Contacts of the helix formed by residues 137 - 155 (chain B) in PDB entry 3RU0
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 137 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LYS 3.5 4.0 + - - +
136B LEU* 1.3 77.3 - - - +
138B GLU* 1.3 59.1 + - - +
139B ASP* 3.7 8.7 + - - +
140B LYS* 3.2 25.2 + - - +
141B LYS* 3.0 25.9 + - - +
254B ARG* 6.3 3.8 - - - -
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU 3.9 0.6 + - - -
137B THR* 1.3 73.3 - - - +
139B ASP* 1.3 57.7 + - - +
141B LYS* 3.1 21.1 + - - +
142B GLU* 2.9 28.8 + - - +
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Residues in contact with ASP 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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137B THR* 3.3 8.2 + - - +
138B GLU* 1.3 78.4 - - - +
140B LYS* 1.3 61.6 + - - +
142B GLU* 3.3 8.6 + - - +
143B GLY* 3.2 17.8 + - - -
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Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 4.4 19.7 - - + +
137B THR* 3.2 24.8 + - - +
139B ASP* 1.3 79.4 - - - +
141B LYS* 1.3 61.3 + - - +
143B GLY* 3.4 4.1 + - - +
144B LEU* 3.2 35.6 + - + +
179B ILE* 3.5 42.2 - - + +
255B ASP* 3.2 29.3 + - - +
256B GLN* 4.2 3.0 - - - +
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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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133B ILE* 4.9 8.5 - - + +
136B LEU* 3.8 29.6 + - + +
137B THR 3.0 21.3 + - - +
138B GLU* 3.1 19.6 + - - +
140B LYS* 1.3 76.7 - - - +
142B GLU* 1.3 56.8 + - - +
144B LEU* 3.4 1.8 + - - -
145B ARG* 3.1 33.3 + - + +
172B PHE* 3.7 30.2 - - + -
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Residues in contact with GLU 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 GLU 2.9 12.3 + - - +
139B ASP* 3.6 11.4 - - - +
140B LYS 3.3 0.2 - - - -
141B LYS* 1.3 72.9 - - - +
143B GLY* 1.3 62.2 + - - +
145B ARG* 3.4 8.3 + - - +
146B GLN* 3.0 35.6 + - + +
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Residues in contact with GLY 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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139B ASP 3.2 13.0 + - - -
140B LYS* 3.4 5.4 + - - -
141B LYS 3.3 0.2 - - - -
142B GLU* 1.3 78.1 - - - +
144B LEU* 1.3 58.3 + - - +
146B GLN* 3.3 9.1 + - - +
147B LEU* 3.0 33.7 + - - +
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Residues in contact with LEU 144 (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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136B LEU* 3.7 29.6 - - + -
140B LYS* 3.2 23.2 + - + +
141B LYS* 3.8 1.6 - - - +
142B GLU 3.3 0.2 - - - -
143B GLY* 1.3 74.2 - - - +
145B ARG* 1.3 60.9 + - - +
147B LEU* 3.6 16.7 - - + +
148B VAL* 2.9 35.4 + - - +
172B PHE* 3.7 26.5 - - + +
175B PHE* 3.9 22.6 - - + +
176B ALA* 4.0 19.3 - - + +
179B ILE* 4.0 23.3 - - + -
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Residues in contact with ARG 145 (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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141B LYS* 3.1 22.3 + - + +
142B GLU* 3.7 9.0 - - - +
143B GLY 3.3 0.2 - - - -
144B LEU* 1.3 76.7 - - - +
146B GLN* 1.3 66.8 + - - +
148B VAL* 3.5 9.7 - - - +
149B MET* 3.2 28.3 + - - +
172B PHE* 4.1 15.5 - - + -
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Residues in contact with GLN 146 (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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142B GLU* 3.0 22.8 + - + +
143B GLY* 3.6 8.5 - - - +
144B LEU 3.2 0.6 - - - -
145B ARG* 1.3 81.2 - - - +
147B LEU* 1.3 57.5 + - + +
149B MET* 3.4 21.6 + - - +
150B THR* 3.0 30.9 + - - -
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Residues in contact with LEU 147 (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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99B PRO* 3.9 17.3 - - + -
101B SER* 3.4 23.1 - - - +
102B VAL* 3.8 16.8 - - + +
143B GLY 3.0 18.5 + - - +
144B LEU* 3.3 23.3 + - + +
146B GLN* 1.3 74.7 - - + +
148B VAL* 1.3 58.7 + - - +
150B THR* 3.2 5.6 + - - -
151B PHE* 2.8 30.7 + - - +
175B PHE* 3.7 27.5 - - + -
179B ILE* 5.2 8.3 - - + -
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Residues in contact with VAL 148 (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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144B LEU 2.9 25.0 + - - +
145B ARG* 3.5 9.4 - - - +
147B LEU* 1.3 75.0 - - - +
149B MET* 1.3 58.8 + - + +
151B PHE* 3.2 4.6 + - - +
152B GLN* 2.9 43.5 + - - +
171B LEU* 3.8 20.8 - - + +
172B PHE* 3.8 35.9 - - + +
175B PHE* 3.9 15.5 - - + -
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Residues in contact with MET 149 (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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145B ARG* 3.2 11.9 + - - +
146B GLN* 3.6 27.6 - - - +
147B LEU 3.3 0.2 - - - -
148B VAL* 1.3 74.0 - - + +
150B THR* 1.3 66.0 + - - +
152B GLN* 3.3 17.6 + - - +
153B HIS* 3.1 23.0 + - - +
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Residues in contact with THR 150 (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 PRO* 4.7 5.2 - - + -
99B PRO* 3.7 32.0 - - + +
102B VAL* 3.9 9.9 - - + -
146B GLN* 3.0 15.3 + - - +
147B LEU* 3.2 12.0 + - - +
149B MET* 1.3 74.3 - - - +
151B PHE* 1.3 58.7 + - - +
153B HIS* 3.4 7.4 + - + +
154B PHE* 2.8 32.0 + - + +
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Residues in contact with PHE 151 (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 VAL* 3.8 24.6 - - + +
105B LEU* 3.8 8.5 - - + -
106B GLY* 3.5 25.8 - - - -
109B VAL* 3.9 24.9 - - + -
147B LEU 2.8 13.2 + - - +
148B VAL 3.4 7.6 - - - +
150B THR* 1.3 77.1 - - - +
152B GLN* 1.3 65.8 + - + +
154B PHE 3.3 0.5 + - - -
155B MET* 3.0 51.4 + - + +
159B ILE* 4.7 4.9 - - + -
165B LEU* 4.6 12.1 - - + -
171B LEU* 3.4 33.0 - - + -
175B PHE* 3.7 21.5 - + + -
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Residues in contact with GLN 152 (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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148B VAL* 2.9 31.4 + - - +
149B MET* 3.3 24.9 + - - +
151B PHE* 1.3 79.0 - - + +
153B HIS* 1.3 62.0 + - - +
155B MET* 3.7 2.5 + - - +
156B ARG* 3.4 21.0 + - - +
159B ILE 4.6 3.2 - - - +
171B LEU* 4.0 15.8 - - + +
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Residues in contact with HIS 153 (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 5.4 0.4 + - - -
93B CYS* 4.1 13.9 - - - +
149B MET 3.1 16.1 + - - +
150B THR* 3.7 7.0 - - + +
152B GLN* 1.3 76.4 - - - +
154B PHE* 1.3 63.7 + - + +
156B ARG* 2.9 68.9 + - - +
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Residues in contact with PHE 154 (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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86B GLU* 4.8 7.0 - - + -
89B CYS* 3.2 55.6 - - + +
90B LEU* 3.8 22.4 - - + -
92B SER* 4.6 0.7 + - - -
93B CYS* 3.7 24.5 - - + -
98B PRO* 3.8 27.8 - - + -
102B VAL* 3.6 34.1 - - + -
103B ARG* 4.3 14.4 - - + -
106B GLY* 5.0 2.0 - - - -
150B THR* 2.8 22.4 + - + +
151B PHE 3.6 2.9 - - - +
153B HIS* 1.3 76.0 - - + +
155B MET* 1.3 89.1 + - + +
156B ARG* 3.5 2.4 + - - -
157B GLU 4.8 0.5 + - - -
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Residues in contact with MET 155 (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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85B ARG 5.0 1.3 - - - +
86B GLU* 5.9 2.2 - - - -
89B CYS* 3.9 19.7 - - - -
106B GLY* 3.9 21.1 - - - +
109B VAL* 4.6 0.9 - - + -
110B PHE* 3.5 33.4 - - + -
151B PHE* 3.0 44.4 + - + +
152B GLN* 4.5 2.0 - - - +
154B PHE* 1.3 102.0 - - + +
156B ARG* 1.3 52.9 + - - +
157B GLU 3.2 2.5 - - - -
158B GLU* 2.7 29.8 + - + +
159B ILE* 2.8 39.0 + - + +
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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