Contacts of the helix formed by residues 145 - 153 (chain D) in PDB entry 2FL0
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 GLY 145 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D ILE 2.8 22.8 + - - -
142D ASP 4.4 1.9 + - - -
143D LYS 3.8 0.6 - - - -
144D ILE* 1.3 74.3 - - - +
146D LEU* 1.3 61.2 + - - -
147D GLU 3.3 2.9 - - - -
148D ASN 3.2 3.3 + - - -
149D TYR* 2.8 30.8 + - - +
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Residues in contact with LEU 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LYS 5.2 2.2 - - - +
82D HIS* 6.1 2.2 - - - +
83D THR* 5.1 5.2 - - - -
84D LYS* 4.9 17.9 - - + +
141D ILE* 3.8 39.3 + - + +
145D GLY* 1.3 69.4 - - - +
147D GLU* 1.3 55.0 + - + +
149D TYR* 3.6 1.6 - - + +
150D LEU* 2.7 66.0 + - + +
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Residues in contact with GLU 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ASP 5.6 1.3 - - - +
143B LYS 3.9 13.5 - - - +
144B ILE* 2.9 44.1 - - - +
145B GLY* 3.8 6.7 + - - -
147B GLU* 5.6 2.6 - - - +
148B ASN* 4.0 10.3 + - - +
145D GLY 3.3 1.2 - - - -
146D LEU* 1.3 79.5 - - + +
148D ASN* 1.3 57.6 + - - +
151D GLN* 2.8 29.3 + - - +
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Residues in contact with ASN 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ASN* 3.6 11.8 + - - -
1607B FE2 2.8 26.6 - - - -
144D ILE* 3.3 39.3 + - + +
145D GLY* 3.2 3.0 + - - +
147D GLU* 1.3 74.7 - - - +
149D TYR* 1.3 68.3 + - - +
151D GLN* 3.1 9.2 + - - +
152D SER* 2.9 25.7 + - - -
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Residues in contact with TYR 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LEU* 3.5 26.1 - - + +
83D THR* 4.4 4.7 - - + -
87D LEU* 4.3 2.5 - - + +
137D GLN* 2.6 54.6 + - + +
140D LEU* 4.2 19.7 - - + -
141D ILE* 3.5 38.1 - - + -
144D ILE* 3.6 15.4 - - + +
145D GLY 2.8 21.2 + - - +
146D LEU* 3.6 3.1 - - + +
148D ASN* 1.3 71.5 - - - +
150D LEU* 1.3 73.8 + - + +
152D SER* 2.8 19.7 + - - -
153D GLN* 3.1 43.2 + - + +
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Residues in contact with LEU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LYS* 3.5 41.1 - - + +
144B ILE* 3.4 15.7 - - + -
37D LEU* 3.5 34.7 - - + +
40D LEU* 4.9 2.2 - - + -
83D THR* 3.5 37.2 - - + +
146D LEU* 2.7 41.2 + - + +
149D TYR* 1.3 80.5 - - + +
151D GLN* 1.3 65.8 + - - +
153D GLN* 3.0 11.3 + - - -
154D MET* 3.5 2.8 + - - +
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Residues in contact with GLN 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ILE* 3.5 19.9 - - + +
148B ASN* 2.8 48.7 + - - +
151B GLN* 3.2 18.9 + - - +
152B SER* 3.0 19.8 + - - +
1607B FE2 3.1 14.0 - - - -
147D GLU 2.8 18.6 + - - +
148D ASN* 3.1 12.1 + - - +
150D LEU* 1.3 71.9 - - - +
152D SER* 1.3 61.5 + - - +
153D GLN 3.1 4.7 + - - -
154D MET* 3.2 22.2 + - - +
155D ASP 4.7 0.5 + - - -
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Residues in contact with SER 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D LYS* 3.9 19.9 + - - -
144D ILE* 4.5 6.9 - - - +
148D ASN 2.9 12.3 + - - -
149D TYR* 2.8 23.2 + - - -
151D GLN* 1.3 78.9 - - - +
153D GLN* 1.3 69.5 + - - +
154D MET 3.3 1.0 + - - -
155D ASP 4.1 3.4 - - - +
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Residues in contact with GLN 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 3.3 11.0 - - + -
38D GLU 3.3 5.5 + - - -
39D LYS* 3.0 39.0 + - + +
40D LEU* 3.2 47.1 + - + +
133D TRP* 5.8 0.2 - - - -
137D GLN* 4.5 4.3 + - - +
149D TYR* 3.1 52.2 + - + +
150D LEU* 3.0 10.5 + - - +
152D SER* 1.3 88.3 + - - +
154D MET* 1.3 59.8 + - - +
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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