Contacts of the helix formed by residues 78 - 86 (chain D) in PDB entry 1PY1
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 GLY 78 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77D CYS* 1.3 76.1 - - - +
79D LYS* 1.3 55.8 + - - -
80D ARG* 2.7 21.8 + - - +
81D PHE 3.2 3.0 + - - +
82D HIS* 3.1 30.2 + - - -
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Residues in contact with LYS 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D GLY* 1.3 69.7 - - - -
80D ARG* 1.3 64.5 + - - +
82D HIS* 3.8 11.2 + - + -
83D ASP* 3.1 54.3 + - - +
128D GLU* 5.2 11.1 + - - +
129D GLU* 4.3 9.5 + - - +
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Residues in contact with ARG 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 5.7 1.1 - - + -
38D ASN* 2.6 49.7 + - + +
39D GLU 4.2 4.0 + - - -
40D ASP 3.8 10.9 + - - -
41D PHE* 4.5 12.3 + - - +
44D PRO* 3.7 24.2 - - + +
77D CYS* 5.7 1.6 - - + -
78D GLY 2.7 10.6 + - - +
79D LYS* 1.3 79.2 - - - +
81D PHE* 1.3 64.5 + - + +
83D ASP* 3.4 7.3 + - - +
84D GLU* 3.6 12.1 + - - +
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Residues in contact with PHE 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 3.9 29.2 - - + -
44D PRO* 4.7 6.4 - - + +
47D ALA* 4.4 6.5 - - + -
48D THR* 3.8 25.8 - - + -
51D LEU* 3.9 25.6 - - + -
70D LEU* 4.0 8.5 - - + -
73D CYS* 3.4 38.1 - - + -
74D MET* 3.7 25.4 - - - -
77D CYS* 3.8 18.6 - - + -
78D GLY 3.2 1.2 + - - -
80D ARG* 1.3 75.8 - - - +
82D HIS* 1.3 68.0 + - + +
84D GLU* 2.7 19.2 + - + +
85D VAL* 2.9 27.4 + - + +
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Residues in contact with HIS 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D MET* 2.5 50.1 + - + +
75D LYS 5.5 0.7 - - - -
77D CYS 3.6 16.9 + - - -
78D GLY* 3.1 21.1 + - - +
79D LYS* 3.8 9.5 + - + +
81D PHE* 1.3 79.3 - - + +
83D ASP* 1.3 56.8 + - - +
85D VAL* 3.5 2.3 + - - +
86D GLY* 2.9 22.9 + - - -
126D LEU* 3.6 43.5 - - + +
129D GLU* 3.2 20.9 - - - +
132D ILE* 5.1 0.2 - - - +
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Residues in contact with ASP 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D LYS* 3.1 54.6 + - - +
80D ARG 3.7 4.3 - - - +
82D HIS* 1.3 76.5 - - - +
84D GLU* 1.3 63.9 + - - +
86D GLY 3.1 9.9 + - - -
87D LYS* 3.3 26.7 + - - +
129D GLU* 3.0 22.8 - - - +
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Residues in contact with GLU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D PRO* 3.6 14.8 - - + +
45D PRO* 3.5 49.2 - - + +
48D THR* 3.5 22.5 + - + +
80D ARG 3.6 3.9 + - - +
81D PHE* 2.7 15.6 + - - +
83D ASP* 1.3 73.2 - - - +
85D VAL* 1.3 64.0 + - - +
87D LYS* 3.2 48.0 + - - +
89D ARG* 5.2 9.2 - - - +
90D PHE* 3.7 12.0 - - - +
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D THR* 4.2 2.0 - - + -
70D LEU* 4.0 6.7 - - + -
74D MET* 3.5 35.7 - - + -
81D PHE* 2.9 38.1 + - + +
82D HIS 4.0 2.0 - - - +
84D GLU* 1.3 76.8 - - - +
86D GLY* 1.3 58.6 + - - +
87D LYS 3.0 5.1 + - - +
90D PHE* 3.6 28.8 - - + -
91D LEU* 3.2 20.5 - - + +
122D TRP* 3.9 27.1 - - + -
132D ILE* 4.4 1.7 - - + +
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Residues in contact with GLY 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D HIS 2.9 16.2 + - - -
83D ASP 3.1 8.0 + - - -
84D GLU 3.1 1.0 - - - -
85D VAL* 1.3 76.5 - - - +
87D LYS* 1.3 58.2 + - - +
91D LEU* 4.1 3.8 - - - -
129D GLU* 3.9 13.5 - - - +
131D LYS* 3.1 29.8 - - - +
132D ILE* 3.8 21.3 - - - +
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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