Contacts of the helix formed by residues 45 - 51 (chain J) in PDB entry 5AN9
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 LYS 45 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35J LYS* 4.0 39.5 - - + +
38J GLY* 3.9 22.3 - - - -
39J TRP* 3.9 14.6 - - + +
43J VAL* 3.2 28.4 + - - +
44J GLU* 1.3 73.8 + - - +
46J ASP* 1.3 88.2 + - - +
49J GLU* 3.2 35.3 - - + +
50J VAL* 4.2 12.3 - - + +
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Residues in contact with ASP 46 (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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25F GLY 5.1 1.7 - - - +
26F VAL 4.8 1.4 - - - +
27F PRO* 3.6 37.6 - - + +
28F ASP* 4.7 5.7 + - - +
39J TRP* 3.4 20.2 - - - -
44J GLU* 3.9 3.8 - - - +
45J LYS* 1.3 88.4 - - - +
47J LEU* 1.3 61.9 + - - +
48J ASP* 3.5 20.0 + - + +
50J VAL* 3.5 10.6 + - - +
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Residues in contact with LEU 47 (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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39J TRP* 3.5 31.4 - - + -
46J ASP* 1.3 73.2 - - - +
48J ASP* 1.3 63.4 + - - +
49J GLU 3.3 0.2 - - - -
50J VAL* 3.9 10.8 - - + -
51J LEU* 3.4 30.6 + - + +
54J HIS* 3.3 17.8 + - + -
81J THR* 4.8 17.7 - - + +
85J LYS* 4.1 42.6 - - + +
88J LEU* 4.9 2.2 - - + -
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Residues in contact with ASP 48 (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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25F GLY 4.0 14.2 - - - +
27F PRO* 4.6 7.2 - - + +
101F LYS* 4.1 16.6 + - - -
121F LYS* 5.1 10.7 - - + +
122F PRO* 3.5 22.0 - - - +
123F MET* 4.4 18.8 - - + -
46J ASP* 3.2 13.6 - - + +
47J LEU* 1.3 79.0 - - - +
49J GLU* 1.3 58.3 + - - +
51J LEU 3.2 16.3 - - - +
54J HIS* 3.5 23.9 + - + -
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Residues in contact with GLU 49 (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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123F MET* 4.2 23.7 - - + +
35J LYS* 3.2 43.5 + - + +
45J LYS* 3.2 36.8 + - + +
46J ASP 3.7 1.4 + - - -
47J LEU 3.3 0.4 - - - -
48J ASP* 1.3 77.2 - - + +
50J VAL* 1.3 65.8 + - - +
51J LEU 3.3 3.6 + - - +
52J GLN* 3.6 10.4 + - - -
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Residues in contact with VAL 50 (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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31J CYS* 3.3 21.8 - - - +
32J TYR 3.7 6.8 + - - -
35J LYS* 3.7 39.1 - - + +
36J VAL 4.2 2.0 - - - +
39J TRP* 3.9 17.9 - - + -
45J LYS* 4.2 6.6 - - + +
46J ASP 3.5 16.4 + - - +
47J LEU* 3.9 13.0 - - + -
49J GLU* 1.3 80.3 - - - +
51J LEU* 1.3 67.0 + - + +
88J LEU* 3.7 38.8 - - + -
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Residues in contact with LEU 51 (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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101F LYS* 5.3 2.3 - - - -
29J ILE* 4.2 13.7 - - + -
30J ALA 3.8 2.2 - - - -
31J CYS* 3.6 22.4 - - - -
47J LEU* 3.4 34.4 + - + +
48J ASP 3.2 19.1 - - - +
49J GLU 3.3 3.6 - - - +
50J VAL* 1.3 85.2 - - + +
52J GLN* 1.3 63.7 + - - +
53J THR 3.7 8.3 - - - +
54J HIS* 3.6 30.6 + - + +
81J THR* 4.9 7.4 - - + +
84J CYS* 3.9 27.6 - - + +
88J LEU* 4.6 7.6 - - + -
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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