS* 1.3 77.9 - - - +
132B ILE* 1.3 65.4 + - - +
134B GLU* 5.2 0.2 - - - -
135B THR* 3.1 51.8 + - + +
136B VAL* 3.3 30.2 + - + -
223B MET* 4.2 9.9 - - + -
245B LEU* 3.9 22.2 - - + +
333B VAL* 3.8 27.6 - - + -
345B ALA* 3.4 37.5 + - + +
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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 ALA 2.9 24.7 + - - +
129B ALA* 3.3 7.4 + - - +
131B TYR* 1.3 78.9 - - - +
133B LEU* 1.3 60.3 + - + +
136B VAL* 4.2 7.2 - - + -
137B LYS 2.9 28.8 + - - -
138B PRO* 3.5 25.2 - - + +
141B ILE* 4.5 4.3 - - + -
158B VAL* 4.0 22.9 - - + -
162B LEU* 3.7 19.7 - - + -
196B PHE* 3.4 42.4 - - + -
198B TYR* 4.5 3.6 - - + -
223B MET* 3.9 14.4 - - - -
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Residues in contact with LEU 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 ALA* 3.1 24.0 + - + +
130B LYS* 4.2 4.7 - - - +
132B ILE* 1.3 78.2 - - + +
134B GLU* 1.3 62.9 + - + +
137B LYS* 3.5 23.2 - - - +
138B PRO* 5.5 0.9 - - + -
141B ILE* 6.1 0.2 - - + -
161B GLY 3.9 14.8 - - - +
162B LEU* 3.7 20.6 - - + -
165B ALA* 3.6 34.8 - - + +
167B ALA* 4.0 17.3 - - + -
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Residues in contact with GLU 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 LYS* 3.1 50.2 + - + +
133B LEU* 1.3 83.0 - - + +
135B THR* 1.3 65.0 + - - +
137B LYS* 3.6 18.5 + - - +
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Residues in contact with THR 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 TYR* 3.1 52.1 + - + +
133B LEU 3.6 0.2 - - - -
134B GLU* 1.3 83.4 + - - +
136B VAL* 1.3 68.2 + - + +
137B LYS* 3.4 7.9 - - - +
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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