Contacts of the helix formed by residues 154 - 158 (chain A) in PDB entry 2FJX
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 ALA 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A LEU* 4.0 9.1 + - + +
152A LYS 3.1 4.9 + - - -
153A ASP* 1.3 75.3 - - - +
155A PHE* 1.3 68.8 - - + +
157A CYS* 3.0 19.5 + - - +
190A GLN* 5.9 0.4 - - - +
199A PHE* 3.2 44.3 - - + -
224A ASP* 3.6 30.7 + - + +
252A TYR* 5.9 0.2 - - - -
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Residues in contact with PHE 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ASP 3.4 0.8 - - - -
154A ALA* 1.3 79.6 - - + +
156A PHE* 1.3 62.9 + - + +
158A LEU* 2.9 15.1 + - - +
188A LEU* 3.2 37.5 - - + +
189A PRO 4.1 6.1 - - - -
190A GLN* 3.1 40.4 - - - +
191A GLY 5.6 0.9 - - - -
195A SER* 3.5 34.5 - - - -
196A PRO* 3.6 27.1 - - + -
199A PHE* 3.8 25.1 - + + -
223A VAL* 3.9 17.5 - - + -
224A ASP* 5.8 1.8 - - - -
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Residues in contact with PHE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A MET* 4.4 5.6 - - + -
40A GLY 4.9 0.7 - - - -
81A LEU* 4.0 18.4 - - + -
86A ILE* 3.9 30.7 - - + -
153A ASP* 3.2 36.2 + - + +
154A ALA 3.2 0.8 - - - -
155A PHE* 1.3 76.8 - - + +
157A CYS* 1.3 52.3 + - - +
158A LEU 3.2 0.4 - - - -
185A TRP* 3.6 35.2 - + - -
187A ARG* 2.6 50.6 + - + +
188A LEU 3.5 17.0 - - - -
189A PRO* 4.5 7.2 - - + -
190A GLN* 4.6 22.9 - - + -
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Residues in contact with CYS 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A MET* 5.4 1.3 - - - -
40A GLY* 3.7 28.7 - - - -
41A LEU* 3.5 12.3 - - - +
42A ALA* 2.7 33.9 + - - +
151A LEU* 6.6 0.2 - - - -
152A LYS 4.4 8.3 - - - -
153A ASP 3.5 13.9 + - - -
154A ALA* 3.0 14.9 + - - +
156A PHE* 1.3 76.9 - - - +
158A LEU* 1.3 59.7 - - - +
159A ARG 3.7 2.1 + - - -
187A ARG* 4.1 2.4 + - - +
251A GLY 3.9 6.3 - - - -
252A TYR* 4.2 28.0 - - + -
253A ARG* 4.8 2.5 - - - -
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA* 3.6 24.9 - - + -
45A GLN* 4.1 11.4 - - + -
48A LEU* 4.1 21.5 - - + -
155A PHE 2.9 8.6 + - - +
157A CYS* 1.3 77.8 - - - +
159A ARG* 1.3 62.6 + - - +
187A ARG* 3.2 6.1 - - - -
188A LEU* 2.9 43.8 + - + +
198A LEU 4.0 2.5 - - - +
199A PHE* 3.7 46.0 - - + -
202A ALA* 3.8 23.6 - - + -
252A TYR* 4.2 8.3 - - + +
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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