Contacts of the helix formed by residues 131 - 139 (chain D) in PDB entry 3T0E
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 131 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119C TYR* 3.4 19.8 - - - +
120C GLN 3.6 23.8 - - - -
121C LEU* 3.9 3.4 - - - +
122C ARG* 5.3 1.1 - - - +
130D PRO* 1.3 75.4 - - - +
132D GLU* 1.3 59.0 + - - +
133D ALA* 2.8 27.8 + - - +
134D GLU* 3.0 12.2 + - - +
135D ILE* 3.3 14.2 + - - +
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Residues in contact with GLU 132 (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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130D PRO 4.4 0.2 + - - -
131D SER* 1.3 68.5 - - - +
133D ALA* 1.3 57.0 + - - +
135D ILE* 3.6 28.7 - - + +
136D SER* 2.7 41.9 + - - +
202D GLN* 4.0 16.7 + - - +
244D ASP* 4.4 15.4 - - - +
245D CYS* 3.5 21.9 + - - +
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Residues in contact with ALA 133 (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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119C TYR* 4.3 18.2 - - + -
120C GLN 5.8 0.9 - - - +
196C PHE* 4.7 20.1 - - + +
131D SER* 2.8 17.1 - - - +
132D GLU* 1.3 80.3 - - - +
134D GLU* 1.3 63.3 + - - +
136D SER* 3.3 5.0 + - - -
137D HIS* 3.1 19.9 + - - +
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Residues in contact with GLU 134 (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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119C TYR* 3.2 42.5 - - + -
121C LEU* 5.1 2.3 - - - +
133C LEU* 4.4 5.7 - - - +
130D PRO* 4.6 3.0 - - - +
131D SER* 3.0 12.4 + - - +
133D ALA* 1.3 78.1 - - - +
135D ILE* 1.3 65.0 + - + +
137D HIS 2.9 1.7 + - - -
138D THR* 2.8 34.6 + - + +
140D LYS 3.4 16.9 - - - +
141D ALA* 4.3 0.2 - - - -
142D THR* 2.8 55.5 + - - +
195D ARG* 3.5 17.2 + - - -
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Residues in contact with ILE 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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130D PRO* 4.2 8.5 - - + -
131D SER 3.3 18.6 - - - +
132D GLU* 3.4 31.6 - - + +
134D GLU* 1.3 76.3 - - + +
136D SER* 1.3 68.8 + - - +
137D HIS 2.9 1.4 + - - -
139D GLN* 3.0 24.3 + - + +
140D LYS 3.5 20.2 - - - +
141D ALA* 4.0 17.5 - - + -
198D ALA* 4.3 20.2 - - + +
201D TRP* 4.8 7.9 - - + +
202D GLN* 3.8 20.9 - - + +
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Residues in contact with SER 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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132D GLU* 2.7 27.9 + - - +
133D ALA* 3.7 6.1 - - - -
135D ILE* 1.3 76.8 - - - +
137D HIS* 1.3 59.1 + - - +
139D GLN* 5.6 1.6 - - - +
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Residues in contact with HIS 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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115C ASP* 2.6 41.1 + - - -
116C PRO 5.5 0.6 + - - -
117C ALA* 5.2 2.7 - - + +
119C TYR* 3.8 18.6 + - + +
196C PHE 4.3 24.2 - - - +
133D ALA 3.1 10.3 + - - +
134D GLU 2.9 7.5 + - - +
135D ILE 2.9 1.0 + - - -
136D SER* 1.3 81.5 - - - +
138D THR* 1.3 67.9 + - - +
139D GLN* 3.4 2.9 + - - +
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Residues in contact with THR 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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115C ASP* 5.4 4.7 - - + +
119C TYR* 3.5 24.5 - - + +
136C ASP* 3.7 23.1 - - - +
134D GLU* 2.8 24.2 + - + +
137D HIS* 1.3 79.5 - - + +
139D GLN* 1.3 68.7 + - - +
140D LYS* 3.1 47.0 + - - +
195D ARG* 4.3 0.7 + - - -
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Residues in contact with GLN 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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164C MET* 6.1 0.5 - - - +
135D ILE* 3.0 19.0 + - + +
136D SER 5.6 1.8 - - - +
137D HIS 3.4 3.7 - - - +
138D THR* 1.3 80.0 - - - +
140D LYS* 1.3 63.4 + - - +
197D SER* 4.6 1.2 - - - -
198D ALA* 3.1 25.6 + - + +
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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