Contacts of the helix formed by residues 67 - 71 (chain w) in PDB entry 5JPQ
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 VAL 67 (chain w).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19o LYS* 2.5 23.1 + - - +
41w ARG 5.2 1.6 - - - -
42w VAL* 3.3 30.1 - - + -
62w LEU 3.9 5.2 - - - +
63w ALA* 3.7 3.4 - - - -
64w ALA 2.6 24.9 - - - +
65w GLN 2.6 8.9 + - - -
66w ASP* 1.3 77.1 - - - +
68w ALA* 1.3 62.6 + - - +
69w ALA 2.8 2.6 + - - -
70w LYS* 3.2 9.9 + - - +
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Residues in contact with ALA 68 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28w VAL* 5.2 14.6 - - + +
30w VAL* 6.4 1.1 - - + -
40w ALA* 5.7 10.4 - - + +
41w ARG 5.4 6.3 - - - +
42w VAL* 4.6 3.1 - - + +
64w ALA* 2.5 28.3 + - + +
67w VAL* 1.3 72.3 - - + +
69w ALA* 1.3 54.4 + - - -
70w LYS* 2.9 6.1 - - - -
71w CYS* 2.9 30.5 + - - +
105w LEU* 5.5 5.2 - - + -
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Residues in contact with ALA 69 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19o LYS* 4.0 4.8 - - - +
64w ALA* 2.4 35.4 + - + +
65w GLN* 3.5 15.5 - - - +
67w VAL 2.8 0.2 + - - -
68w ALA* 1.3 61.5 - - - +
70w LYS* 1.3 54.8 + - - +
71w CYS* 3.1 7.6 + - - -
72w LYS* 3.6 19.7 - - - +
73w GLU 4.3 0.2 + - - -
108w SER* 4.7 20.0 - - - -
109w GLY 5.9 1.8 - - - +
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Residues in contact with LYS 70 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19o LYS* 3.4 31.8 - - + +
21o ARG* 2.7 4.2 + - - -
67w VAL 3.2 8.5 + - - +
68w ALA 2.9 1.6 + - - -
69w ALA* 1.3 75.6 - - - +
71w CYS* 1.3 55.3 + - - +
73w GLU* 2.2 42.5 - - + +
74w VAL* 3.6 1.2 + - - +
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Residues in contact with CYS 71 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21o ARG* 1.9 31.8 + - - +
30w VAL* 5.9 4.3 - - + -
39w ILE 5.6 3.4 - - - +
40w ALA* 5.5 10.1 - - + -
68w ALA* 2.9 16.9 + - + +
69w ALA* 4.8 0.7 - - - -
70w LYS* 1.3 74.1 - - - +
72w LYS* 1.3 51.2 + - - +
74w VAL 3.4 0.2 + - - -
76w ILE* 2.9 41.9 + - + +
109w GLY 5.1 7.2 - - - +
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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