Contacts of the helix formed by residues 134 - 142 (chain D) in PDB entry 3ARE
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 SER 134 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C TYR* 3.3 26.7 - - - +
127C GLN 3.2 26.2 - - - -
128C LEU* 4.4 3.8 - - - +
132D GLU 3.8 0.6 + - - -
133D PRO* 1.3 73.6 - - - +
135D GLU* 1.3 62.8 + - - +
136D ALA* 3.5 5.9 + - - +
137D GLU* 3.0 23.4 + - - +
138D ILE* 3.0 24.0 + - - +
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Residues in contact with GLU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D PRO 4.0 0.6 + - - -
134D SER* 1.3 73.2 - - - +
136D ALA* 1.3 52.6 + - - +
138D ILE* 3.7 28.5 - - - +
139D SER* 2.7 47.1 + - - +
204D TRP* 5.0 1.4 + - - -
205D GLN* 5.5 1.4 + - - -
245D ARG* 3.8 22.6 + - - +
247D ASP 5.0 13.6 - - - -
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Residues in contact with ALA 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C TYR* 3.8 4.6 - - + -
203C PHE* 4.4 6.6 - - + -
205C PRO* 3.7 36.8 - - + -
134D SER* 3.1 10.2 - - - +
135D GLU* 1.3 79.6 - - - +
137D GLU* 1.3 57.2 + - - +
139D SER* 4.0 3.7 - - - -
140D HIS* 3.0 33.3 + - - +
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Residues in contact with GLU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C TYR* 3.5 39.4 - - + +
128C LEU* 5.6 1.4 - - - +
140C LEU* 4.8 2.9 - - - +
133D PRO* 4.4 5.2 - - - +
134D SER* 3.0 23.4 + - - +
136D ALA* 1.3 75.2 - - - +
138D ILE* 1.3 58.6 + - - +
141D THR* 2.5 43.9 + - - +
143D LYS 3.4 10.6 - - - +
144D ALA* 3.6 2.1 - - - -
145D THR* 2.4 51.6 + - - +
198D ARG* 3.1 22.3 + - - +
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Residues in contact with ILE 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D PRO* 3.8 13.9 - - + -
134D SER 3.0 15.5 + - - +
135D GLU* 3.3 31.2 + - - +
137D GLU* 1.3 76.9 - - - +
139D SER* 1.3 63.0 + - - +
142D GLN* 3.3 26.1 + - - +
143D LYS 3.6 6.5 - - - +
144D ALA* 4.0 18.6 - - + -
201D ALA* 3.8 11.9 - - + -
204D TRP* 3.5 34.3 - - + +
205D GLN* 3.6 26.0 - - + +
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Residues in contact with SER 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D GLU* 2.7 32.6 + - - +
136D ALA* 4.0 5.1 - - - -
138D ILE* 1.3 75.1 - - - +
140D HIS* 1.3 60.7 + - - +
142D GLN* 3.4 17.8 + - - +
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Residues in contact with HIS 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ASP* 2.8 42.7 + - - +
124C ALA* 5.6 0.2 - - + -
126C TYR* 3.6 19.5 - - - +
203C PHE* 4.3 25.9 - + + +
136D ALA 3.0 18.6 + - - +
139D SER* 1.3 79.9 - - - +
141D THR* 1.3 60.2 + - + +
142D GLN* 3.7 0.9 - - - -
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Residues in contact with THR 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ASP* 3.8 10.1 - - - +
126C TYR* 3.6 23.8 - - - +
143C ASP* 4.1 14.1 - - - +
137D GLU* 2.5 26.1 + - + +
140D HIS* 1.3 90.1 - - + +
142D GLN* 1.3 70.6 + - - +
143D LYS* 2.9 51.4 + - - +
198D ARG* 4.2 3.6 - - - +
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Residues in contact with GLN 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D ILE* 3.3 19.9 + - - +
139D SER* 3.4 24.8 + - - +
140D HIS 5.5 0.7 - - - -
141D THR* 1.3 79.1 - - - +
143D LYS* 1.3 60.6 + - - +
200D SER* 3.8 5.0 - - - -
201D ALA* 2.9 34.1 + - + +
202D THR* 5.8 3.1 - - - +
205D GLN* 5.8 0.7 + - - -
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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