Contacts of the strand formed by residues 147 - 154 (chain A) in PDB entry 1MHP
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 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A THR 3.5 29.7 + - - +
146A GLN* 1.3 80.2 - - - +
148A ASP* 1.3 60.0 + - - +
149A ILE* 3.7 13.9 + - + -
182A GLN 3.9 1.4 + - - -
183A THR* 3.5 10.2 - - + +
184A GLN 3.0 15.9 + - - +
245A ARG* 2.8 18.2 + - - +
248A VAL* 3.6 0.4 - - - -
249A LYS* 3.6 19.1 - - + +
251A VAL* 3.9 23.6 - - + -
335A ILE* 4.0 32.8 - - + +
336A PHE* 4.5 14.6 - - + +
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Residues in contact with ASP 148 (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 LEU* 1.3 69.0 - - - +
149A ILE* 1.3 61.8 + - - +
184A GLN* 3.6 11.3 - - - +
200A LEU* 3.8 20.6 - - + -
238A PHE* 3.2 16.6 - - + -
244A ALA* 3.3 9.7 - - - +
245A ARG* 2.7 67.2 + - - +
248A VAL* 3.9 7.5 - - - +
249A LYS 2.9 13.7 + - - +
250A LYS* 4.8 3.5 - - + +
251A VAL 3.0 21.4 + - - -
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Residues in contact with ILE 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 LEU* 4.1 11.7 - - + -
148A ASP* 1.3 73.9 - - - +
150A VAL* 1.3 67.7 + - - +
151A ILE* 4.1 9.2 - - + -
172A LEU* 6.5 0.4 - - + -
176A MET* 4.0 18.4 - - + -
183A THR* 3.6 24.9 - - + -
184A GLN 2.9 11.4 + - - +
185A VAL* 3.2 10.6 - - + +
186A GLY 3.0 22.7 + - - +
200A LEU* 3.4 2.1 - - - +
251A VAL* 3.2 28.9 - - + +
253A VAL* 4.2 17.7 - - + -
335A ILE* 3.3 25.6 - - + -
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Residues in contact with VAL 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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149A ILE* 1.3 76.9 - - - +
151A ILE* 1.3 66.8 + - - +
186A GLY* 3.1 11.2 - - - +
188A VAL* 4.2 11.4 - - + -
200A LEU* 4.1 14.6 - - + -
233A ALA* 3.8 26.2 - - + -
237A ALA* 3.9 20.0 - - + -
238A PHE* 3.3 42.8 - - + -
251A VAL 2.8 6.1 + - - +
252A MET* 3.3 6.3 - - - +
253A VAL 3.0 22.3 + - - -
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Residues in contact with ILE 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 ILE* 4.4 11.9 - - + -
150A VAL* 1.3 75.9 - - - +
152A VAL* 1.3 58.9 + - - +
153A LEU* 3.4 28.0 + - + -
168A PHE* 5.5 0.7 - - + -
169A LEU* 3.8 23.8 - - + -
172A LEU* 4.4 11.7 - - + -
173A LEU* 4.0 27.6 - - + -
176A MET* 5.5 0.9 - - + -
185A VAL* 4.2 4.3 - - + -
186A GLY 2.7 11.9 + - - +
187A ILE* 3.4 17.4 - - + +
188A VAL* 2.7 34.1 + - - +
253A VAL* 3.5 26.7 - - + +
255A VAL* 4.8 1.3 - - + -
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Residues in contact with VAL 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 VAL* 4.4 1.6 - - + +
151A ILE* 1.3 73.7 - - - +
153A LEU* 1.3 60.9 + - - +
188A VAL* 3.3 10.5 - - + +
190A TYR* 3.7 26.8 - - + -
229A GLY* 3.9 21.3 - - - +
230A ILE* 4.2 3.8 - - + +
233A ALA* 3.7 21.8 - - + -
252A MET* 3.6 33.0 - - + -
253A VAL 2.7 11.8 + - - +
254A ILE* 3.6 11.9 - - + +
255A VAL 3.2 24.8 + - - +
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Residues in contact with LEU 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 ILE* 3.4 22.9 + - + -
152A VAL* 1.3 71.3 - - - +
154A ASP* 1.3 61.0 + - - +
155A GLY 3.5 0.3 + - - -
162A TRP* 4.5 17.0 - - + -
165A VAL* 4.1 22.2 - - + -
168A PHE* 5.3 1.6 - - + -
169A LEU* 3.4 38.6 - - + -
187A ILE* 3.8 17.7 - - + -
188A VAL 2.7 13.6 + - - +
189A GLN* 3.2 7.8 - - + +
190A TYR* 3.0 30.8 + - - -
216A ILE* 5.0 4.3 - - + -
255A VAL* 3.6 24.0 - - + -
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Residues in contact with ASP 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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153A LEU* 1.3 72.9 - - - +
155A GLY* 1.3 57.7 + - - +
156A SER* 2.7 33.0 + - - -
159A ILE* 3.3 21.8 - - + +
162A TRP* 3.5 13.0 - - - -
165A VAL* 5.2 2.3 - - - +
190A TYR* 3.5 27.5 - - - +
224A THR* 3.7 5.8 - - - +
255A VAL* 3.0 25.5 + - - +
256A THR* 2.9 24.4 + - - -
257A ASP* 3.5 15.4 + - - +
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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