Contacts of the helix formed by residues 118 - 129 (chain B) in PDB entry 2P1Q
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 THR 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B TYR* 5.9 3.1 - - + -
94B TYR* 4.8 3.8 - - + +
116B VAL* 4.6 15.3 - - + +
117B VAL* 1.3 78.3 - - - +
119B ASP* 1.3 65.2 + - - +
120B ASP* 3.5 11.5 + - - +
121B CYS* 3.1 30.3 + - - +
122B LEU* 3.1 22.7 + - - +
142B GLY 3.4 13.5 - - - +
143B PHE* 3.9 4.7 - - - -
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Residues in contact with ASP 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 THR* 1.3 74.5 - - - +
120B ASP* 1.3 58.9 + - - +
122B LEU* 3.1 2.5 + - - +
123B GLU* 2.8 41.2 + - + +
142B GLY 4.3 1.8 + - - -
143B PHE* 3.6 4.1 - - - +
144B SER* 2.6 48.3 + - - +
146B ASP* 3.9 7.0 - - + +
147B GLY* 3.1 28.5 + - - +
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Residues in contact with ASP 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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94B TYR* 4.2 18.6 - - + -
118B THR* 3.2 10.0 + - - +
119B ASP* 1.3 79.6 - - - +
121B CYS* 1.3 61.7 + - - +
123B GLU* 3.9 14.1 - - - +
124B LEU* 3.0 25.3 + - - +
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Residues in contact with CYS 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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93B VAL* 3.6 23.1 - - + -
94B TYR* 3.7 32.1 - - - -
97B ILE* 3.9 12.8 - - + +
116B VAL 4.8 0.7 - - - -
117B VAL* 4.0 11.7 - - + -
118B THR* 3.1 35.5 + - - +
120B ASP* 1.3 77.7 - - - +
122B LEU* 1.3 59.0 + - - +
124B LEU* 3.3 4.3 + - - +
125B ILE* 3.0 35.0 + - + +
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Residues in contact with LEU 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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117B VAL* 4.2 13.9 - - + -
118B THR 3.1 7.1 + - - +
119B ASP 3.1 7.6 + - - +
121B CYS* 1.3 79.7 - - - +
123B GLU* 1.3 64.3 + - - +
125B ILE* 3.3 20.5 + - + +
126B ALA* 3.1 20.0 + - - +
135B LEU* 4.0 27.1 - - + -
137B LEU* 4.4 3.4 - - + -
143B PHE* 3.7 38.8 - - + -
147B GLY* 3.7 37.0 - - - +
148B LEU* 4.1 7.2 - - + +
150B ALA* 4.8 0.4 - - - -
151B ILE* 3.6 15.0 - - + +
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Residues in contact with GLU 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 ASP* 2.8 23.2 + - + +
120B ASP* 3.9 15.4 - - - +
122B LEU* 1.3 77.0 - - + +
124B LEU* 1.3 61.4 + - - +
126B ALA* 3.4 3.6 + - - +
127B LYS* 3.1 28.0 + - + +
146B ASP 5.0 3.6 - - - +
147B GLY* 5.1 2.2 - - - -
150B ALA* 3.8 27.5 - - + +
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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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94B TYR* 4.1 20.2 - - + +
97B ILE* 3.7 15.9 - - + -
98B GLU* 3.7 33.2 - - + +
101B SER* 3.9 11.9 - - - +
120B ASP 3.0 18.1 + - - +
121B CYS* 3.7 5.2 - - - +
123B GLU* 1.3 73.2 - - - +
125B ILE* 1.3 61.2 + - - +
127B LYS* 3.9 21.5 - - + +
128B SER* 2.6 58.8 + - - +
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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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97B ILE* 3.9 21.3 - - + -
110B ILE* 3.8 26.0 - - + -
112B LEU* 6.0 1.8 - - + -
117B VAL* 5.7 2.5 - - + -
121B CYS* 3.0 22.1 + - + +
122B LEU* 3.5 26.0 - - + +
123B GLU 3.3 0.2 - - - -
124B LEU* 1.3 73.8 - - - +
126B ALA* 1.3 66.0 + - - +
129B PHE* 3.1 41.0 + - + +
132B PHE* 3.7 37.1 - - + +
135B LEU* 4.5 9.9 - - + -
151B ILE* 4.0 8.5 - - + -
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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 LEU 3.1 15.9 + - - +
123B GLU* 3.7 6.7 - - - +
125B ILE* 1.3 78.4 - - - +
127B LYS* 1.3 62.0 + - + +
129B PHE 4.1 9.5 + - - +
130B LYS* 5.1 3.3 - - - +
150B ALA* 3.7 28.5 - - + +
151B ILE* 4.4 1.3 - - + -
154B THR* 3.4 26.5 - - + +
155B CYS* 3.8 20.9 - - - -
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Residues in contact with LYS 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 GLU* 3.1 17.9 + - + +
124B LEU* 3.6 25.1 - - + +
126B ALA* 1.3 81.9 - - + +
128B SER* 1.3 63.5 + - - +
130B LYS* 2.8 26.2 + - - +
154B THR* 4.7 6.1 - - + -
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Residues in contact with SER 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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101B SER* 3.4 32.8 + - - +
105B THR* 4.1 12.0 - - - +
124B LEU* 2.6 42.0 + - - +
125B ILE 3.3 0.2 + - - -
127B LYS* 1.3 83.6 + - - +
129B PHE* 1.3 73.5 + - - +
130B LYS* 3.8 11.8 + - - +
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Residues in contact with PHE 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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97B ILE* 4.5 8.1 - - + -
100B MET* 3.6 20.6 - - + -
101B SER* 3.7 27.8 - - - -
104B TYR 3.2 30.7 - - - -
105B THR* 4.1 5.2 - - - -
107B LEU* 3.6 46.2 - - + +
110B ILE* 4.3 3.6 - - + -
125B ILE* 3.1 54.8 + - + +
126B ALA 4.1 5.3 + - - +
127B LYS 3.7 1.0 - - - -
128B SER* 1.3 83.4 - - - +
130B LYS* 1.3 67.3 + - - +
131B ASN 3.2 2.2 - - - -
132B PHE* 3.0 24.4 + + + +
155B CYS* 5.4 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