Contacts of the helix formed by residues 240 - 250 (chain A) in PDB entry 2FNJ
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 PRO 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A PRO 4.3 2.9 - - - +
239A LEU* 1.3 94.2 - - + +
241A LEU* 1.3 67.9 + - - +
242A MET* 4.4 10.8 - - + +
243A ASP* 2.7 44.2 + - - +
244A LEU* 3.1 10.0 + - - +
76C TYR* 3.2 7.6 - - - +
80C LYS* 6.0 0.2 - - - -
112C CYS* 3.4 15.3 - - - +
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Residues in contact with LEU 241 (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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240A PRO* 1.3 70.0 - - - +
242A MET* 1.3 62.7 + - - +
244A LEU* 3.1 5.5 + - + +
245A CYS* 2.9 42.2 + - - -
73C VAL* 4.3 13.0 - - + -
76C TYR* 3.3 34.6 + - + -
93C PHE* 3.8 30.3 - - + -
95C ILE* 4.3 4.0 - - + -
103C LEU* 3.8 25.1 - - + -
107C ALA* 3.8 16.2 - - + -
112C CYS* 2.7 32.1 + - - +
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Residues in contact with MET 242 (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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240A PRO* 4.8 9.2 - - + -
241A LEU* 1.3 76.7 - - - +
243A ASP* 1.3 64.3 + - - +
245A CYS* 3.4 3.2 + - - +
246A ARG* 3.1 37.0 + - - +
104C LEU* 4.2 3.6 - - - +
107C ALA* 3.6 19.3 - - - +
108C ASN* 3.1 40.2 - - - +
111C ASP* 3.5 18.6 - - - +
112C CYS* 3.1 41.3 + - - +
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Residues in contact with ASP 243 (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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43A ILE* 3.8 31.6 - - + +
47A MET* 5.1 14.1 - - - +
239A LEU* 5.1 0.8 - - + +
240A PRO* 2.7 37.1 + - + +
242A MET* 1.3 74.9 - - - +
244A LEU* 1.3 66.5 + - - +
246A ARG* 2.8 37.8 + - - +
247A ARG* 3.1 23.6 + - - +
250A ARG* 4.6 1.0 + - - -
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Residues in contact with LEU 244 (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 ALA* 5.9 4.5 - - + -
43A ILE* 3.5 24.2 - - + -
239A LEU* 3.7 33.0 - - + +
240A PRO 3.1 13.1 + - - +
241A LEU* 3.1 8.4 + - - +
243A ASP* 1.3 76.3 - - - +
245A CYS* 1.3 60.7 + - - +
247A ARG* 3.3 7.9 + - + +
248A THR* 3.1 24.6 + - - -
76C TYR* 4.0 14.4 - - + -
79C TYR* 4.8 4.9 - - + +
93C PHE* 3.8 35.4 - - + +
95C ILE* 3.8 13.9 - - + +
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Residues in contact with CYS 245 (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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241A LEU* 2.9 29.3 + - - +
242A MET 3.7 4.5 - - - +
244A LEU* 1.3 74.7 - - - +
246A ARG* 1.3 66.0 + - - +
248A THR* 3.1 5.7 + - - +
249A ILE* 3.0 28.3 + - - +
95C ILE* 4.0 7.9 - - - -
100C ALA* 3.9 5.1 - - - +
103C LEU* 3.5 46.2 - - - -
104C LEU* 3.7 26.2 - - + -
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Residues in contact with ARG 246 (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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43A ILE* 5.7 0.8 + - - +
46A ASP* 3.0 32.7 + - - +
47A MET* 5.5 4.8 - - - +
242A MET* 3.1 26.6 + - - +
243A ASP* 2.8 36.3 + - - +
245A CYS* 1.3 77.4 - - - +
247A ARG* 1.3 57.0 + - - +
249A ILE* 3.4 10.2 + - - +
250A ARG* 2.9 43.7 + - - +
104C LEU* 4.1 22.9 - - + -
108C ASN* 5.4 2.8 - - - +
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Residues in contact with ARG 247 (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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37A LYS 4.8 4.6 + - - -
39A ALA* 3.5 34.8 - - - +
42A ASP* 3.7 22.8 - - + +
43A ILE* 3.8 18.0 - - + +
243A ASP 3.1 14.7 + - - +
244A LEU* 3.4 12.7 + - - +
245A CYS 3.1 0.2 - - - -
246A ARG* 1.3 74.9 - - - +
248A THR* 1.3 71.4 + - - +
250A ARG* 3.2 34.9 + - - +
251A GLN* 2.7 53.2 + - - +
92C GLU* 3.8 24.4 + - - +
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Residues in contact with THR 248 (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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244A LEU 3.1 10.9 + - - -
245A CYS 3.1 8.2 + - - -
247A ARG* 1.3 83.2 + - - +
249A ILE* 1.3 62.0 + - - +
251A GLN* 3.3 34.1 + - - +
95C ILE* 3.6 38.8 + - + +
97C PRO* 4.3 16.9 - - + +
100C ALA* 3.9 20.4 - - + -
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Residues in contact with ILE 249 (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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245A CYS 3.0 17.2 + - - +
246A ARG* 3.6 8.7 - - - +
248A THR* 1.3 73.6 - - - +
250A ARG* 1.3 61.0 + - + +
251A GLN 2.8 16.7 + - - -
100C ALA* 3.8 29.4 - - + +
101C LEU* 4.1 19.1 - - + +
104C LEU* 3.7 30.1 - - + -
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Residues in contact with ARG 250 (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 ASP* 2.6 39.3 + - - +
43A ILE* 4.0 5.1 - - - +
46A ASP* 3.1 47.2 + - - +
243A ASP 4.6 0.8 + - - -
246A ARG* 2.9 32.5 + - - +
247A ARG* 3.2 30.4 + - - +
249A ILE* 1.3 76.2 - - + +
251A GLN* 1.3 59.5 + - - +
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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