Contacts of the helix formed by residues 154 - 160 (chain A) in PDB entry 2R5N
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 GLY 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ASN* 4.0 11.7 - - - +
153A MET* 1.3 74.6 - - - +
155A ASP* 1.3 66.0 + - - -
156A GLY 3.2 2.9 - - - -
157A CYS* 3.3 6.5 + - - +
158A MET* 3.1 25.3 + - - +
182A TYR* 3.7 6.3 - - - -
183A ASP* 4.2 16.4 - - - -
672A TPP 3.7 13.0 - - - -
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Residues in contact with ASP 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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154A GLY* 1.3 72.1 - - - -
156A GLY* 1.3 58.6 + - - +
158A MET* 3.2 2.7 + - - +
159A MET* 2.9 50.4 + - + +
182A TYR* 2.5 34.5 + - - -
183A ASP 4.2 3.5 + - - +
184A ASP* 4.7 3.3 - - - +
185A ASN* 3.2 8.8 - - - +
186A GLY 4.0 8.3 + - - -
187A ILE 3.4 4.3 + - - +
188A SER* 5.0 0.2 - - - -
193A VAL* 4.3 13.9 - - + +
197A PHE* 3.6 13.1 - - + -
672A TPP 3.2 11.5 + - - +
2000A CA 2.3 26.2 - - - -
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Residues in contact with GLY 156 (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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116A LEU* 4.0 15.0 - - - -
154A GLY 3.2 0.6 - - - -
155A ASP* 1.3 79.6 - - - +
157A CYS* 1.3 60.6 + - - +
159A MET* 3.3 2.5 + - - +
160A GLU* 3.2 27.4 + - - +
672A TPP 3.5 22.5 + - - -
409B VAL* 3.8 22.1 - - - +
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Residues in contact with CYS 157 (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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63A SER* 3.1 46.2 - - - +
64A ASN* 4.1 2.2 - - - -
116A LEU* 3.9 10.0 - - - +
117A GLY* 3.3 27.1 - - - +
120A ILE* 4.9 0.4 - - + -
153A MET* 3.9 22.2 - - + -
154A GLY 3.3 11.3 + - - +
155A ASP 3.3 0.4 - - - -
156A GLY* 1.3 75.2 - - - +
158A MET* 1.3 61.4 + - - +
160A GLU* 3.4 10.6 + - - +
163A SER* 3.1 22.1 + - - -
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Residues in contact with MET 158 (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 MET* 3.8 19.7 - - + -
154A GLY 3.1 18.7 + - - +
155A ASP 3.2 8.5 + - - +
157A CYS* 1.3 77.3 - - - +
159A MET* 1.3 57.1 + - - +
163A SER* 3.1 5.3 + - - -
182A TYR* 3.7 39.0 - - + -
197A PHE* 3.7 19.1 - - + -
201A THR* 3.9 12.3 - - + -
204A ARG* 3.0 14.3 + - - +
205A PHE* 3.5 32.5 - - + -
240A LEU* 3.7 24.9 - - + -
164B HIS* 2.8 23.6 + - - -
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Residues in contact with MET 159 (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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155A ASP* 2.9 42.8 + - + +
156A GLY 3.3 3.3 + - - +
158A MET* 1.3 74.9 - - - +
160A GLU* 1.3 66.7 + - - +
161A GLY 3.4 2.3 + - - -
188A SER* 4.5 7.9 - - - -
193A VAL* 4.8 0.7 - - + -
196A TRP* 4.0 12.3 - - + +
197A PHE* 3.6 45.3 - - + -
164B HIS* 3.5 13.5 + - - -
165B GLU* 3.7 9.7 - - - +
408B GLY* 3.8 11.7 - - - -
409B VAL* 3.5 46.4 - - + +
410B ARG* 3.9 18.7 + - + +
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Residues in contact with GLU 160 (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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116A LEU* 3.9 15.9 - - + +
117A GLY* 4.5 0.9 - - - -
156A GLY 3.2 15.7 + - - +
157A CYS 3.7 9.4 - - - +
158A MET 3.3 0.6 - - - -
159A MET* 1.3 77.7 - - - +
161A GLY* 1.3 63.7 + - - +
162A ILE* 4.2 16.3 + - + -
163A SER* 2.7 28.6 + - - -
412A PHE* 5.6 0.3 - - - -
672A TPP 3.3 11.3 - - - +
164B HIS* 3.6 1.9 - - - -
165B GLU* 3.3 14.8 - - - +
409B VAL* 3.3 25.9 - - + +
411B GLU* 2.6 29.0 - - - +
440B TYR* 3.4 19.2 - - - -
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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