Contacts of the helix formed by residues 131 - 143 (chain B) in PDB entry 4BL8
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 131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B THR* 3.3 20.5 - - - +
130B TRP* 1.3 78.5 + - - +
132B GLU* 1.3 61.9 + - - +
133B ILE 3.2 0.2 - - - -
134B PRO* 3.2 13.1 - - - +
135B ALA* 4.8 3.5 + - - +
195B PHE* 3.9 21.8 - - + -
250B THR* 4.0 3.1 + - - +
251B PHE* 3.7 14.5 - - + -
252B LYS* 2.9 35.6 + - - +
253B GLY 5.5 0.2 + - - -
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Residues in contact with GLU 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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127B PRO* 3.0 31.2 - - + +
128B LYS* 3.2 19.2 + - - +
129B THR* 3.1 35.5 + - - +
130B TRP 3.0 0.4 - - - -
131B GLU* 1.3 78.7 - - - +
133B ILE* 1.3 57.2 + - - +
134B PRO 3.6 0.7 - - - -
135B ALA* 3.5 9.4 + - - +
136B LEU* 3.0 26.2 + - + +
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Residues in contact with ILE 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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127B PRO* 4.1 9.9 - - + -
129B THR 4.1 8.1 - - - +
130B TRP* 3.0 30.7 + - + +
132B GLU* 1.3 77.2 - - - +
134B PRO* 1.3 71.5 - - + +
136B LEU* 3.5 5.5 - - + -
137B ASP* 2.8 23.8 + - + +
147B ALA* 4.3 18.6 - - + -
148B LEU* 3.8 30.1 - - + -
199B LEU* 4.7 13.2 - - + -
204B HIS* 5.7 2.5 - - + -
225B MET* 3.7 25.8 - - + -
249B PRO* 4.7 10.3 - - + -
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Residues in contact with PRO 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 TRP 3.6 8.3 - - - +
131B GLU* 3.2 18.2 - - - +
133B ILE* 1.3 94.4 - - + +
135B ALA* 1.3 60.7 + - - +
137B ASP* 3.2 9.2 + - - +
138B LYS* 3.4 20.6 + - - +
195B PHE* 4.4 12.6 - - + -
199B LEU* 4.1 15.0 - - + -
202B ASN* 6.0 0.7 - - - +
204B HIS* 3.6 34.4 - - + +
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Residues in contact with ALA 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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131B GLU 4.8 2.0 + - - +
132B GLU* 3.5 12.0 + - - +
133B ILE 3.2 0.4 - - - -
134B PRO* 1.3 79.1 - - - +
136B LEU* 1.3 63.6 + - - +
137B ASP 3.1 1.1 + - - -
138B LYS* 3.2 24.8 + - - +
139B GLU* 3.5 16.7 + - - +
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Residues in contact with LEU 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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123B LEU* 3.7 45.5 - - + -
127B PRO* 3.9 23.3 - - + -
132B GLU* 3.0 18.8 + - + +
133B ILE* 3.1 7.8 + - - +
135B ALA* 1.3 76.0 - - - +
137B ASP* 1.3 59.4 + - - +
138B LYS 3.4 0.2 - - - -
139B GLU* 3.7 23.5 + - + +
140B LEU* 3.4 30.4 + - + +
147B ALA* 4.2 6.3 - - + -
225B MET* 4.2 10.8 - - + -
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Residues in contact with ASP 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 ILE* 2.8 16.6 + - + +
134B PRO 3.5 1.1 - - - +
135B ALA 3.1 0.4 - - - -
136B LEU* 1.3 76.7 - - - +
138B LYS* 1.3 59.0 + - - +
140B LEU* 3.8 1.6 - - - +
141B LYS* 2.9 56.8 + - - +
146B SER* 3.8 5.9 - - - -
147B ALA* 3.0 36.7 + - + +
148B LEU 4.5 0.3 + - - -
204B HIS* 2.7 51.1 + - + +
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Residues in contact with LYS 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 PRO* 3.4 24.8 + - - +
135B ALA* 3.2 14.2 + - - +
137B ASP* 1.3 76.2 - - - +
139B GLU* 1.3 65.2 + - + +
141B LYS* 3.3 7.4 + - - +
142B ALA* 3.2 22.3 + - - +
204B HIS* 4.4 16.8 - - + -
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Residues in contact with GLU 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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135B ALA* 3.7 14.1 - - - +
136B LEU* 3.8 27.6 - - + +
138B LYS* 1.3 79.7 - - + +
140B LEU* 1.3 61.9 + - + +
142B ALA* 3.5 17.1 - - - +
143B LYS* 3.7 17.7 - - - +
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Residues in contact with LEU 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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122B LEU* 4.3 25.6 - - + +
123B LEU* 5.4 2.2 - - + -
136B LEU* 3.4 32.3 + - + +
137B ASP 3.4 3.6 + - - +
138B LYS 3.2 0.2 - - - -
139B GLU* 1.3 80.0 - - + +
141B LYS* 1.3 59.0 + - - +
142B ALA 3.2 0.8 + - - -
143B LYS* 3.5 23.8 + - - +
144B GLY 3.3 3.3 + - - -
145B LYS* 2.7 57.9 + - + +
146B SER 3.8 6.3 - - - +
147B ALA* 3.6 25.8 - - + -
224B ALA* 3.8 16.6 - - + -
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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 ASP* 2.9 40.4 + - - +
138B LYS* 3.3 7.8 + - - +
140B LEU* 1.3 75.7 - - - +
142B ALA* 1.3 64.0 + - - +
143B LYS 3.3 0.2 - - - -
144B GLY* 3.1 13.6 + - - +
145B LYS 3.2 18.8 - - - +
146B SER* 3.8 18.8 - - - +
203B LYS 3.2 25.1 + - - -
204B HIS* 4.3 5.1 + - - +
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Residues in contact with ALA 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 LYS 3.2 11.1 + - - +
139B GLU* 3.5 15.0 - - - +
140B LEU 3.2 0.4 - - - -
141B LYS* 1.3 78.8 - - - +
143B LYS* 1.3 57.3 + - + +
144B GLY 3.4 2.3 + - - -
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Residues in contact with LYS 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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35A LYS* 4.8 13.7 - - - +
122B LEU* 4.9 12.3 + - + +
139B GLU* 3.7 20.6 - - - +
140B LEU* 3.7 27.3 - - + +
141B LYS 3.3 0.2 - - - -
142B ALA* 1.3 74.6 - - + +
144B GLY* 1.3 55.7 + - - +
145B LYS* 3.0 28.6 + - + +
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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