Contacts of the helix formed by residues 147 - 155 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132I TYR* 3.3 18.6 - - - +
133I GLN* 3.0 42.4 - - - -
134I LEU* 3.7 10.3 - - - +
135I ARG* 5.1 1.3 - - - +
146J PRO* 1.3 75.7 - - - +
148J GLU* 1.3 62.7 + - - +
149J ALA* 3.4 4.9 + - - +
150J GLU* 2.9 29.9 + - - +
151J ILE* 3.3 16.3 + - - +
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Residues in contact with GLU 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135I ARG* 3.7 18.4 + - - +
146J PRO 3.7 1.8 + - - -
147J SER* 1.3 69.6 - - - +
149J ALA* 1.3 66.0 + - - +
151J ILE* 3.2 25.5 + - - +
152J SER* 3.1 27.2 + - - -
218J GLN* 5.3 2.4 + - - -
260J ASP* 2.8 39.8 - - - +
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Residues in contact with ALA 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I TYR* 3.9 6.7 - - + -
133I GLN 5.9 0.4 - - - +
209I PHE* 5.5 2.0 - - + -
211I PRO* 3.7 37.7 - - + -
147J SER* 3.4 7.8 + - - +
148J GLU* 1.3 77.2 - - - +
150J GLU* 1.3 61.8 + - - +
152J SER* 3.2 12.4 - - - +
153J HIS* 3.1 21.8 - - - +
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Residues in contact with GLU 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I TYR* 3.4 36.5 - - + -
134I LEU* 4.3 1.6 - - - +
146I LEU* 4.0 7.4 - - - +
146J PRO* 4.2 1.0 - - - +
147J SER* 2.9 29.7 + - - +
149J ALA* 1.3 74.6 - - - +
151J ILE* 1.3 64.7 + - - +
154J THR* 2.7 34.6 + - - +
155J GLN 3.8 0.2 + - - -
156J LYS 3.0 15.3 - - - +
157J ALA* 4.0 1.3 - - - -
158J THR* 2.8 57.2 + - - +
211J ARG* 3.4 9.7 + - - +
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Residues in contact with ILE 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146J PRO* 3.8 10.3 - - + +
147J SER 3.3 18.2 - - - +
148J GLU* 3.2 25.8 + - - +
150J GLU* 1.3 76.9 - - - +
152J SER* 1.3 58.7 + - - +
153J HIS 2.9 7.3 + - - -
155J GLN* 3.1 25.1 + - - +
156J LYS 4.3 4.7 - - - +
157J ALA* 3.7 31.6 - - + +
214J ALA* 3.9 17.3 - - + -
217J TRP* 3.8 13.9 - - + +
218J GLN* 3.3 31.0 - - + +
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Residues in contact with SER 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209I PHE* 5.8 0.3 - - - -
148J GLU* 3.1 17.8 + - - -
149J ALA* 3.2 7.3 - - - +
151J ILE* 1.3 75.7 - - - +
153J HIS* 1.3 62.4 + - - +
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Residues in contact with HIS 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I ASP* 3.4 35.5 + - + +
130I ALA* 4.8 1.8 - - + -
132I TYR* 2.8 24.9 + - - +
209I PHE* 3.5 36.6 - + + -
213I CD 2.8 23.5 - - - -
149J ALA 3.1 14.1 - - - +
150J GLU 4.2 0.2 - - - +
151J ILE 2.9 5.3 + - - -
152J SER* 1.3 75.3 - - - +
154J THR* 1.3 65.7 + - + +
155J GLN* 3.7 2.6 - - - +
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Residues in contact with THR 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I ASP* 4.9 7.6 - - + +
132I TYR* 3.4 16.6 - - - +
149I ASP* 3.4 24.0 - - - +
179I PHE* 6.5 0.2 - - + -
150J GLU* 2.7 28.0 + - - +
153J HIS* 1.3 88.1 - - + +
155J GLN* 1.3 72.9 + - - +
156J LYS* 3.4 26.5 + - - +
211J ARG* 3.6 17.5 + - - -
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Residues in contact with GLN 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151J ILE 3.1 19.0 + - - +
153J HIS 5.5 2.0 - - - +
154J THR* 1.3 80.8 + - - +
156J LYS* 1.3 61.4 + - - +
213J SER* 4.1 4.0 - - - -
214J ALA* 3.2 27.9 + - + +
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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