Contacts of the helix formed by residues 138 - 145 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137D ASP* 1.3 70.4 - - - +
139D GLN* 1.4 54.5 + - - +
141D ILE* 3.3 10.5 + - + -
142D TYR* 2.8 36.0 + - - +
149D PHE* 3.6 11.5 - - + -
157D LEU* 3.6 36.1 - - + -
180D ALA* 3.1 19.5 + - + +
183D LEU* 2.8 43.5 + - + +
185D LEU* 4.3 10.3 - - + -
193D VAL* 4.0 4.7 - - + -
254D TRP* 5.0 1.6 - - + -
341D LEU* 4.0 36.8 - - + -
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Residues in contact with GLN 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ASP* 3.1 11.5 + - - +
138D LEU* 1.4 76.1 - - - +
140D LYS* 1.3 57.4 + - + +
142D TYR* 3.4 22.4 + - - +
143D GLU* 2.9 67.8 + - - +
147D LYS* 5.4 3.0 - - - +
180D ALA* 3.3 22.5 + - - +
181D SER* 3.8 24.2 + - - +
227D PHE* 5.9 3.3 - - - -
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Residues in contact with LYS 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D SER* 3.8 21.5 - - - +
137D ASP* 3.1 32.0 + - - +
138D LEU 3.3 0.2 - - - -
139D GLN* 1.3 76.7 - - + +
141D ILE* 1.4 57.6 + - + +
143D GLU* 3.9 10.2 - - - +
144D ALA* 3.0 29.1 + - - +
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Residues in contact with ILE 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D SER* 3.7 19.5 - - - +
137D ASP 3.4 20.2 - - - +
138D LEU* 3.3 13.6 + - + +
140D LYS* 1.4 72.8 - - + +
142D TYR* 1.4 58.6 + - - +
144D ALA* 3.3 9.4 + - + +
145D ASN* 3.0 30.6 + - + +
149D PHE* 4.1 4.5 - - + -
185D LEU* 3.7 29.8 - - + -
341D LEU* 3.9 42.0 - - + +
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Residues in contact with TYR 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LEU 2.8 22.1 + - - +
139D GLN* 3.5 33.2 - - - +
140D LYS 3.4 0.2 - - - -
141D ILE* 1.4 71.8 - - - +
143D GLU* 1.4 58.7 + - - +
145D ASN* 3.1 11.5 + - - +
147D LYS* 3.0 59.3 + - + +
148D ARG 3.6 11.4 + - - -
149D PHE* 3.6 33.4 - + + -
180D ALA* 5.1 1.3 - - + -
253D GLN* 2.8 47.3 + - + -
254D TRP* 3.7 27.4 - + - -
257D GLY* 3.2 11.3 + - - -
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Residues in contact with GLU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D GLN* 2.9 53.3 + - - +
140D LYS* 3.9 9.2 - - - +
142D TYR* 1.4 75.7 - - + +
144D ALA* 1.4 60.9 + - - +
146D ALA* 3.4 13.0 + - - -
147D LYS* 4.0 26.7 + - - +
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Residues in contact with ALA 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D LYS 3.0 19.1 + - - +
141D ILE* 3.5 9.0 - - + +
142D TYR 3.3 0.2 - - - -
143D GLU* 1.4 75.2 - - - +
145D ASN* 1.3 56.5 + - - +
146D ALA 3.3 3.4 + - - -
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Residues in contact with ASN 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D ILE* 3.0 18.3 + - + +
142D TYR* 3.1 3.2 + - - +
144D ALA* 1.3 76.5 - - - +
146D ALA* 1.4 65.4 + - - +
147D LYS 3.4 2.0 - - - -
148D ARG* 2.8 39.0 + - - +
149D PHE* 4.4 12.1 - - + +
150D SER 5.2 2.2 - - - +
341D LEU* 6.4 0.6 - - - +
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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