Contacts of the helix formed by residues 74 - 80 (chain A) in PDB entry 4PJO
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 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ALA* 4.1 7.6 - - + -
16A HIS* 3.9 24.5 - - + -
17A ILE 3.6 22.7 - - - +
18A VAL* 4.4 1.1 - - + -
73A LEU* 1.4 91.5 - - + +
75A ASP* 1.3 67.6 + - - +
76A MET 4.5 0.9 - - - +
77A LEU* 3.0 34.8 + - + +
69B LEU* 3.7 2.0 - - - +
13K PHE* 4.1 28.3 - - + +
14K ALA 4.4 8.7 - - - +
15K PRO* 5.3 2.9 - - + -
16K ARG 5.9 0.9 - - - +
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Residues in contact with ASP 75 (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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72A ILE* 6.0 0.2 - - - +
73A LEU 4.1 2.3 - - - +
74A PRO* 1.3 69.9 - - - +
76A MET* 1.3 63.5 + - - +
77A LEU 2.9 1.7 + - - -
78A LYS* 3.0 41.4 + - + +
44B ASP* 6.0 0.7 - - - -
68B GLY 4.1 0.2 - - - -
69B LEU* 3.3 28.1 + - + +
12K LEU 5.6 0.2 + - - -
14K ALA 4.7 4.9 + - - -
16K ARG* 2.4 49.0 + - - +
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Residues in contact with MET 76 (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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74A PRO* 3.1 1.0 + - - +
75A ASP* 1.3 78.3 - - - +
77A LEU* 1.3 55.5 - - - +
79A ASN* 2.9 47.3 + - - +
12K LEU* 3.5 44.1 + - + +
13K PHE* 3.5 41.0 - - + -
38L TYR* 4.8 8.3 - - + -
41L TRP* 3.5 43.1 - - + -
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Residues in contact with LEU 77 (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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9A VAL* 4.1 13.3 - - + +
12A GLU* 3.5 44.2 - - + +
13A ALA* 3.5 30.7 - - + +
73A LEU* 3.7 15.3 - - + -
74A PRO* 3.0 24.1 + - + +
75A ASP 2.9 0.8 + - - -
76A MET* 1.3 76.5 - - - +
78A LYS* 1.3 56.6 + - - +
79A ASN 3.0 0.2 - - - -
80A ALA* 2.8 33.5 + - + +
83A LEU* 3.6 8.2 - - - +
69B LEU* 3.8 9.0 - - + -
13K PHE* 4.0 21.1 - - + -
38L TYR* 5.2 0.7 - - - +
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Residues in contact with LYS 78 (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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75A ASP* 3.0 35.4 + - + +
77A LEU* 1.3 75.5 - - - +
79A ASN* 1.3 78.4 + - - +
80A ALA 3.3 1.7 + - - -
83A LEU* 3.5 26.3 - - + +
84A LYS* 4.1 8.7 + - - -
32B LYS* 5.1 6.8 + - + -
43B CYS* 3.6 33.7 - - - -
44B ASP* 3.7 24.4 + - - +
69B LEU* 4.2 6.8 - - + +
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Residues in contact with ASN 79 (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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76A MET* 2.9 41.4 + - - +
78A LYS* 1.3 98.8 + - - +
80A ALA* 1.3 65.0 + - - +
84A LYS* 3.9 18.4 - - - +
37L TYR* 3.3 22.7 + - - -
38L TYR* 4.4 4.1 - - + -
41L TRP* 3.6 39.1 - - + +
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Residues in contact with ALA 80 (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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9A VAL* 5.7 0.4 - - + -
12A GLU* 4.8 2.2 - - + -
76A MET 4.1 0.4 + - - -
77A LEU* 2.8 21.9 + - + +
78A LYS 3.3 1.0 - - - -
79A ASN* 1.3 82.7 - - - +
81A PRO* 1.4 71.3 - - + +
82A MET* 2.9 38.3 + - + -
83A LEU* 3.4 11.1 + - + +
84A LYS* 3.5 11.1 - - - +
37L TYR* 3.9 0.2 - - - -
38L TYR* 3.9 14.6 - - - +
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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