Contacts of the helix formed by residues 83 - 93 (chain E) in PDB entry 2PPB
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 ASP 83 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81E PRO 3.3 1.0 - - - -
82E GLU* 1.3 76.0 - - + +
84E ARG* 1.3 77.2 + - + +
85E LEU 3.0 6.5 + - - -
86E GLN* 3.1 38.0 + - - +
87E LYS* 3.7 19.8 + - - +
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Residues in contact with ARG 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1495D ILE* 5.0 8.9 - - + +
1498D ALA* 2.9 47.5 + - - +
1499D ARG* 5.2 7.6 - - - +
80E VAL* 5.2 0.9 - - + -
81E PRO* 3.3 29.3 + - + +
83E ASP* 1.3 86.0 - - + +
85E LEU* 1.3 56.7 + - - +
87E LYS* 3.6 19.3 - - + +
88E GLU* 3.1 35.1 + - + +
91E ARG* 5.7 2.6 - - - +
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Residues in contact with LEU 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1485D GLN* 5.6 10.8 - - + -
1486D VAL 4.3 18.2 - - - +
1487D VAL* 5.2 4.5 - - + -
1491D THR* 4.6 17.2 - - + +
1495D ILE* 4.5 4.6 - - - +
29E GLN* 5.9 6.7 - - - +
33E HIS* 6.0 2.7 - - - +
80E VAL* 3.9 35.4 - - + +
81E PRO 3.4 9.3 + - - +
82E GLU* 4.3 10.1 - - - +
83E ASP 3.0 1.0 + - - -
84E ARG* 1.3 72.8 - - - +
86E GLN* 1.3 66.9 + - + +
87E LYS 3.1 1.3 - - - -
88E GLU* 3.4 2.1 + - - +
89E MET* 2.9 39.1 + - + +
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Residues in contact with GLN 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E HIS* 4.1 12.6 - - + -
82E GLU 4.1 4.1 + - - +
83E ASP* 3.1 36.7 + - - +
85E LEU* 1.3 85.4 - - + +
87E LYS* 1.3 62.5 + - + +
89E MET* 3.9 6.3 - - - +
90E GLU* 2.6 45.1 + - - +
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Residues in contact with LYS 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E ASP* 3.7 29.3 + - - +
84E ARG* 3.5 19.3 + - - +
85E LEU 3.1 0.2 - - - -
86E GLN* 1.3 85.9 - - + +
88E GLU* 1.3 65.0 + - + +
90E GLU* 3.2 11.4 + - - +
91E ARG* 3.1 50.6 + - - +
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Residues in contact with GLU 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1491D THR* 4.9 2.4 - - + +
1494D ALA* 2.5 50.5 - - + +
1495D ILE* 3.5 26.7 - - + -
1497D GLU 4.7 0.2 - - - -
1498D ALA* 2.9 20.4 - - + +
84E ARG* 3.1 16.7 + - + +
85E LEU 4.0 0.7 - - - +
87E LYS* 1.3 78.7 - - + +
89E MET* 1.3 62.3 + - - +
91E ARG* 2.9 42.2 + - - +
92E LEU* 3.4 31.6 + - - +
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Residues in contact with MET 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1488D ASP* 2.9 24.7 - - - +
1491D THR* 3.2 29.4 - - + +
26E ARG* 3.6 5.8 - - - +
29E GLN* 3.2 27.1 - - - +
33E HIS* 3.4 37.8 + - + +
37E ASN* 4.0 9.2 - - - +
85E LEU* 2.9 23.8 + - + +
86E GLN 4.0 0.7 - - - +
87E LYS 3.1 0.2 - - - -
88E GLU* 1.3 79.1 - - - +
90E GLU* 1.3 60.8 + - - +
92E LEU* 3.4 1.4 + - - -
93E TYR* 3.1 43.7 + - + +
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Residues in contact with GLU 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E HIS* 4.0 18.6 - - + +
86E GLN* 2.6 33.4 + - - +
87E LYS* 3.2 11.6 + - - +
89E MET* 1.3 77.6 - - - +
91E ARG* 1.3 63.2 + - + +
92E LEU 3.4 0.3 + - - -
93E TYR 3.8 15.7 + - - +
94E PRO* 5.0 1.0 - - - +
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Residues in contact with ARG 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1498D ALA* 4.7 7.7 - - - +
1501D GLU* 5.5 4.9 + - - -
84E ARG* 5.7 2.0 - - - +
87E LYS* 3.1 43.1 + - - +
88E GLU* 2.9 49.4 + - - +
89E MET 3.3 0.2 - - - -
90E GLU* 1.3 80.3 - - + +
92E LEU* 1.3 68.3 + - + +
94E PRO* 4.9 3.3 - - - +
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Residues in contact with LEU 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1490D LYS* 4.4 10.3 - - + +
1491D THR* 5.2 4.3 - - + +
1494D ALA* 3.4 33.4 - - + -
88E GLU* 3.4 16.7 + - - +
89E MET* 3.4 3.4 + - - +
90E GLU 3.3 0.2 - - - -
91E ARG* 1.3 85.2 - - + +
93E TYR* 1.3 78.7 + - + +
94E PRO* 3.4 12.1 - - - +
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Residues in contact with TYR 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1488D ASP* 4.5 5.6 + - - +
1490D LYS* 3.4 42.3 - - + +
1491D THR* 4.1 6.9 + - - -
33E HIS* 3.2 17.0 - - - +
36E LYS* 4.9 6.3 - - + -
37E ASN* 2.9 60.0 - - + +
38E THR 5.1 3.7 + - - -
39E VAL* 5.7 0.5 - - - +
89E MET* 3.1 43.6 + - + +
90E GLU* 3.8 11.0 + - - +
91E ARG 3.8 0.8 - - - -
92E LEU* 1.3 94.8 - - + +
94E PRO* 1.4 60.0 - - - +
95E VAL* 4.1 1.6 - - - -
96E GLU 5.0 1.0 + - - -
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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