Contacts of the helix formed by residues 82 - 89 (chain T) in PDB entry 2P8W
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 SER 82 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81T MET* 1.3 76.6 - - - +
83T ASP* 1.3 65.9 + - - +
84T GLU* 3.3 16.3 + - - +
85T ASP* 3.0 39.0 + - - +
86T VAL* 3.0 12.5 + - - +
96T ASN* 4.2 0.9 - - - +
223T ARG* 4.6 0.3 + - - -
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Residues in contact with ASP 83 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82T SER* 1.3 73.9 - - - +
84T GLU* 1.3 63.5 + - - +
86T VAL* 3.6 3.7 + - - +
87T LYS* 3.4 26.8 + - - +
96T ASN* 3.0 30.5 + - - +
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Residues in contact with GLU 84 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82T SER* 3.1 13.4 + - - +
83T ASP* 1.3 76.0 - - - +
85T ASP* 1.3 68.5 + - - +
87T LYS* 3.0 26.2 + - - +
88T GLU* 3.5 8.0 + - - +
223T ARG* 2.0 38.7 + - - +
227T THR* 3.3 9.7 + - - +
237T LYS* 1.6 54.4 + - - -
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Residues in contact with ASP 85 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81T MET* 3.9 26.9 - - + +
82T SER* 3.0 24.9 + - - +
84T GLU* 1.3 81.2 - - - +
86T VAL* 1.3 53.2 + - - +
88T GLU* 2.7 32.4 + - - +
89T ILE 3.6 2.9 + - - -
223T ARG* 2.2 59.5 + - - +
224T GLN* 6.2 0.2 - - - +
336T GLU* 5.5 4.8 - - - +
340T LEU* 3.6 14.2 - - + +
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Residues in contact with VAL 86 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81T MET* 3.7 19.3 - - + +
82T SER 3.0 13.1 + - - +
83T ASP* 3.9 5.6 - - - +
85T ASP* 1.3 76.3 - - - +
87T LYS* 1.3 61.7 + - + +
89T ILE* 3.4 24.2 + - + +
93T THR* 3.4 32.2 + - + -
95T GLY 3.9 5.4 - - - +
96T ASN* 3.5 32.8 - - - +
98T PHE* 4.2 7.6 - - + -
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Residues in contact with LYS 87 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83T ASP* 3.4 16.8 + - - +
84T GLU* 3.0 17.1 + - - +
86T VAL* 1.3 79.7 - - + +
88T GLU* 1.3 61.1 + - + +
89T ILE 3.5 5.4 + - - +
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Residues in contact with GLU 88 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84T GLU* 4.0 6.6 - - - +
85T ASP 2.7 12.0 + - - +
87T LYS* 1.3 77.7 - - + +
89T ILE* 1.3 61.7 + - - -
90T LYS* 3.1 15.1 + - - +
223T ARG* 1.9 56.5 + - - +
237T LYS* 5.2 0.5 - - - +
241T MET* 4.3 17.4 - - - +
340T LEU* 4.6 15.3 - - + +
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Residues in contact with ILE 89 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20T ARG* 4.1 9.6 - - - +
81T MET* 5.3 0.2 - - + -
86T VAL* 3.6 26.8 - - + +
87T LYS 3.3 6.9 - - - +
88T GLU* 1.3 73.6 - - - +
90T LYS* 1.3 60.8 + - - +
91T GLN* 2.8 36.9 + - + +
93T THR* 3.6 20.0 - - - +
98T PHE* 3.6 33.2 - - + -
339T VAL* 3.9 15.9 - - + +
340T LEU* 3.2 30.7 - - + +
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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