Contacts of the helix formed by residues 139 - 144 (chain F) in PDB entry 3F0D
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 139 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E VAL* 3.6 30.1 - - + -
12E HIS* 4.0 12.3 - - - +
13E GLN* 3.9 26.0 - - + +
141E TYR* 3.9 38.6 - - + -
146E GLU* 3.8 21.5 - - + +
147E GLY* 4.3 2.7 - - - -
136F ASN* 2.9 34.1 + - - +
137F GLU* 3.2 6.9 - - + +
138F LYS* 1.3 77.2 - - - +
140F GLY* 1.3 63.9 + - - +
142F LEU 4.0 0.5 + - - -
143F GLY* 2.9 12.9 + - - -
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Residues in contact with GLY 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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141E TYR* 3.6 25.8 - - - +
138F LYS 4.1 1.4 + - - -
139F LEU* 1.3 72.0 - - - +
141F TYR* 1.3 67.4 + - - -
142F LEU 3.2 0.4 - - - -
143F GLY 3.0 1.0 + - - -
144F ARG* 2.9 42.8 + - - +
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Residues in contact with TYR 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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136D ASN* 3.1 20.1 + - - -
139D LEU* 3.8 36.6 - - + -
140D GLY* 3.5 35.7 - - - +
141D TYR* 6.2 3.1 - + - -
142D LEU* 5.6 1.2 - - - +
141E TYR* 6.2 3.4 - + - -
9F TYR* 3.8 12.5 + - - -
11F VAL* 4.1 4.7 - - + -
140F GLY* 1.3 72.5 - - - -
142F LEU* 1.3 99.6 + - + +
144F ARG* 3.4 17.5 + - - +
145F GLY 3.3 3.5 + - - -
146F GLU* 2.9 48.4 + - - +
147F GLY 5.0 1.8 - - - -
149F GLU* 4.6 5.6 + - - -
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Residues in contact with LEU 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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9E TYR* 5.1 1.6 - - - +
141E TYR* 5.7 0.7 - - - +
11F VAL* 4.6 0.9 - - + -
101F ILE* 3.8 28.3 - - + +
103F GLN* 3.5 17.9 + - - +
136F ASN* 3.8 26.9 - - + +
139F LEU 4.0 0.2 + - - -
140F GLY 3.2 0.8 - - - -
141F TYR* 1.3 101.0 - - + +
143F GLY* 1.3 63.2 + - - +
145F GLY* 3.0 13.2 + - - -
147F GLY 3.4 30.6 - - - +
148F ILE* 4.0 1.1 - - - -
149F GLU* 3.5 44.4 - - + +
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Residues in contact with GLY 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F GLN* 3.4 32.8 - - - +
136F ASN* 4.1 1.5 - - - +
138F LYS* 3.7 17.5 - - - +
139F LEU 2.9 33.4 + - - -
140F GLY 3.0 1.7 + - - -
142F LEU* 1.3 78.7 - - - +
144F ARG* 1.3 57.6 + - - +
145F GLY 3.3 0.7 - - - -
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Residues in contact with ARG 144 (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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140D GLY* 6.0 1.8 - - - -
144D ARG* 5.7 5.3 - - - +
31F ARG* 5.5 0.2 + - - -
138F LYS 5.5 2.9 - - - +
140F GLY* 2.9 36.8 + - - +
141F TYR* 3.5 16.2 - - - +
142F LEU 3.2 0.2 - - - -
143F GLY* 1.3 75.7 - - - +
145F GLY* 1.3 60.6 + - - +
146F GLU* 2.9 47.5 + - - +
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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