Contacts of the strand formed by residues 144 - 149 (chain D) in PDB entry 3OMA
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 TYR 144 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141D TYR* 2.9 76.2 + + + +
142D GLN 3.9 10.5 - - - -
143D TRP* 1.3 83.7 - - - +
145D TRP* 1.3 75.6 + - - +
157D GLU* 3.7 28.0 - - + -
158D SER 3.3 15.7 - - - +
159D TYR* 3.4 37.0 - + + +
263D MET* 3.5 14.1 - - - +
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Residues in contact with TRP 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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138D VAL* 3.6 20.0 - - + -
139D THR 3.4 3.6 - - - -
140D GLY* 3.5 29.8 - - - -
144D TYR* 1.3 85.0 - - - +
146D GLY* 1.3 59.7 + - - +
147D TYR* 3.7 25.5 - - + +
157D GLU* 3.3 2.8 - - - -
158D SER* 2.8 39.1 + - - +
210D VAL* 4.7 0.7 - - + -
217D HIS* 3.6 13.0 - - + -
218D SER* 3.4 36.8 - - - -
219D TRP* 3.6 17.3 - + + -
230D ALA* 4.1 7.9 - - + -
252D CYS* 4.1 7.9 - - + -
263D MET* 2.8 38.6 + - + +
264D PRO 3.3 21.3 - - - -
265D ILE* 3.6 19.3 - - + +
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Residues in contact with GLY 146 (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 LYS 3.7 0.7 - - - +
138D VAL* 3.3 6.6 - - - +
139D THR* 2.8 37.9 + - - -
141D TYR* 3.7 16.8 - - - -
145D TRP* 1.3 74.0 - - - +
147D TYR* 1.3 62.6 + - - -
156D PHE 3.5 7.4 - - - -
157D GLU* 4.3 8.7 - - - -
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Residues in contact with TYR 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D VAL* 4.0 6.1 - - + -
137D LYS 3.6 1.6 - - - -
138D VAL* 3.7 19.5 - - + -
145D TRP* 3.7 27.9 - - + +
146D GLY* 1.3 74.4 - - - -
148D GLU* 1.3 61.2 + - - +
149D TYR* 4.7 3.1 - - + -
155D SER* 3.1 7.1 - - - -
156D PHE* 2.8 63.1 + + + +
158D SER* 3.2 29.2 - - - -
198D MET* 3.6 40.4 - - + -
219D TRP* 3.1 27.9 + - - -
264D PRO 5.0 0.2 + - - -
265D ILE* 3.6 20.1 - - - +
266D THR 4.8 2.2 + - - -
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Residues in contact with GLU 148 (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 VAL* 3.4 3.5 - - - +
137D LYS* 2.7 53.9 + - + +
147D TYR* 1.3 76.2 - - - +
149D TYR* 1.3 66.2 + - - +
150D PRO* 3.2 5.7 - - + +
154D ILE 3.2 8.1 - - - +
155D SER* 4.2 9.6 - - - -
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Residues in contact with TYR 149 (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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134D VAL* 4.4 5.2 - - + -
135D THR 3.8 6.7 - - - +
136D VAL* 3.7 31.0 - - + -
147D TYR* 4.7 2.5 - - + -
148D GLU* 1.3 77.7 - - - +
150D PRO* 1.3 69.3 - - - +
151D ASP 3.3 2.0 - - - +
152D GLU* 3.0 21.8 + - + -
153D GLU* 3.0 19.6 + - - -
154D ILE* 2.7 31.9 + - + +
156D PHE* 3.7 16.4 - + - -
198D MET* 3.5 8.4 - - + +
199D VAL 2.5 46.3 + - - -
200D VAL* 4.4 0.2 - - - +
275D TYR* 3.7 22.9 - - - -
278D TRP* 3.5 22.8 - + - -
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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