Contacts of the helix formed by residues 147 - 155 (chain E) in PDB entry 3FFC
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 147 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D TYR* 3.1 32.5 - - - +
133D GLN 3.2 29.4 - - - -
134D LEU* 3.8 7.7 - - - +
135D ARG* 5.4 2.9 - - - +
145E GLU 3.7 1.6 + - - -
146E PRO* 1.3 73.2 - - - +
148E GLU* 1.3 62.9 + - - +
149E ALA* 3.8 4.9 + - - -
150E GLU* 3.1 23.1 + - - +
151E ILE* 3.2 17.9 - - - +
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Residues in contact with GLU 148 (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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135D ARG* 5.0 10.9 + - - +
146E PRO 3.7 5.5 + - - +
147E SER* 1.3 70.1 - - - +
149E ALA* 1.3 66.4 + - - +
151E ILE* 3.2 19.6 + - + +
152E SER* 3.1 25.6 + - - +
217E TRP* 5.4 0.9 + - - -
260E ASP* 2.9 46.4 - - - +
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Residues in contact with ALA 149 (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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132D TYR* 3.9 7.4 - - + -
209D PHE* 5.2 2.5 - - + -
211D PRO* 3.6 38.4 - - + -
147E SER* 3.2 5.1 - - - +
148E GLU* 1.3 78.6 - - - +
150E GLU* 1.3 62.6 + - - +
152E SER* 3.1 26.7 - - - +
153E HIS* 3.1 8.3 - - - +
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Residues in contact with GLU 150 (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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132D TYR* 3.6 33.3 - - + -
134D LEU* 5.0 1.1 - - - +
146D LEU* 3.6 13.3 - - - +
146E PRO* 3.6 14.9 - - - +
147E SER* 3.1 23.9 + - - +
148E GLU 3.3 0.2 - - - -
149E ALA* 1.3 72.1 - - - +
151E ILE* 1.3 68.0 + - + +
154E THR* 2.6 31.2 + - - +
155E GLN 3.8 0.2 + - - -
156E LYS 3.3 14.5 - - - +
157E ALA* 3.8 0.4 - - - -
158E THR* 2.5 54.3 + - - +
211E ARG* 4.0 9.1 + - - +
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Residues in contact with ILE 151 (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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146E PRO* 3.9 11.0 - - + +
147E SER 3.2 19.1 - - - +
148E GLU* 3.3 23.8 - - + +
150E GLU* 1.3 74.1 - - + +
152E SER* 1.3 61.4 + - - +
153E HIS 2.9 7.3 + - - -
155E GLN* 3.1 30.3 + - - +
156E LYS 4.3 5.6 - - - +
157E ALA* 3.7 30.7 - - + -
214E ALA* 4.1 17.0 - - + -
217E TRP* 4.0 12.6 - - + +
218E GLN* 3.2 33.7 - - + +
260E ASP* 5.6 0.2 - - - +
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Residues in contact with SER 152 (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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148E GLU* 3.1 16.2 + - - +
149E ALA* 3.1 7.8 - - - +
151E ILE* 1.3 75.4 - - - +
153E HIS* 1.3 63.7 + - - +
155E GLN* 4.3 8.1 - - - +
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Residues in contact with HIS 153 (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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128D ASP* 4.3 8.3 + - - +
130D ALA* 5.7 0.6 - - - +
132D TYR* 3.8 21.9 + + + +
209D PHE* 3.4 55.4 - + + +
149E ALA 3.1 13.9 - - - +
150E GLU 4.2 0.2 - - - +
151E ILE 2.9 4.8 + - - -
152E SER* 1.3 76.0 + - - +
154E THR* 1.3 71.7 + - + +
155E GLN* 3.7 8.0 + - - +
261E CD 2.7 27.3 - - - -
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Residues in contact with THR 154 (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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128D ASP* 3.4 26.5 - - - +
132D TYR* 3.7 18.1 + - - +
149D ASP* 3.5 19.7 - - - +
150E GLU* 2.6 32.8 + - - +
153E HIS* 1.3 78.6 - - + +
155E GLN* 1.3 71.1 + - - +
156E LYS* 3.4 33.0 + - - -
211E ARG* 4.2 2.9 + - - -
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Residues in contact with GLN 155 (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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151E ILE* 3.1 26.6 + - - +
152E SER* 4.3 5.5 - - - +
153E HIS* 4.0 12.8 + - - +
154E THR* 1.3 81.7 + - - +
156E LYS* 1.3 61.1 + - - +
213E SER* 4.3 2.8 - - - -
214E ALA* 3.2 31.2 + - + +
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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