Contacts of the helix formed by residues 128 - 143 (chain B) in PDB entry 3Q02
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 GLU 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B ASP* 3.2 26.0 + - - +
126B PHE 3.1 1.5 - - - -
127B SER* 1.3 82.5 + - - +
129B VAL* 1.3 65.6 + - - +
130B GLU 3.5 1.8 - - - -
131B ARG* 3.3 41.2 + - + +
132B ALA* 2.9 18.5 + - - +
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Residues in contact with VAL 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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126B PHE* 3.3 20.2 - - + +
127B SER 3.5 1.9 + - - +
128B GLU* 1.3 72.1 - - - +
130B GLU* 1.3 70.7 + - + +
132B ALA* 3.2 5.0 + - - +
133B ARG* 3.0 26.7 + - - +
155B GLY 6.3 0.2 - - - +
157B VAL* 3.4 32.6 - - + +
158B ASP* 3.6 4.3 - - + +
159B GLN* 3.4 37.0 - - + +
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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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128B GLU 3.5 0.2 - - - -
129B VAL* 1.3 86.2 - - + +
131B ARG* 1.3 66.6 + - - +
133B ARG* 3.3 34.8 + - - +
134B PHE* 3.0 45.1 + - + -
154B LYS* 3.2 31.8 + - - +
155B GLY 5.4 2.6 + - - -
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Residues in contact with ARG 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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125B ASP* 4.4 18.1 + - - +
128B GLU* 3.3 42.6 + - + +
130B GLU* 1.3 77.8 - - - +
132B ALA* 1.3 57.0 + - - +
134B PHE* 3.3 10.4 + - + +
135B ILE* 3.0 53.0 + - + +
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Residues in contact with ALA 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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124B VAL* 4.8 8.7 - - + +
125B ASP 3.5 25.1 + - - +
126B PHE* 3.9 27.8 - - + -
128B GLU 2.9 11.1 + - - +
129B VAL 3.6 4.3 - - - +
131B ARG* 1.3 75.0 - - - +
133B ARG* 1.3 65.7 + - - +
135B ILE* 3.4 8.8 + - - +
136B ILE* 3.2 30.1 + - - +
157B VAL* 5.7 0.2 - - + -
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Residues in contact with ARG 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 VAL 3.0 16.1 + - - +
130B GLU* 3.3 35.7 + - - +
132B ALA* 1.3 76.9 - - - +
134B PHE* 1.3 80.2 + - + +
136B ILE* 3.5 2.4 + - - +
137B ASN* 3.1 38.7 + - - +
150B ASN* 2.7 32.3 + - - +
152B LEU* 3.5 22.2 + - + +
153B GLY* 3.3 24.4 - - - +
154B LYS* 3.5 31.0 - - - +
155B GLY 5.0 1.3 - - - +
157B VAL* 4.4 15.0 - - + +
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Residues in contact with PHE 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 36.9 + - + +
131B ARG* 3.7 6.7 - - - +
132B ALA 3.2 0.2 - - - -
133B ARG* 1.3 105.4 - - - +
135B ILE* 1.3 61.2 + - + +
137B ASN* 4.5 8.1 - - + +
138B ASP* 2.8 36.9 + - - +
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Residues in contact with ILE 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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98B PHE* 4.9 5.8 - - + -
124B VAL* 4.4 26.0 - - + -
125B ASP 6.2 0.4 - - - +
131B ARG* 3.0 44.0 + - + +
132B ALA* 3.4 8.3 + - - +
134B PHE* 1.3 76.2 - - + +
136B ILE* 1.3 57.2 + - - +
138B ASP* 3.9 5.1 - - - +
139B TRP* 3.1 27.4 + - + +
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Residues in contact with ILE 136 (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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98B PHE* 3.6 52.9 - - + -
124B VAL* 4.9 3.4 - - + -
126B PHE* 3.8 26.5 - - + -
132B ALA 3.2 17.1 + - - +
133B ARG 3.8 3.4 - - - +
134B PHE 3.1 0.6 - - - -
135B ILE* 1.3 77.8 - - + +
137B ASN* 1.3 64.2 + - - +
139B TRP* 3.3 3.5 + - - +
140B VAL* 3.0 31.3 + - + +
151B LEU* 5.4 0.9 - - + -
152B LEU* 3.6 36.8 - - + -
164B VAL* 4.6 3.8 - - + -
166B VAL* 4.5 11.7 - - + -
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Residues in contact with ASN 137 (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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133B ARG* 3.1 32.6 + - - +
134B PHE* 4.0 9.4 - - + +
136B ILE* 1.3 74.6 - - - +
138B ASP* 1.3 56.2 + - - +
140B VAL* 3.2 4.5 + - - +
141B LYS* 2.8 38.0 + - - +
148B ILE 4.7 0.7 - - - +
150B ASN* 3.7 27.0 + - - +
151B LEU* 3.0 17.1 + - - +
152B LEU* 2.8 39.7 + - - +
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Residues in contact with ASP 138 (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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134B PHE* 2.8 23.9 + - - +
135B ILE* 3.9 6.5 - - - +
137B ASN* 1.3 72.9 - - - +
139B TRP* 1.3 57.3 + - - +
141B LYS* 3.3 5.6 + - - +
142B THR* 2.8 51.8 + - - +
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Residues in contact with TRP 139 (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 THR* 3.5 19.1 + - - -
95B ASP 4.5 3.6 + - - -
96B ALA* 3.8 14.1 - - + +
98B PHE* 4.1 21.8 - + + -
122B LYS* 3.3 43.7 - - + -
135B ILE* 3.1 17.9 + - + +
136B ILE 3.6 4.0 - - - +
137B ASN 3.2 0.2 - - - -
138B ASP* 1.3 80.2 - - - +
140B VAL* 1.3 72.2 + - + +
142B THR* 4.2 2.5 - - - -
143B HIS* 2.9 70.1 + + - +
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Residues in contact with VAL 140 (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 THR* 4.2 9.4 - - + -
136B ILE* 3.0 24.3 + - + +
137B ASN 3.2 4.0 + - - +
139B TRP* 1.3 84.8 - - + +
141B LYS* 1.3 64.3 + - - +
143B HIS 3.1 11.3 + - - -
144B THR* 3.0 16.8 + - - +
148B ILE* 3.7 16.6 - - + +
151B LEU* 3.8 35.0 - - + -
166B VAL* 4.0 27.6 - - + -
168B ALA* 3.8 18.6 - - + -
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Residues in contact with LYS 141 (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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137B ASN 2.8 21.2 + - - +
138B ASP* 3.9 6.3 - - - +
140B VAL* 1.3 74.4 - - - +
142B THR* 1.3 63.1 + - + +
144B THR* 3.3 5.5 + - - -
146B GLY* 2.8 56.9 + - - -
148B ILE 3.1 19.6 + - - +
149B SER* 3.8 25.1 - - - -
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Residues in contact with THR 142 (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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138B ASP* 2.8 45.0 + - - +
139B TRP* 3.6 1.9 + - - -
141B LYS* 1.3 76.4 - - + +
143B HIS* 1.3 80.0 + - - +
144B THR 3.3 1.4 + - - -
145B LYS* 3.9 8.4 + - - -
146B GLY* 4.8 1.6 - - - +
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Residues in contact with HIS 143 (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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92B SER* 4.5 1.7 + - - -
93B THR 3.4 21.7 + - - +
94B THR* 3.6 20.2 - - - +
139B TRP* 2.9 78.4 + + - +
140B VAL 3.1 0.6 + - - +
142B THR* 1.3 89.5 + - - +
144B THR* 1.3 62.1 + - - +
145B LYS 3.7 0.9 - - - -
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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