Contacts of the strand formed by residues 66 - 69 (chain Q) in PDB entry 2D2I
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 66 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40Q ALA* 3.4 3.5 - - - +
63Q ASP* 2.9 48.3 + - - +
65Q ASN* 1.3 81.2 - - - +
67Q ILE* 1.3 71.7 + - - +
68Q THR* 4.5 2.9 + - - -
73Q THR* 3.7 24.5 - - - +
74Q MET 3.4 10.5 - - - -
75Q LYS* 4.4 4.3 - - - -
76Q ILE* 3.8 4.6 - - - +
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Residues in contact with ILE 67 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10Q PHE* 4.9 5.2 - - + -
34Q ILE* 5.2 4.7 - - + -
40Q ALA 3.6 11.7 - - - +
43Q ALA* 3.2 36.8 - - + -
44Q ALA* 3.6 13.7 - - + +
47Q LEU* 4.7 8.5 - - + -
60Q ILE* 5.3 0.4 - - + -
61Q SER 3.5 8.3 - - - +
62Q TYR* 4.1 8.1 - - + +
66Q SER* 1.3 83.5 - - - +
68Q THR* 1.3 65.2 + - - +
69Q VAL* 4.1 20.6 - - + -
72Q LYS 3.8 0.9 - - - +
73Q THR* 3.4 0.5 - - - -
74Q MET* 2.7 44.2 + - + +
76Q ILE* 3.4 19.1 - - + -
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Residues in contact with THR 68 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Q ASP 3.3 3.7 - - - +
60Q ILE* 3.4 2.3 - - - +
61Q SER* 2.7 56.6 + - - +
62Q TYR* 4.7 0.4 - - - +
66Q SER* 4.5 3.3 + - - -
67Q ILE* 1.3 76.2 - - - +
69Q VAL* 1.3 68.3 + - - +
70Q ASN 4.7 0.2 - - - +
71Q GLY* 3.8 24.2 - - - +
72Q LYS 3.4 7.6 - - - +
73Q THR* 2.9 31.6 + - - +
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Residues in contact with VAL 69 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22Q PHE* 3.1 43.2 - - + -
47Q LEU* 3.6 27.8 - - + -
56Q PHE* 3.9 20.6 - - + -
58Q ALA* 4.0 14.8 - - + -
59Q ASP 3.3 2.9 - - - -
60Q ILE* 4.3 8.3 - - + -
67Q ILE* 4.1 4.7 - - + -
68Q THR* 1.3 79.6 - - - +
70Q ASN* 1.3 73.2 + - - +
72Q LYS 3.0 14.1 + - - -
74Q MET* 3.7 15.3 - - + -
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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