Contacts of the strand formed by residues 133 - 139 (chain C) in PDB entry 1H5R
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 ALA 133 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129C LYS* 2.8 21.3 + - - +
132C GLY* 1.3 75.5 - - - +
134C THR* 1.3 63.8 + - - +
135C VAL* 5.7 0.2 - - + -
178C PHE 3.2 13.2 - - - +
179C TYR* 3.7 13.9 - - + -
207C TYR* 3.6 30.5 - - + -
212C ARG 3.0 6.4 + - - +
213C LEU* 4.0 12.3 - - + -
214C SER 2.9 12.5 + - - -
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Residues in contact with THR 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C ALA* 3.7 37.3 + - + +
129C LYS* 3.5 17.5 - - - +
133C ALA* 1.3 78.5 + - - +
135C VAL* 1.3 81.1 + - - +
136C PHE* 4.5 2.7 - - + -
176C LEU 4.4 0.2 - - - +
177C TYR* 3.7 2.4 - - - +
178C PHE* 2.9 36.4 + - - +
214C SER* 3.3 19.9 - - - +
216C ALA* 4.4 13.2 - - + -
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Residues in contact with VAL 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ALA* 5.7 0.7 - - + -
134C THR* 1.3 82.9 - - - +
136C PHE* 1.3 70.6 + - - +
160C LEU* 6.2 0.9 - - + -
173C VAL* 3.7 25.4 - - + -
176C LEU 4.2 3.1 - - - +
177C TYR* 3.7 25.1 - - + -
179C TYR* 4.9 0.7 - - + +
204C ASN* 3.8 19.1 - - - +
213C LEU* 3.9 19.3 - - + -
214C SER 2.9 15.0 + - - +
215C VAL* 3.9 22.0 - - + -
216C ALA* 2.9 23.9 + - - +
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Residues in contact with PHE 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C PHE* 5.2 2.0 - + - -
122C LEU* 3.7 44.0 - - + -
123C MET* 4.3 6.3 - - + -
126C ALA* 4.1 14.8 - - + -
134C THR* 4.5 5.4 - - + -
135C VAL* 1.3 82.7 - - - +
137C ALA* 1.3 59.8 + - - +
173C VAL* 3.5 4.4 - - - -
174C THR* 2.9 39.9 + - - +
176C LEU* 3.6 34.5 + - + -
178C PHE* 3.7 35.9 - + - -
216C ALA* 3.2 26.7 - - + +
218C MET* 4.5 15.3 - - + -
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Residues in contact with ALA 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C PHE* 1.3 73.5 - - - +
138C TYR* 1.4 62.6 + - - +
149C VAL* 3.7 20.4 - - + -
171C TYR* 4.1 4.3 - - + -
172C ALA 3.2 4.9 - - - +
215C VAL* 3.6 23.5 - - + +
216C ALA 2.9 7.1 + - - -
217C MET* 3.7 24.2 - - + +
218C MET* 2.8 30.8 + - - +
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Residues in contact with TYR 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B ILE* 5.5 0.5 - - - +
246B ARG* 3.9 22.4 - - - +
247B GLN* 3.0 23.8 + - + +
137C ALA* 1.4 74.8 - - - +
139C HIS* 1.3 86.1 + - - +
140C VAL* 3.4 6.7 + - + +
171C TYR* 3.9 3.1 - - - -
172C ALA* 2.8 38.6 + - - +
174C THR* 3.9 8.7 - - + -
218C MET* 3.7 32.3 - - + -
219C GLY 4.0 11.2 - - - -
220C ARG* 5.2 0.7 - - - -
222C TYR 2.6 31.3 + - - -
223C ALA* 3.5 8.1 - - - -
224C TRP* 3.5 43.8 + + + -
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Residues in contact with HIS 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B GLN* 2.8 44.0 + - + +
248B GLY* 4.4 5.4 - - - -
249B LEU* 3.7 39.5 - - + +
138C TYR* 1.3 87.2 - - - +
140C VAL* 1.3 70.1 + - - +
141C ASN* 5.5 0.4 - - - -
170C ASN* 3.3 35.7 + - + +
171C TYR* 3.6 37.9 - + + +
218C MET 5.0 1.6 + - - -
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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