Contacts of the strand formed by residues 148 - 155 (chain A) in PDB entry 1ONE
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 VAL 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A LEU 4.0 0.2 + - - -
147A PRO* 1.3 71.6 - - - +
149A PRO* 1.3 72.3 - - + +
150A PHE* 3.6 6.2 + - + -
172A ALA* 3.8 28.7 - - + -
173A PRO 3.9 12.3 - - - +
174A THR* 4.0 11.2 - - + +
393A GLY 2.9 17.6 + - - +
394A GLN* 3.6 2.1 - - - -
395A ILE 3.2 21.3 + - - +
425A PHE* 3.9 8.1 - - + -
427A GLY* 3.2 45.3 - - - +
430A PHE* 3.8 9.0 - - + -
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Residues in contact with PRO 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A PRO 3.5 8.1 - - - +
148A VAL* 1.3 86.2 - - + +
150A PHE* 1.4 60.7 + - - +
151A LEU* 3.5 15.3 + - + +
171A ILE 3.3 2.8 - - - +
172A ALA* 3.6 1.6 - - - -
173A PRO* 3.2 30.7 - - + +
179A PHE* 3.7 25.1 - - + -
182A ALA* 3.9 27.4 - - + -
183A LEU* 4.7 6.7 - - + -
395A ILE* 3.5 11.0 - - + +
397A THR* 6.0 0.4 - - + -
409A LEU* 4.1 19.3 - - + -
425A PHE* 4.4 0.2 - - + -
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Residues in contact with PHE 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A VAL* 3.7 18.6 - - + -
149A PRO* 1.4 69.5 - - - +
151A LEU* 1.3 61.3 + - - +
152A ASN 3.7 2.6 + - - -
170A MET* 3.7 24.3 - - + +
171A ILE 3.4 5.6 - - - -
172A ALA* 3.5 26.5 - - + -
244A GLY* 4.3 19.5 - - - -
292A VAL* 4.5 6.3 - - + -
293A SER* 4.1 16.8 - - - -
370A MET* 3.7 28.9 - - + -
394A GLN* 4.0 15.9 - - + -
395A ILE 2.7 16.6 + - - +
396A LYS* 3.6 22.0 - - + +
397A THR 4.2 4.5 + - - +
398A GLY 4.3 0.9 + - - +
430A PHE* 3.9 31.9 - + - -
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PRO* 4.0 25.1 - - + +
150A PHE* 1.3 72.3 - - - +
152A ASN* 1.4 59.8 + - - +
153A VAL* 3.0 19.4 + - + +
170A MET* 3.1 2.1 - - - -
171A ILE* 2.7 50.8 + - + +
173A PRO* 4.4 8.1 - - + -
182A ALA 4.8 1.6 - - - +
183A LEU* 4.5 7.9 - - + -
186A GLY* 3.8 31.0 - - - -
398A GLY 3.3 23.8 - - - +
400A PRO* 4.2 12.8 - - + -
409A LEU* 3.7 26.2 - - + -
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Residues in contact with ASN 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A PHE 3.7 3.0 + - - +
151A LEU* 1.4 66.5 - - - +
153A VAL* 1.3 56.8 + - - +
154A LEU 3.1 17.6 + - - -
155A ASN* 3.0 38.1 + - - +
159A HIS* 4.4 1.4 + - - -
167A GLN 4.5 0.3 - - - +
168A GLU* 3.5 22.3 - - + +
169A PHE 3.3 15.3 - - - +
170A MET* 3.6 15.7 - - + -
211A GLU* 2.7 33.0 - - + +
213A GLY* 3.5 1.0 + - - -
373A HIS* 5.7 0.4 - - + +
398A GLY* 3.5 11.1 + - - +
399A ALA* 3.2 23.8 + - - +
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Residues in contact with VAL 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU* 3.0 17.7 + - + +
152A ASN* 1.3 71.2 - - - +
154A LEU* 1.4 59.1 + - - +
169A PHE 3.2 9.9 + - - +
171A ILE* 4.1 39.0 - - + -
189A VAL* 5.6 1.8 - - + -
190A TYR* 3.7 26.5 - - + -
193A LEU* 3.4 31.6 - - + +
213A GLY* 3.2 7.0 - - - -
214A VAL 2.9 19.4 + - - -
228A ILE* 4.3 8.5 - - + -
399A ALA* 4.2 1.3 - - - -
400A PRO* 3.8 18.2 - - + -
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ASN* 3.1 12.0 + - - -
153A VAL* 1.4 79.5 - - - +
155A ASN* 1.3 65.7 + - - +
164A LEU* 3.8 29.2 - - + -
168A GLU 4.1 0.2 - - - -
169A PHE* 3.2 22.4 + - + -
193A LEU* 4.4 3.1 - - + -
214A VAL* 3.4 19.1 - - + +
216A PRO* 3.9 15.7 - - + -
224A ALA* 3.7 39.5 - - + +
227A LEU* 4.0 19.7 - - + -
228A ILE* 4.0 20.0 - - + -
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Residues in contact with ASN 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ASN* 3.0 39.7 + - - +
154A LEU* 1.3 81.8 - - - +
156A GLY* 1.4 58.1 + - - +
159A HIS* 4.5 7.7 + - + +
160A ALA* 3.6 24.0 - - + +
164A LEU* 4.4 2.8 - - - +
167A GLN 3.8 5.2 - - - +
209A GLY* 3.4 12.6 - - - -
210A ASP 3.6 0.4 - - - +
211A GLU* 2.9 33.1 - - - +
212A GLY 3.3 1.4 - - - +
213A GLY* 3.1 19.3 + - - +
214A VAL 2.9 15.2 + - - +
215A ALA* 4.3 5.0 - - - -
216A PRO* 4.9 1.7 - - - +
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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