Contacts of the helix formed by residues 138 - 151 (chain B) in PDB entry 1WG8
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 PRO 138 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B ARG 3.4 8.5 - - - +
137B LEU* 1.3 91.9 - - + +
139B LEU* 1.3 67.9 + - - +
140B GLU* 3.3 5.4 - - + +
141B ALA* 3.2 17.0 + - + +
142B LEU* 2.8 20.1 + - - +
166B ARG* 4.2 5.2 - - - +
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Residues in contact with LEU 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 LEU 3.9 0.4 + - - -
138B PRO* 1.3 71.9 - - - +
140B GLU* 1.3 65.9 + - + +
142B LEU* 3.3 3.9 + - - +
143B ALA* 2.8 25.5 + - - +
156B TYR* 4.3 20.9 - - + -
159B ALA* 3.7 18.8 - - + -
160B ARG* 4.3 26.0 - - + +
163B VAL* 4.2 28.9 - - + +
166B ARG* 4.8 1.0 - - - +
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Residues in contact with GLU 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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138B PRO* 3.3 3.4 - - + +
139B LEU* 1.3 88.5 - - + +
141B ALA* 1.3 52.7 + - - +
143B ALA* 3.1 3.0 + - - +
144B ARG* 2.7 46.4 + - - +
147B ARG* 4.8 0.9 + - - -
156B TYR* 2.6 44.8 + - - -
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Residues in contact with ALA 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 LEU* 4.0 21.1 - - + +
138B PRO* 3.2 24.8 + - + +
140B GLU* 1.3 78.1 - - - +
142B LEU* 1.3 58.6 + - - +
144B ARG* 3.1 28.5 + - - +
145B LEU* 2.8 31.4 + - - +
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Residues in contact with LEU 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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133B VAL* 6.3 0.9 - - + -
134B VAL* 4.6 11.2 - - + +
137B LEU* 4.0 19.7 - - + +
138B PRO 2.8 17.0 + - - +
139B LEU 3.5 4.5 - - - +
141B ALA* 1.3 76.3 - - - +
143B ALA* 1.3 62.1 + - - +
145B LEU* 3.5 8.4 - - + +
146B LEU* 3.2 35.9 + - + +
159B ALA* 3.7 17.7 - - + +
162B ILE* 3.7 50.5 - - + -
163B VAL* 4.3 4.3 - - + -
166B ARG* 4.2 13.0 - - - +
201B LEU* 5.8 2.2 - - + -
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Residues in contact with ALA 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 LEU 2.8 17.8 + - - +
140B GLU 3.5 3.8 - - - +
142B LEU* 1.3 74.2 - - - +
144B ARG* 1.3 65.0 + - - +
146B LEU* 3.4 1.1 + - - -
147B ARG* 3.1 27.5 + - - +
155B ALA* 3.6 10.8 - - - +
156B TYR* 3.6 45.8 - - + -
159B ALA* 3.9 12.3 - - + +
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Residues in contact with ARG 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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140B GLU* 2.7 21.8 + - - +
141B ALA* 3.1 36.8 - - - +
143B ALA* 1.3 73.2 - - - +
145B LEU* 1.3 61.8 + - - +
147B ARG* 3.8 23.0 - - - +
148B GLU* 3.2 48.7 + - - +
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Residues in contact with LEU 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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133B VAL* 4.0 9.0 - - + -
137B LEU* 3.6 23.6 - - + -
141B ALA 2.8 15.2 + - - +
142B LEU* 3.5 9.2 - - + +
144B ARG* 1.3 75.5 - - - +
146B LEU* 1.3 71.9 + - + +
149B LEU* 3.1 31.6 + - + +
150B GLY 3.8 0.2 + - - -
200B ALA* 3.5 33.2 - - + +
201B LEU* 4.1 13.5 - - + -
204B TYR* 3.5 41.7 - - + -
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Residues in contact with LEU 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 LEU* 3.2 34.2 + - + +
143B ALA 3.4 0.4 + - - +
145B LEU* 1.3 86.1 - - + +
147B ARG* 1.3 57.9 + - - +
150B GLY* 3.0 21.3 + - - -
151B GLU 3.2 6.8 + - - -
152B GLU* 3.4 11.9 + - + +
155B ALA* 3.6 37.0 - - + +
158B ILE* 3.9 23.3 - - + -
159B ALA 4.1 2.9 - - - +
162B ILE* 4.6 0.4 - - + -
197B THR* 3.6 42.0 - - + +
200B ALA* 4.2 9.0 - - + -
201B LEU* 5.3 2.7 - - + -
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Residues in contact with ARG 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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140B GLU* 4.8 1.0 + - - -
143B ALA* 3.1 13.0 + - - +
144B ARG* 3.8 37.0 - - - +
145B LEU 3.2 0.2 - - - -
146B LEU* 1.3 77.1 - - - +
148B GLU* 1.3 73.9 + - - +
151B GLU* 2.9 30.9 + - - +
152B GLU 4.4 5.6 - - - +
155B ALA* 3.9 12.7 - - + +
156B TYR* 3.3 41.3 + - - -
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Residues in contact with GLU 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 ARG* 3.2 39.5 + - - +
147B ARG* 1.3 97.0 + - + +
149B LEU* 1.3 69.8 + - + +
151B GLU* 4.6 2.9 - - - +
237B LEU* 3.2 21.7 - - - +
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Residues in contact with LEU 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 LEU* 3.1 20.2 + - + +
148B GLU* 1.3 93.2 - - + +
150B GLY* 1.3 60.6 + - - +
151B GLU* 3.6 0.6 - - - +
199B GLN* 3.6 14.9 - - - +
200B ALA* 3.9 16.3 - - - +
203B ILE* 3.6 26.7 - - + +
204B TYR* 4.0 42.4 - - + +
209B LEU* 4.7 9.4 - - + -
237B LEU* 3.6 20.3 - - + +
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Residues in contact with GLY 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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146B LEU 3.0 12.6 + - - -
149B LEU* 1.3 79.1 - - - +
151B GLU* 1.3 72.1 + - - +
152B GLU* 3.1 4.2 + - - -
196B LYS* 3.0 45.0 - - - +
199B GLN* 4.5 7.1 - - - +
200B ALA* 3.6 6.3 - - - +
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Residues in contact with GLU 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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147B ARG* 2.9 21.5 + - - +
148B GLU 4.9 7.2 - - - +
149B LEU 5.2 1.8 - - - +
150B GLY* 1.3 77.5 - - - +
152B GLU* 1.3 55.0 + - - +
153B PRO* 3.2 8.3 - - - +
196B LYS* 2.5 33.5 + - - +
236B SER* 4.2 15.9 + - - -
237B LEU* 4.1 12.4 - - + +
240B ARG* 3.2 32.0 + - - -
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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