Contacts of the helix formed by residues 53 - 62 (chain P) in PDB entry 4ADV
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 ASP 53 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35P ARG 5.3 0.3 - - - +
36P VAL* 4.0 8.7 - - + -
37P GLY* 2.7 33.1 + - - -
51P ARG* 2.8 33.5 + - - +
52P LEU* 1.3 80.3 - - - +
54P LEU* 1.3 66.5 + - - +
55P ASP* 2.7 7.3 + - + -
56P ARG* 2.9 22.2 + - + +
57P ILE 3.3 3.6 + - - -
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Residues in contact with LEU 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52P LEU* 3.2 8.1 - - + +
53P ASP* 1.3 72.8 - - - +
55P ASP* 1.3 67.3 + - - +
57P ILE* 3.1 29.5 + - + +
58P ALA* 3.2 7.8 + - - +
75P ILE* 3.9 29.8 - - + -
79P ASN 4.7 4.0 - - - +
80P LYS* 3.2 40.8 - - + +
81P ALA 5.3 0.7 - - - +
82P ALA 5.6 1.6 - - - +
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Residues in contact with ASP 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53P ASP 2.7 5.7 + - - +
54P LEU* 1.3 81.5 - - - +
56P ARG* 1.3 61.8 + - - +
57P ILE 3.3 0.2 + - - -
58P ALA* 3.4 17.9 + - - +
59P HIS* 4.1 2.6 + - - +
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Residues in contact with ARG 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34P GLU* 2.9 53.8 + - - +
35P ARG 5.2 0.7 - - - -
36P VAL* 4.7 4.3 - - + +
53P ASP* 2.9 21.0 + - + +
55P ASP* 1.3 73.2 - - - +
57P ILE* 1.3 65.9 - - - +
58P ALA 3.4 0.3 + - - -
59P HIS* 3.4 20.8 + - + +
60P TRP* 3.9 22.9 + - - +
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Residues in contact with ILE 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P ILE* 3.9 20.2 - - + -
19P VAL* 5.9 0.7 - - + -
21P VAL* 5.3 2.2 - - + -
36P VAL* 3.4 29.8 - - + -
52P LEU* 3.1 28.7 - - + +
53P ASP 3.3 0.8 + - - +
54P LEU* 3.1 21.2 + - + +
56P ARG* 1.3 79.4 - - - +
58P ALA* 1.3 64.0 + - - +
59P HIS 3.2 0.5 + - - -
60P TRP* 3.3 6.3 + - + +
61P VAL* 3.0 44.0 + - + +
71P VAL* 5.9 0.9 - - + -
75P ILE* 4.3 27.4 - - + -
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Residues in contact with ALA 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54P LEU 3.2 6.6 + - - +
55P ASP* 3.5 13.9 - - - +
56P ARG 3.3 0.4 - - - -
57P ILE* 1.3 80.1 - - - +
59P HIS* 1.3 55.2 + - - +
61P VAL* 3.0 11.0 - - - +
62P GLY* 2.7 34.5 + - - -
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Residues in contact with HIS 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A A 6.2 1.0 - - - -
55P ASP 4.1 2.1 + - - +
56P ARG* 3.4 17.3 + - + +
57P ILE 3.3 0.6 - - - -
58P ALA* 1.3 78.2 - - - +
60P TRP* 1.3 80.7 + + + +
63P GLN* 2.5 57.7 + - + +
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Residues in contact with TRP 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A A 3.5 22.7 - - - -
229A U 3.2 32.1 - - - -
2P VAL* 4.9 5.4 - - + -
4P ILE* 5.3 1.3 - - + -
21P VAL* 3.5 34.9 - - + +
33P ILE* 3.5 26.2 - - + -
34P GLU* 3.5 25.3 - - + +
36P VAL* 5.9 0.7 - - + -
56P ARG* 3.9 26.5 - - - +
57P ILE* 3.3 7.4 + - + +
59P HIS* 1.3 96.3 - + + +
61P VAL* 1.3 57.2 + - + +
63P GLN* 2.7 28.2 + - + +
64P GLY 3.2 0.7 + - - -
65P ALA* 2.9 30.3 + - + +
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Residues in contact with VAL 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A U 6.1 0.2 - - - +
4P ILE* 3.6 28.0 - - + -
57P ILE* 3.0 42.5 + - + +
58P ALA* 3.0 20.4 - - - +
60P TRP* 1.3 74.9 - - - +
62P GLY* 1.3 60.5 + - - +
63P GLN 3.4 0.7 + - - -
64P GLY* 3.5 8.7 + - - -
65P ALA* 3.3 17.4 - - - +
67P ILE* 5.1 9.0 - - + -
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Residues in contact with GLY 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A U 4.6 8.9 + - - -
58P ALA 2.7 22.6 + - - -
59P HIS 3.7 0.2 - - - -
61P VAL* 1.3 74.2 - - - +
63P GLN* 1.3 70.1 + - - +
64P GLY 3.4 2.0 - - - -
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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