Contacts of the helix formed by residues 58 - 69 (chain p) in PDB entry 6AH0
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 58 (chain p).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7p HIS* 5.0 2.0 - - - +
36p HIS 4.9 2.0 + - - +
56p PHE* 4.0 10.6 - - - +
57p LYS* 1.3 76.0 - - - +
59p LEU* 1.3 62.8 + - - +
60p GLY 3.4 3.1 - - - +
61p SER* 3.4 13.7 + - - +
62p SER* 3.5 8.0 + - - -
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Residues in contact with LEU 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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6p ASN 4.9 4.1 - - - +
7p HIS* 4.7 16.2 - - - +
57p LYS 4.0 1.4 + - - -
58p GLU* 1.3 67.6 - - - +
60p GLY* 1.3 66.1 + - - +
61p SER 3.1 1.8 - - - -
62p SER* 3.0 11.9 + - - +
63p THR* 3.1 10.4 + - - -
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Residues in contact with GLY 60 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58p GLU* 3.4 1.0 - - - +
59p LEU* 1.3 75.8 - - - +
61p SER* 1.3 56.4 + - - +
63p THR* 3.3 1.7 + - - -
64p ASN* 3.0 25.8 + - - -
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Residues in contact with SER 61 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34p PHE* 3.7 28.9 - - - +
35p GLY* 5.3 2.7 - - - -
56p PHE* 6.4 0.2 - - - -
58p GLU* 3.4 11.0 + - - +
59p LEU 3.1 1.0 - - - -
60p GLY* 1.3 77.4 - - - +
62p SER* 1.3 59.5 + - - +
64p ASN* 3.4 1.1 + - - +
65p ALA* 3.0 21.1 + - - -
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Residues in contact with SER 62 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6p ASN 4.6 12.8 - - - -
7p HIS 4.7 9.9 - - - -
8p THR 6.4 0.7 - - - -
56p PHE* 5.9 1.9 - - - +
58p GLU 3.5 8.0 + - - -
59p LEU 3.0 6.9 + - - -
61p SER* 1.3 76.2 - - - +
63p THR* 1.3 61.5 + - - +
65p ALA* 3.4 1.3 + - - +
66p LEU* 2.9 21.3 + - - -
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Residues in contact with THR 63 (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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6p ASN 5.2 0.8 + - - -
59p LEU 3.1 12.3 + - - -
60p GLY* 3.8 3.4 - - - -
62p SER* 1.3 74.4 - - - +
64p ASN* 1.3 63.7 + - - +
66p LEU* 3.4 2.2 + - - +
67p ARG* 3.2 19.1 + - - -
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Residues in contact with ASN 64 (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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60p GLY 3.0 16.4 + - - -
61p SER* 3.9 1.3 - - - +
63p THR* 1.3 72.3 - - - +
65p ALA* 1.3 65.5 + - - +
67p ARG* 3.5 0.7 + - - +
68p GLN* 2.9 22.3 + - - -
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Residues in contact with ALA 65 (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 PHE* 5.9 4.1 - - - +
61p SER 3.0 15.4 + - - -
62p SER* 3.8 3.1 - - - +
64p ASN* 1.3 75.6 - - - +
66p LEU* 1.3 62.2 + - - +
68p GLN* 5.3 0.2 - - - +
69p LEU* 2.9 26.0 + - - -
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Residues in contact with LEU 66 (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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62p SER 2.9 14.9 + - - -
63p THR* 3.8 3.8 - - - +
65p ALA* 1.3 76.7 - - - +
67p ARG* 1.3 59.3 + - - +
69p LEU 4.3 0.4 - - - -
70p GLN* 3.5 18.5 + - - -
81p ILE* 5.7 10.4 - - - +
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Residues in contact with ARG 67 (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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63p THR 3.2 13.4 + - - -
64p ASN 4.0 1.6 - - - -
66p LEU* 1.3 76.6 - - - +
68p GLN* 1.3 60.6 + - - +
69p LEU 3.7 0.2 + - - -
70p GLN* 3.9 5.4 + - - +
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Residues in contact with GLN 68 (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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64p ASN 2.9 16.5 + - - -
67p ARG* 1.3 77.3 - - - +
69p LEU* 1.3 58.4 + - - +
70p GLN 3.5 1.3 + - - +
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Residues in contact with LEU 69 (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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65p ALA* 2.9 14.4 + - - +
66p LEU 4.3 1.6 - - - -
68p GLN* 1.3 75.7 - - - +
70p GLN* 1.3 65.4 + - - +
71p GLY 3.2 1.0 + - - -
72p PHE* 3.2 18.8 + - - +
79p MET* 4.4 3.1 - - - +
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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