Contacts of the helix formed by residues 45 - 54 (chain F) in PDB entry 3J41
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 GLU 45 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29F THR* 4.6 3.1 + - - +
30F LYS* 2.7 39.6 + - - -
43F PRO 3.8 2.1 + - - +
44F THR* 1.3 70.9 - - - +
46F ALA* 1.3 69.5 + - - +
48F LEU* 3.0 36.2 + - + +
49F GLN* 4.1 0.5 + - - +
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Residues in contact with ALA 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D LEU* 4.3 31.2 - - + -
224D PHE* 6.1 2.7 - - + -
44F THR* 3.6 5.1 - - - -
45F GLU* 1.3 79.7 - - + +
47F GLU* 1.3 57.0 + - + +
49F GLN* 2.8 34.4 + - - +
50F ASP* 3.3 7.9 - - - +
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Residues in contact with GLU 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D PHE* 5.6 0.9 - - - +
222D LEU* 3.7 19.3 + - - +
223D LEU* 4.1 21.1 - - + +
226D ARG* 4.7 1.4 - - + +
229D SER* 2.6 35.8 + - - -
230D VAL* 4.3 15.3 - - + +
233D ARG* 2.8 44.6 + - - +
44F THR* 2.7 31.6 + - - +
45F GLU 3.2 1.0 + - - -
46F ALA* 1.3 71.7 - - + +
48F LEU* 1.3 56.2 + - - +
50F ASP* 3.4 20.9 - - - +
51F MET* 3.5 15.9 + - - +
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Residues in contact with LEU 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D ARG* 3.5 20.6 - - - +
29F THR* 3.3 41.5 - - + +
30F LYS* 5.5 0.7 - - - -
32F LEU* 3.9 32.1 - - + +
33F GLY* 4.0 14.8 - - - +
36F MET* 6.0 0.7 - - + -
43F PRO* 5.1 8.7 - - + -
44F THR 4.4 2.0 - - - +
45F GLU* 3.0 31.8 + - + +
46F ALA 2.9 0.6 + - - -
47F GLU* 1.3 76.5 - - - +
49F GLN* 1.3 63.7 + - - +
51F MET* 3.2 21.9 - - + +
52F ILE* 3.5 17.0 - - + +
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Residues in contact with GLN 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F THR* 3.6 21.2 + - + +
45F GLU 4.1 0.4 + - - -
46F ALA* 2.8 14.0 + - - +
48F LEU* 1.3 74.8 - - - +
50F ASP* 1.3 60.5 + - - +
52F ILE* 3.2 3.4 + - - +
53F ASN* 2.9 68.1 + - - +
59F GLY 3.6 5.3 + - - -
60F ASN 4.0 2.7 + - - +
61F GLY* 3.6 18.2 - - - +
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Residues in contact with ASP 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D LEU* 4.9 3.1 - - - +
224D PHE* 5.2 5.7 - - - -
226D ARG* 3.0 36.5 - - + +
230D VAL* 3.7 24.2 - - + -
46F ALA* 3.3 18.4 + - - +
47F GLU* 3.4 14.1 - - - +
48F LEU 3.5 0.2 - - - -
49F GLN* 1.3 75.2 - - - +
51F MET* 1.3 61.1 + - - +
52F ILE 3.2 0.2 + - - -
53F ASN* 3.5 3.3 + - - +
54F GLU* 3.1 29.5 + - - +
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Residues in contact with MET 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C LYS* 4.0 5.9 + - - -
230D VAL* 3.3 22.5 - - + +
233D ARG* 3.4 28.7 - - + +
234D LEU* 3.4 50.2 - - + +
237D LEU* 4.5 15.3 - - + -
32F LEU* 4.6 6.7 - - + -
47F GLU 3.5 12.9 + - - +
48F LEU* 3.2 31.4 - - + +
50F ASP* 1.3 77.4 - - - +
52F ILE* 1.3 66.1 + - + +
54F GLU* 3.8 18.2 - - - +
55F VAL 4.9 0.2 + - - -
71F MET* 4.0 12.0 - - - +
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Residues in contact with ILE 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D LEU* 6.2 1.3 - - + -
27F ILE* 5.8 2.7 - - + +
28F THR 5.3 1.1 - - - -
29F THR* 4.2 21.5 - - + +
32F LEU* 4.7 23.3 - - + -
48F LEU 3.5 19.3 - - - +
49F GLN* 3.2 4.6 + - - +
51F MET* 1.3 86.8 - - + +
53F ASN* 1.3 58.2 + - - +
54F GLU 3.2 1.1 - - - -
55F VAL* 2.8 23.7 + - - +
56F ASP* 2.8 31.9 + - - +
61F GLY* 4.3 9.9 - - - +
63F ILE* 3.7 27.8 - - + -
71F MET* 4.1 18.3 - - + +
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Residues in contact with ASN 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F GLN* 2.9 47.8 + - - +
50F ASP* 4.3 3.1 - - - +
52F ILE* 1.3 69.8 - - - +
54F GLU* 1.3 53.8 + - - +
55F VAL 3.1 4.0 - - - -
56F ASP* 3.1 24.5 + - - +
59F GLY* 3.0 32.0 + - - +
61F GLY* 3.8 1.0 - - - +
77F LYS* 2.9 27.5 + - - -
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Residues in contact with GLU 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C LYS* 2.6 41.9 + - - +
241C ARG 5.6 0.5 - - - +
227D LEU* 4.8 5.0 - - - +
230D VAL* 3.4 27.6 - - - +
231D SER* 5.1 4.1 + - - -
234D LEU* 5.3 1.4 - - - +
50F ASP* 3.1 21.6 + - - +
51F MET* 3.8 11.5 - - - +
52F ILE 3.2 0.2 + - - -
53F ASN* 1.3 73.9 - - - +
55F VAL* 1.3 61.1 + - - +
75F LYS* 4.8 3.1 + - - -
76F MET* 4.8 11.1 - - - +
77F LYS* 4.1 5.7 + - - -
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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