Contacts of the strand formed by residues 158 - 163 (chain M) in PDB entry 5X22
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 158 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148M PHE* 5.4 0.2 - - + -
149M THR 3.8 4.3 - - - +
150M PRO* 3.7 28.0 - - + -
151M ASP* 4.1 1.1 - - - +
156M GLY* 4.4 9.6 - - - -
157M ARG* 1.3 82.0 - - - +
159M ILE* 1.3 71.2 + - - +
174M LEU 4.2 3.3 - - - +
175M GLU* 4.8 0.5 - - - +
176M VAL* 4.4 12.0 + - - +
310M LEU* 3.8 21.6 - - + +
313M LEU* 3.6 53.3 + - + +
314M THR* 4.0 20.6 + - - -
322M VAL* 3.5 24.7 - - + +
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Residues in contact with ILE 159 (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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147M TYR 3.8 0.2 - - - +
148M PHE* 3.4 3.9 - - - -
149M THR* 2.9 52.6 + - + +
150M PRO 4.9 0.2 - - - -
151M ASP* 3.7 29.4 - - + +
152M PRO* 5.0 4.0 - - + -
158M TYR* 1.3 76.5 - - - +
160M ALA* 1.3 69.7 + - - +
161M SER* 4.1 7.0 - - - +
173M ASP* 3.7 26.0 - - + +
174M LEU 3.8 4.3 - - - +
175M GLU* 3.6 39.7 - - + +
310M LEU* 4.7 2.2 - - - -
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Residues in contact with ALA 160 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147M TYR 3.5 4.9 - - - -
148M PHE* 3.7 27.1 - - + -
158M TYR 4.2 0.6 + - - -
159M ILE* 1.3 75.7 - - - +
161M SER* 1.3 61.2 + - - +
162M ILE* 4.3 0.9 - - - -
172M ILE 4.4 0.2 - - - -
173M ASP* 3.4 5.7 - - - -
174M LEU* 2.9 51.8 + - + +
306M THR* 4.2 11.9 - - + -
310M LEU* 4.3 9.5 - - + +
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Residues in contact with SER 161 (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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142M ARG* 5.4 3.0 + - - -
145M GLY 3.6 1.6 - - - +
146M VAL* 3.3 7.1 - - - +
147M TYR* 2.9 44.8 + - - +
149M THR* 4.2 10.0 - - - +
159M ILE* 4.1 12.3 + - - +
160M ALA* 1.3 77.2 + - - +
162M ILE* 1.3 63.1 + - - +
163M ILE* 3.9 18.1 + - - -
171M TRP* 5.5 4.3 - - - -
172M ILE 3.5 4.3 - - - -
173M ASP* 4.0 11.3 + - - -
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Residues in contact with ILE 162 (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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145M GLY 3.6 5.8 - - - +
146M VAL* 4.1 15.7 - - + -
160M ALA 5.7 0.4 - - - -
161M SER* 1.3 75.0 - - - +
163M ILE* 1.3 62.2 + - - +
164M PRO* 3.6 3.3 - - - +
170M PRO 4.1 1.0 - - - +
171M TRP* 3.6 6.2 - - - -
172M ILE* 2.9 44.5 + - + +
174M LEU* 4.9 4.3 - - + -
267M TYR* 3.3 22.0 - - - +
269M LEU* 4.9 4.0 - - + -
290M LEU* 3.7 26.5 - - + -
302M VAL* 3.9 20.2 - - + -
303M PHE* 4.4 19.3 - - + -
306M THR* 4.3 16.6 - - + +
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Residues in contact with ILE 163 (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 46.2 - - + +
143M SER 5.0 1.8 - - - +
144M PRO* 3.1 11.6 - - + +
145M GLY 2.9 42.0 + - - +
147M TYR* 3.8 15.5 - - + -
161M SER* 4.5 11.9 - - - -
162M ILE* 1.3 76.5 - - - +
164M PRO* 1.3 74.1 - - - +
171M TRP* 3.5 49.4 - - + +
269M LEU* 3.6 7.1 - - - +
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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