Contacts of the helix formed by residues 75 - 81 (chain B) in PDB entry 2PI8
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 ARG 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B GLN* 3.4 49.7 + - + +
73B ASP* 2.9 11.8 + - - +
74B THR* 1.3 91.2 - - + +
76B ASN* 1.3 63.8 + - - +
77B MSE 3.2 7.6 + - - -
78B ARG* 4.1 11.6 + - - +
30D VAL* 4.8 17.9 - - - +
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Residues in contact with ASN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ALA* 6.2 1.3 - - + -
73B ASP* 3.0 44.3 + - + -
75B ARG* 1.3 77.9 - - - +
77B MSE 1.3 58.7 + - - +
78B ARG* 3.1 7.5 + - - -
79B GLN* 3.2 43.3 + - - +
80B PHE* 3.4 18.9 - - + -
30D VAL* 6.2 0.4 - - - +
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Residues in contact with MSE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ASN 4.2 6.7 - - - +
26B GLN* 5.7 0.2 - - - -
27B PRO* 3.8 14.1 - - + -
67B TRP* 3.4 46.4 - - + +
73B ASP 3.2 2.8 + - - -
74B THR 3.4 24.5 - - - +
75B ARG 3.2 1.3 - - - +
76B ASN* 1.3 77.6 - - - +
78B ARG* 1.3 65.4 + - + +
79B GLN 3.2 0.4 - - - -
80B PHE* 3.2 20.3 + - - +
82B ILE* 3.3 62.6 + - + +
84B ALA* 3.7 28.9 - - + +
272B ILE* 5.6 0.4 - - - -
333B LEU* 4.1 7.2 - - + -
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Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 5.9 2.1 - - - +
25B ASN* 3.6 54.0 - - + +
26B GLN* 5.0 3.8 - - + +
75B ARG 4.2 13.2 - - - +
76B ASN 3.1 0.8 - - - -
77B MSE 1.3 78.1 - - + +
79B GLN* 1.3 60.9 + - + +
80B PHE 3.1 0.4 - - - -
81B GLY* 3.0 24.5 + - - -
82B ILE 2.9 24.8 + - - -
83B ASP* 3.2 37.7 + - - +
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Residues in contact with GLN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ASN* 3.2 43.6 + - - +
77B MSE 3.2 0.4 - - - -
78B ARG* 1.3 80.1 - - + +
80B PHE* 1.3 72.2 + - + +
81B GLY 3.2 1.0 + - - -
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Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ALA* 4.2 16.0 - - + +
66B GLU* 3.6 40.6 - - + -
67B TRP* 3.9 24.5 - + + -
70B ALA* 3.6 26.0 - - + -
76B ASN* 3.4 25.6 - - + -
77B MSE 3.6 14.1 - - - +
78B ARG 3.1 0.6 - - - -
79B GLN* 1.3 90.5 - - + +
81B GLY* 1.3 62.0 + - - +
82B ILE* 3.2 16.0 + - + +
287D GLN* 5.3 2.9 - - - -
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Residues in contact with GLY 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ARG* 3.0 17.8 + - - -
79B GLN 3.2 2.2 + - - -
80B PHE* 1.3 78.6 - - - +
82B ILE* 1.3 58.8 + - - +
83B ASP* 2.8 21.3 + - - +
335B THR* 4.2 4.5 - - - +
336B ALA* 4.2 10.8 + - - +
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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