Contacts of the helix formed by residues 138 - 145 (chain B) in PDB entry 3OP5
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 LEU 138 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B ASP* 1.3 69.8 - - - +
139B GLN* 1.4 54.4 + - - +
141B ILE* 3.3 8.7 + - + -
142B TYR* 2.8 35.7 + - - +
149B PHE* 3.6 12.7 - - + -
157B LEU* 3.6 34.5 - - + -
180B ALA* 3.1 19.7 + - + +
183B LEU* 2.8 44.3 + - + +
185B LEU* 4.3 11.2 - - + -
193B VAL* 4.0 4.5 - - + -
254B TRP* 5.0 1.3 - - + -
341B LEU* 3.8 38.6 - - + -
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Residues in contact with GLN 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 ASP* 3.1 13.7 + - - +
138B LEU* 1.4 75.3 - - - +
140B LYS* 1.3 54.8 + - + +
142B TYR* 3.4 21.2 + - - +
143B GLU* 2.9 69.4 + - - +
147B LYS* 5.3 4.2 - - - +
180B ALA* 3.3 22.5 + - - +
181B SER* 3.8 24.5 + - - +
227B PHE* 5.9 2.8 - - - -
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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
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136B SER* 3.8 22.0 + - - +
137B ASP* 2.7 39.4 + - - +
138B LEU 3.3 0.2 - - - -
139B GLN* 1.3 74.7 - - + +
141B ILE* 1.4 56.7 + - + +
143B GLU* 3.5 10.9 + - - +
144B ALA* 3.0 28.8 + - - +
365B REB 5.9 4.9 - - - -
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Residues in contact with ILE 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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136B SER* 3.7 20.2 - - - +
137B ASP 3.4 19.5 + - - +
138B LEU* 3.3 13.8 + - + +
140B LYS* 1.4 72.6 - - + +
142B TYR* 1.4 60.0 + - - +
144B ALA* 3.3 8.2 + - - +
145B ASN* 3.0 30.3 + - + +
149B PHE* 4.1 4.3 - - + -
185B LEU* 3.7 29.8 - - + -
341B LEU* 3.8 37.2 - - + -
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Residues in contact with TYR 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 LEU 2.8 21.2 + - - +
139B GLN* 3.4 32.3 - - - +
141B ILE* 1.4 72.6 - - - +
143B GLU* 1.4 58.8 + - - +
145B ASN* 3.1 11.0 + - - +
147B LYS* 3.0 67.6 + - + +
148B ARG 3.6 9.3 + - - -
149B PHE* 3.7 31.6 - + + -
180B ALA* 5.0 0.9 - - + -
253B GLN* 2.7 44.6 + - + -
254B TRP* 3.7 27.6 - + - -
257B GLY* 3.2 10.2 + - - -
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Residues in contact with GLU 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 GLN* 2.9 50.5 + - - +
140B LYS* 3.9 9.4 - - - +
142B TYR* 1.4 74.4 - - + +
144B ALA* 1.3 62.0 + - - +
146B ALA* 3.4 12.8 + - - -
147B LYS* 4.1 21.0 + - + +
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Residues in contact with ALA 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 LYS 3.0 19.3 + - - +
141B ILE* 3.5 9.4 - - - +
142B TYR 3.3 0.2 - - - -
143B GLU* 1.3 75.2 - - - +
145B ASN* 1.4 56.0 + - - +
146B ALA 3.3 3.3 + - - -
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Residues in contact with ASN 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 ILE* 3.0 18.1 + - + +
142B TYR* 3.1 3.0 + - - +
144B ALA* 1.4 75.0 - - - +
146B ALA* 1.4 67.7 + - - +
147B LYS 3.3 2.0 - - - -
148B ARG* 2.8 39.7 + - - +
149B PHE* 4.4 12.7 - - + +
150B SER 5.2 1.4 - - - +
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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