Contacts of the helix formed by residues 137 - 142 (chain D) in PDB entry 2AMT
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 LEU 137 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134D THR* 2.5 39.7 + - - +
135D GLU 3.1 8.2 + - - +
136D LYS* 1.3 78.3 - - + +
138D GLY* 1.3 63.2 + - - +
140D THR* 3.8 0.5 + - - -
141D GLY 3.2 5.5 + - - -
9F VAL* 3.8 15.5 - - + -
11F ALA* 3.7 33.0 - - + -
139F PHE* 3.6 33.1 - - + -
144F GLU* 3.8 41.1 - - + +
145F GLY* 4.1 2.9 - - - -
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Residues in contact with GLY 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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136D LYS 4.2 0.2 + - - -
137D LEU* 1.3 74.5 - - - +
139D PHE* 1.3 60.3 + - - -
140D THR* 3.3 1.1 - - - -
142D ARG* 3.0 47.5 + - - +
8903D GPP 3.3 28.3 - - - -
139F PHE* 3.5 11.1 - - - +
142F ARG* 5.6 0.2 - - - +
144F GLU* 5.9 0.2 + - - -
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Residues in contact with PHE 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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7D PHE* 5.2 0.7 - + - -
9D VAL* 3.6 42.6 - - + -
138D GLY* 1.3 71.7 - - - -
140D THR* 1.3 81.0 + - + +
142D ARG* 3.6 6.3 + - - +
143D GLY 3.5 1.9 + - - -
144D GLU* 2.9 55.6 + - + +
145D GLY 3.5 4.6 + - - -
147D ALA* 4.4 6.5 - - + -
8903D GPP 3.2 44.3 + - + -
134E THR* 4.4 9.6 - - + -
137E LEU* 3.7 33.4 - - + -
138E GLY* 3.7 20.9 - - - +
140E THR* 5.7 0.4 - - - -
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Residues in contact with THR 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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99D ILE* 3.5 34.5 - - + +
100D ALA* 4.8 2.5 - - - -
101D GLN* 3.2 18.7 + - - +
102D ALA* 5.9 0.3 - - - +
134D THR* 2.7 32.7 + - - +
137D LEU 3.8 1.7 + - - -
138D GLY* 4.6 0.9 - - - -
139D PHE* 1.3 97.3 + - + +
141D GLY* 1.3 57.4 + - - -
143D GLY* 3.2 12.8 + - - -
145D GLY 3.6 13.8 - - - +
147D ALA* 3.7 22.0 - - + +
8903D GPP 5.5 3.6 + - + +
139F PHE* 5.7 0.5 - - - -
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Residues in contact with GLY 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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101D GLN* 3.3 31.3 - - - +
134D THR* 3.1 3.9 + - - -
136D LYS* 3.3 29.7 - - - +
137D LEU 3.2 16.0 + - - -
140D THR* 1.3 82.8 + - - +
142D ARG* 1.3 57.1 + - - +
143D GLY 3.2 1.9 + - - -
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Residues in contact with ARG 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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13C GLY* 6.2 0.2 - - - -
29C LYS* 3.3 18.5 - - - -
142C ARG* 4.0 10.8 + - - +
143C GLY 4.7 0.4 - - - +
144C GLU* 3.5 48.7 + - - +
136D LYS 4.0 10.8 - - - +
138D GLY* 3.0 33.6 + - - +
139D PHE* 3.6 5.0 + - - +
140D THR 3.3 0.2 - - - -
141D GLY* 1.3 77.5 - - - +
143D GLY* 1.3 61.4 + - - +
144D GLU* 2.8 46.3 + - + +
8903D GPP 2.8 44.0 + - - -
138E GLY 4.9 0.4 - - - +
142E ARG* 4.2 5.7 - - - +
142F ARG* 4.6 0.4 - - - +
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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