Contacts of the helix formed by residues 144 - 152 (chain A) in PDB entry 1R00
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 PRO 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A PRO* 6.5 1.3 - - + -
137A TYR* 4.3 1.3 - - + -
138A ALA* 3.9 17.9 - - + +
143A ARG* 1.3 92.0 - - + +
145A PHE* 1.3 57.6 + - - +
146A TRP 3.4 2.2 - - - +
147A GLU* 3.1 32.1 + - + +
148A ASP* 2.8 31.0 + - - +
261A TRP* 6.1 5.4 - - + -
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Residues in contact with PHE 145 (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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115A ALA* 4.9 4.7 - - + -
119A ALA* 4.4 8.1 - - + -
137A TYR* 3.5 37.1 - + + +
144A PRO* 1.3 73.1 - - - +
146A TRP* 1.3 92.1 + + + +
148A ASP* 3.2 4.2 + - - +
149A LEU* 2.9 56.5 + - + +
159A PHE* 3.6 29.2 - + - -
311A PHE* 3.6 36.9 + + + +
312A MET* 3.3 34.0 - - + +
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Residues in contact with TRP 146 (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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144A PRO* 3.4 0.8 - - - +
145A PHE* 1.3 95.9 - + + +
147A GLU* 1.3 61.6 + - + +
149A LEU* 3.9 18.0 - - + +
150A SER* 2.9 30.3 + - - -
159A PHE* 3.5 31.2 - + - -
160A ASP* 5.7 2.7 - - - -
214A LEU* 3.6 8.2 - - + +
217A PRO* 6.0 1.8 - - + -
260A ASN* 3.6 31.7 + - + +
261A TRP* 4.1 16.8 - + + +
312A MET* 3.6 25.3 - - + -
635A SAH 3.5 75.8 + + + +
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Residues in contact with GLU 147 (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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143A ARG* 4.2 20.1 + - + +
144A PRO* 3.1 36.6 + - + +
146A TRP* 1.3 78.0 - - + +
148A ASP* 1.3 63.5 + - - +
150A SER* 3.4 7.9 + - - -
151A ALA* 3.4 21.8 + - - +
214A LEU* 4.3 15.5 - - + -
635A SAH 6.3 0.2 - - - +
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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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118A HIS* 4.2 5.7 - - - -
137A TYR* 2.4 39.3 + - + +
141A TYR* 4.3 9.1 - - - +
143A ARG* 2.6 45.3 + - + +
144A PRO 2.8 13.6 + - - +
145A PHE 3.4 8.3 - - - +
147A GLU* 1.3 79.1 - - - +
149A LEU* 1.3 62.4 + - + +
151A ALA 3.4 0.5 + - - -
152A ASP* 3.2 26.6 + - - +
155A LEU* 3.6 15.6 - - - +
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Residues in contact with LEU 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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115A ALA* 4.6 4.3 - - + -
137A TYR* 4.5 8.5 - - - +
145A PHE* 2.9 50.8 + - + +
146A TRP* 3.9 16.4 - - + +
147A GLU 3.4 0.2 - - - -
148A ASP* 1.3 73.6 - - - +
150A SER* 1.3 66.2 + - - +
152A ASP 3.1 24.2 + - - +
153A VAL* 4.6 0.2 - - - -
155A LEU* 3.8 21.1 - - + -
156A ALA* 3.4 26.6 - - + +
159A PHE* 3.6 42.0 - - + -
220A ARG* 5.0 0.8 + - - +
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Residues in contact with SER 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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146A TRP 2.9 19.2 + - - -
147A GLU* 3.5 7.4 - - - -
149A LEU* 1.3 76.9 - - - +
151A ALA* 1.3 60.0 + - - +
152A ASP 5.0 0.5 - - - -
153A VAL* 5.2 4.5 + - - +
214A LEU* 3.5 26.2 - - - +
215A ALA* 3.5 6.8 + - - +
216A GLY* 3.2 40.7 + - - -
217A PRO* 4.4 6.5 - - - +
220A ARG* 5.4 0.2 - - - +
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Residues in contact with ALA 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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143A ARG* 3.8 33.2 - - - +
147A GLU 3.4 7.0 + - - +
148A ASP 3.4 0.2 + - - -
149A LEU 3.2 0.2 - - - -
150A SER* 1.3 79.3 - - - +
152A ASP* 1.3 60.0 + - - +
153A VAL* 4.0 5.8 + - - +
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Residues in contact with ASP 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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143A ARG* 5.2 4.7 - - - +
148A ASP* 3.2 15.7 + - - +
149A LEU 3.1 13.4 + - - +
151A ALA* 1.3 76.8 - - - +
153A VAL* 1.3 63.3 + - - +
154A ALA* 3.2 20.4 + - - +
155A LEU* 3.2 39.6 + - + +
156A ALA 3.2 4.7 + - - -
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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