Contacts of the helix formed by residues 137 - 142 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B GLU* 5.0 9.6 - - - +
9E VAL* 3.7 16.8 - - + -
11E ALA* 3.7 26.7 - - + -
139E PHE* 3.7 32.3 - - + -
144E GLU* 3.7 39.3 - - + +
145E GLY* 3.8 3.6 - - - -
134F THR* 2.6 39.9 + - - +
135F GLU 3.5 8.1 - - - +
136F LYS* 1.3 81.9 - - + +
138F GLY* 1.3 64.2 + - - +
140F THR* 3.8 0.5 + - - -
141F GLY 3.0 6.6 + - - -
142F ARG* 5.3 0.2 - - - -
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Residues in contact with GLY 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8903D GPP 3.3 24.5 - - - -
139E PHE* 3.6 12.0 - - - +
144E GLU* 5.1 0.4 + - - -
137F LEU* 1.3 74.5 - - - +
139F PHE* 1.3 61.2 + - - -
140F THR 3.3 0.4 - - - -
142F ARG* 3.1 53.7 + - - +
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Residues in contact with PHE 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D THR* 4.6 7.0 - - + -
137D LEU* 3.6 34.1 - - + -
138D GLY* 3.5 23.1 - - - +
140D THR* 5.7 0.2 - - - -
8903D GPP 3.3 40.4 + - + -
7F PHE* 5.4 0.9 - + - -
9F VAL* 3.6 43.1 - - + -
138F GLY* 1.3 72.2 - - - -
140F THR* 1.3 77.4 + - + +
142F ARG* 3.4 17.2 - - - +
143F GLY 3.3 2.1 + - - -
144F GLU* 2.7 51.2 + - + +
145F GLY 3.5 3.9 + - - -
146F ILE 4.8 1.3 - - - -
147F ALA* 4.5 6.3 - - + -
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Residues in contact with THR 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8903D GPP 4.4 7.0 - - + +
12F PHE* 5.7 0.2 - - - -
99F ILE* 3.4 34.0 - - + +
100F ALA* 4.7 2.5 - - - -
101F GLN* 3.4 17.3 + - - +
134F THR* 2.8 32.5 + - - +
137F LEU 3.8 1.4 + - - -
138F GLY* 4.7 0.7 - - - -
139F PHE* 1.3 96.6 + - + +
141F GLY* 1.3 56.4 + - - +
143F GLY* 3.1 17.0 + - - -
145F GLY 3.6 13.2 - - - +
147F ALA* 3.6 22.4 - - + +
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Residues in contact with GLY 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ARG* 4.6 0.3 - - - -
101F GLN* 3.3 28.0 - - - +
134F THR* 3.0 16.3 + - - -
136F LYS* 3.4 30.7 + - - +
137F LEU 3.0 16.6 + - - -
140F THR* 1.3 75.2 - - - +
142F ARG* 1.3 59.0 + - - +
143F GLY 3.2 1.0 + - - -
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Residues in contact with ARG 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ARG* 4.3 7.6 + - - -
144A GLU* 4.1 10.2 - - - +
7903A GPP 4.4 3.6 - - - +
142B ARG* 3.4 46.9 + - - +
144B GLU* 5.0 1.1 - - - +
142C ARG* 3.3 36.7 - - - +
144C GLU* 3.9 1.8 + - - -
142D ARG* 4.6 0.6 - - - +
8903D GPP 2.4 42.8 + - - -
142E ARG* 4.0 3.0 - - - +
144E GLU* 5.2 0.8 + - - -
136F LYS 4.1 8.1 - - - +
137F LEU* 5.3 0.2 - - - -
138F GLY* 3.1 36.6 + - - +
139F PHE* 3.4 12.1 - - - +
140F THR 3.3 0.2 - - - -
141F GLY* 1.3 75.9 - - - +
143F GLY* 1.3 60.8 + - - +
144F GLU* 2.7 38.7 + - + -
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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