Contacts of the helix formed by residues 117 - 133 (chain B) in PDB entry 2H8R
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 ASP 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116B GLU* 1.4 70.6 - - - +
118B PRO* 1.3 88.9 - - - +
119B TRP* 2.6 18.4 + - - +
120B ARG* 2.7 38.7 + - + +
121B ALA* 3.0 11.3 + - - +
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Residues in contact with PRO 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLU 3.1 8.9 - - - +
117B ASP* 1.3 94.4 - - - +
119B TRP* 1.3 58.4 + - + +
121B ALA* 3.3 5.5 - - + +
122B ALA* 3.0 21.7 + - - +
153B HIS* 4.3 13.6 + - + +
160B MET 6.4 0.2 - - - +
165B ARG* 3.9 26.2 - - - +
169B TYR* 3.7 16.7 + - - +
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Residues in contact with TRP 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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117B ASP* 2.6 17.5 + - - +
118B PRO* 1.3 76.5 - - + +
120B ARG* 1.3 72.7 + - - +
121B ALA 3.0 1.3 - - - -
122B ALA* 3.0 23.4 + - + +
123B LYS* 3.1 51.2 + - + +
153B HIS* 4.6 2.1 + + - -
154B LEU 4.9 5.9 + - - -
155B ASN 5.5 3.5 - - - -
156B LYS* 4.3 4.2 + - - +
157B GLY* 3.6 35.8 - - - +
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Residues in contact with ARG 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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116B GLU* 4.8 17.9 - - + +
117B ASP* 2.7 24.7 + - + +
119B TRP* 1.3 87.1 - - - +
121B ALA* 1.3 61.6 + - - +
123B LYS* 3.3 21.9 - - - +
124B MET* 3.5 24.3 + - + +
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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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113B MET* 4.7 18.4 - - + +
116B GLU* 5.9 3.5 + - + +
117B ASP 3.0 7.1 + - - +
118B PRO* 3.3 11.9 - - + +
120B ARG* 1.3 79.0 - - - +
122B ALA* 1.3 68.7 + - - +
123B LYS 3.1 0.5 + - - -
124B MET* 3.2 10.6 - - - +
125B ILE* 3.1 27.3 + - - +
169B TYR* 3.9 24.7 - - + +
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PRO 3.0 10.6 + - - +
119B TRP* 3.0 20.6 + - + +
121B ALA* 1.3 79.6 - - - +
123B LYS* 1.3 67.8 + - - +
125B ILE* 3.4 3.1 + - - +
126B LYS* 2.9 23.4 + - - +
153B HIS* 4.1 26.7 - - + +
154B LEU* 3.8 24.3 - - + +
169B TYR* 5.1 1.0 + - - -
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Residues in contact with LYS 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 TRP* 3.4 53.5 - - + +
120B ARG* 3.3 11.2 - - - +
122B ALA* 1.3 79.9 - - - +
124B MET* 1.3 55.9 + - - +
125B ILE 2.6 1.4 + - - -
126B LYS* 2.8 7.7 + - - +
127B GLY* 2.5 35.7 + - - -
154B LEU 5.9 0.4 - - - -
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Residues in contact with MET 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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113B MET* 5.2 5.6 - - + -
120B ARG* 3.5 26.9 + - + +
121B ALA* 3.2 14.5 + - - +
123B LYS* 1.3 76.0 - - - +
125B ILE* 1.3 53.2 + - + +
127B GLY* 3.0 4.4 + - - -
128B TYR* 2.6 33.5 + - - +
172B TYR* 3.4 29.6 - - + +
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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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113B MET* 5.0 1.8 - - + -
121B ALA 3.1 15.7 + - - +
122B ALA* 3.9 4.3 - - - +
123B LYS 2.6 4.8 + - - -
124B MET* 1.3 76.9 - - + +
126B LYS* 1.3 57.8 + - - +
127B GLY 2.8 1.6 - - - -
128B TYR* 2.7 7.9 - - - +
129B MET* 2.6 54.6 + - + +
154B LEU* 4.7 7.2 - - + -
168B LEU* 4.0 26.7 - - + -
169B TYR* 3.9 30.7 - - + -
171B TRP* 4.5 13.0 - - + -
172B TYR* 4.0 30.5 - - + -
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Residues in contact with LYS 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 ALA 2.9 15.3 + - - +
123B LYS* 2.8 4.4 + - - +
125B ILE* 1.3 79.1 - - - +
127B GLY* 1.3 58.6 - - - +
129B MET* 3.6 12.3 - - + +
130B GLN* 2.7 54.9 + - + +
154B LEU* 3.9 19.0 + - + +
155B ASN* 3.0 48.5 + - - +
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Residues in contact with GLY 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 LYS 2.5 18.4 + - - -
124B MET* 3.0 7.0 - - - -
126B LYS* 1.3 76.9 - - - +
128B TYR* 1.3 57.2 - - - +
130B GLN* 3.5 4.3 - - - +
131B GLN* 2.9 27.3 + - - +
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Residues in contact with TYR 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 MET 2.6 14.9 + - - +
125B ILE* 2.7 15.0 - - - +
127B GLY* 1.3 68.4 - - - +
129B MET* 1.3 76.6 + - + +
130B GLN 2.8 3.0 + - - -
131B GLN* 2.9 25.1 + - - +
132B HIS* 3.0 47.7 + + + -
134B ILE* 5.7 4.0 - - + -
171B TRP* 5.4 4.5 - + - -
172B TYR* 3.2 30.3 - + + -
175B LYS* 5.2 13.2 - - + -
176B GLN* 3.7 33.2 + - + +
179B ILE* 3.6 19.5 - - + +
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Residues in contact with MET 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ILE* 2.6 34.1 + - + +
126B LYS* 3.6 7.9 - - + +
128B TYR* 1.3 83.8 - - + +
130B GLN* 1.3 61.4 + - + +
132B HIS 3.6 0.6 + - - +
133B ASN 2.7 22.9 + - - -
134B ILE* 3.1 40.7 + - + +
136B GLN* 4.0 23.6 - - + +
139B VAL* 4.4 18.6 - - + -
150B LEU* 6.2 0.4 - - + -
154B LEU* 4.0 23.1 - - + -
168B LEU* 5.9 0.9 - - - -
171B TRP* 4.3 17.3 - - + -
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Residues in contact with GLN 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 LYS* 2.7 38.0 + - + +
127B GLY* 3.5 3.8 - - - +
128B TYR 2.8 0.8 + - - -
129B MET* 1.3 80.5 - - + +
131B GLN* 1.3 70.0 + - - +
133B ASN* 3.3 18.9 - - - +
240B PRO* 5.3 13.1 - - + +
275B GLN* 3.4 6.4 + - - -
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Residues in contact with GLN 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 GLY 2.9 12.6 + - - +
128B TYR* 2.9 19.5 + - - +
130B GLN* 1.3 78.4 - - - +
132B HIS* 1.3 82.0 + - + +
275B GLN* 2.5 63.7 + - + +
276B ARG* 3.5 28.2 + - - +
277B GLY* 5.2 1.4 - - - -
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Residues in contact with HIS 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 TYR* 3.0 54.6 + + + +
131B GLN* 1.3 89.7 + - + +
133B ASN* 1.3 73.0 + - - +
134B ILE* 3.8 18.7 - - + +
179B ILE* 4.4 23.0 - - + +
183B PHE* 5.7 5.2 - + - -
276B ARG* 2.5 66.8 + - + +
289B ASN* 3.1 3.1 + - - -
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Residues in contact with ASN 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 MET 2.7 14.3 + - - -
130B GLN* 3.3 16.7 + - - +
131B GLN 3.3 2.6 - - - -
132B HIS* 1.3 82.7 - - - +
134B ILE* 1.3 61.2 + - - +
135B PRO* 4.2 1.1 - - - +
237B LYS* 3.4 53.6 + - - +
238B TRP 4.1 2.4 + - - -
239B GLY* 4.0 15.9 - - - -
240B PRO* 4.9 1.4 - - - +
272B GLU* 5.4 0.2 - - - -
275B GLN* 4.3 5.9 + - - -
276B ARG* 4.3 7.1 + - - +
289B ASN* 3.0 26.1 + - - +
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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