Contacts of the helix formed by residues 138 - 147 (chain E) in PDB entry 2DFS
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 TYR 138 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E ALA 6.2 0.2 - - - -
90E ARG* 4.2 25.4 + - + -
93E ASP* 2.6 33.7 + - + +
96E GLY* 4.8 3.5 - - - -
98E GLY* 3.1 41.1 + - - -
99E TYR 3.4 18.4 - - - -
100E ILE* 3.8 27.6 - - + -
136E VAL* 3.1 3.7 + - + -
137E ASN* 1.3 72.6 - - - +
139E GLU* 1.3 62.0 + - + +
141E PHE* 3.7 12.5 - - + +
142E VAL* 3.0 37.7 + - + +
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Residues in contact with GLU 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E GLY* 4.4 0.9 + - - +
137E ASN* 3.3 12.7 + - - +
138E TYR* 1.3 84.4 - - + +
140E GLU* 1.3 59.2 + - - +
142E VAL* 3.1 26.5 - - + +
143E GLN* 3.2 29.6 + - + +
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Residues in contact with GLU 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ASN* 2.9 38.0 + - + +
139E GLU* 1.3 76.6 - - - +
141E PHE* 1.3 58.2 + - - +
143E GLN* 3.1 19.9 + - + +
144E MET* 2.8 50.3 + - + +
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Residues in contact with PHE 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845A LEU* 5.1 6.3 - - + -
849A LEU* 4.9 4.3 - - + -
100E ILE* 5.8 1.8 - - + -
105E LEU* 3.6 43.1 - - + -
109E MET* 6.3 0.2 - - - -
124E MET* 3.8 31.2 - - + -
128E ALA* 3.9 29.8 - - + -
136E VAL* 3.8 20.2 - - + +
137E ASN 3.0 17.7 + - - +
138E TYR* 3.7 13.5 - - + +
140E GLU* 1.3 74.5 - - - +
142E VAL* 1.4 63.9 + - + +
144E MET* 3.5 11.2 + - + +
145E MET* 3.1 47.8 + - + +
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Residues in contact with VAL 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845A LEU* 4.3 22.9 - - + -
86E ARG 4.6 14.6 - - - +
87E GLU* 5.7 0.9 - - - -
88E ALA* 4.9 24.2 - - + +
138E TYR* 3.0 25.4 + - + +
139E GLU* 3.1 29.6 - - + +
141E PHE* 1.4 76.1 - - + +
143E GLN* 1.3 56.2 + - + +
145E MET* 3.4 9.6 - - + +
146E THR* 2.8 39.8 + - + +
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Residues in contact with GLN 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E ARG 5.6 2.2 - - - +
139E GLU* 3.2 38.2 + - + +
140E GLU* 3.1 21.7 + - + +
142E VAL* 1.3 77.8 - - + +
144E MET* 1.3 57.1 + - + +
146E THR* 3.2 7.1 + - - -
147E ALA* 2.9 29.6 + - - +
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Residues in contact with MET 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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852A TYR* 3.2 26.9 + - + +
124E MET* 6.4 0.4 - - + -
127E GLU 3.9 22.0 - - - +
128E ALA* 4.3 3.4 - - - -
129E ASP* 3.3 42.2 - - + +
140E GLU* 2.8 36.1 + - + +
141E PHE* 3.8 13.9 - - + +
142E VAL 3.5 0.2 - - - -
143E GLN* 1.3 71.2 - - - +
145E MET* 1.3 62.0 + - - +
147E ALA* 3.2 16.1 + - - +
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Residues in contact with MET 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845A LEU* 3.7 35.4 - - + +
848A LEU* 3.9 34.1 - - + +
849A LEU* 4.5 4.7 - - + -
852A TYR* 3.2 32.3 - - + +
855A ARG* 4.0 6.9 + - - -
124E MET* 3.7 20.8 - - + +
141E PHE* 3.1 54.1 + - + +
142E VAL* 3.4 15.3 - - - +
144E MET* 1.3 76.5 - - - +
146E THR* 1.3 67.1 + - + +
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Residues in contact with THR 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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848A LEU* 3.7 25.6 - - + -
855A ARG* 5.4 0.8 + - - +
85E ILE 3.3 26.2 - - - +
86E ARG* 3.8 25.4 + - - +
142E VAL* 2.8 23.6 + - + +
143E GLN* 3.2 11.1 + - - -
145E MET* 1.3 75.6 - - + +
147E ALA* 1.3 63.6 + - - +
148E LYS* 3.5 12.2 + - - +
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Residues in contact with ALA 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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852A TYR* 3.4 14.4 + - - +
855A ARG* 3.1 15.4 + - - -
143E GLN 2.9 19.0 + - - +
144E MET* 3.2 14.5 + - - +
146E THR* 1.3 76.5 - - - +
148E LYS* 1.3 63.0 + - - +
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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