Contacts of the strand formed by residues 145 - 149 (chain M) in PDB entry 3AOI
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 GLY 145 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143M SER 2.6 9.1 + - - -
144M PRO* 1.3 76.6 - - - +
146M VAL* 1.3 69.7 + - - +
147M TYR* 4.0 4.3 - - - -
162M ILE* 3.8 0.7 - - - +
163M ILE* 2.9 31.1 + - - +
164M PRO* 5.2 0.3 - - - +
267M TYR* 5.6 1.6 - - - -
273M GLY* 5.0 0.9 - - - -
276M LYS* 3.3 21.1 - - - -
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Residues in contact with VAL 146 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145M GLY* 1.3 82.2 - - - +
147M TYR* 1.3 73.8 + - - +
148M PHE* 4.0 22.8 - - + -
160M ALA* 5.8 0.2 - - + -
161M SER 3.2 16.2 - - - +
162M ILE* 3.9 28.0 - - + -
276M LYS* 3.9 9.6 - - + +
277M ALA* 6.0 1.1 - - - -
280M LYS* 3.7 19.8 - - - +
281M LEU* 4.0 30.7 - - + -
302M VAL* 5.7 4.3 - - + -
306M THR* 4.6 2.5 - - + -
323M ASP* 4.4 0.7 - - - +
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Residues in contact with TYR 147 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142M ARG* 3.4 34.5 - - + +
143M SER* 2.2 46.7 + - - -
145M GLY* 4.1 0.7 - - - -
146M VAL* 1.3 91.9 - - - +
148M PHE* 1.3 67.1 + - - +
149M THR* 4.2 1.1 - - - -
161M SER* 2.8 42.4 + - - +
163M ILE* 3.6 22.4 - - + -
280M LYS* 3.6 15.2 + - + -
323M ASP* 3.9 20.2 - - + +
325M ILE* 6.4 4.0 - - + -
330M ASN* 2.8 43.9 - - + -
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Residues in contact with PHE 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146M VAL* 4.0 18.6 - - + -
147M TYR* 1.3 84.6 - - - +
149M THR* 1.3 60.7 + - - +
150M PRO* 4.4 0.9 - - - +
158M TYR* 5.1 3.8 - - + +
159M ILE 3.5 7.6 - - - +
160M ALA* 3.5 28.7 - - + -
280M LYS* 4.7 4.0 - - + -
281M LEU* 3.5 33.0 - - + -
306M THR* 4.3 4.7 - - - -
309M TYR* 3.4 37.5 - + + -
310M LEU* 5.6 1.1 - - + -
313M LEU* 3.5 32.1 - - + -
321M GLU* 3.8 19.4 - - + +
322M VAL* 4.1 2.9 - - - -
323M ASP* 3.2 33.9 + - - +
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Residues in contact with THR 149 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142M ARG* 5.9 5.4 - - - +
147M TYR* 4.2 2.1 + - - -
148M PHE* 1.3 73.0 - - - +
150M PRO* 1.3 83.0 + - - +
158M TYR* 3.7 3.8 - - - -
159M ILE* 3.0 49.1 + - + +
161M SER* 5.9 3.8 - - - -
323M ASP 4.9 2.7 - - - -
325M ILE* 4.1 23.4 - - - +
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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