Contacts of the helix formed by residues 63 - 69 (chain E) in PDB entry 2Y1T
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 63 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ARG* 3.5 21.9 + - - +
62E SER* 1.3 74.3 - - - +
64E THR* 1.3 62.5 + - - +
65E TYR 3.4 1.1 - - - -
66E LYS* 3.5 26.0 + - - +
67E ASN* 3.0 39.0 + - - +
143E DUD 2.6 31.7 + - - -
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Residues in contact with THR 64 (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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60E PRO* 4.4 6.1 - - + -
61E ARG* 3.4 22.1 + - - +
62E SER 3.1 2.4 - - - -
63E SER* 1.3 75.7 + - - +
65E TYR* 1.3 62.3 + - - +
68E PHE* 2.8 43.3 + - + +
69E GLY 3.6 0.5 + - - -
70E VAL* 3.7 28.8 + - + +
92E PHE* 4.6 8.5 - - + -
107E ARG 4.6 1.2 + - - -
108E ILE* 2.7 38.3 + - + +
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Residues in contact with TYR 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E PRO* 6.0 0.2 - - - +
61E ARG 4.7 0.6 + - - -
62E SER 4.0 7.2 + - - +
63E SER 3.4 0.4 - - - -
64E THR* 1.3 80.3 - - - +
66E LYS* 1.3 63.4 + - - +
69E GLY* 2.8 44.9 + - - +
70E VAL 3.6 23.0 + - - +
71E ILE* 4.6 0.7 - - + -
97E LEU* 3.9 22.8 - - + +
98E ARG* 4.2 5.2 + - - +
39F PHE* 3.6 43.5 - + + +
73F THR* 3.8 33.7 - - + +
74F ASN* 6.1 0.9 - - + +
95F TYR* 3.2 28.5 - + - -
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Residues in contact with LYS 66 (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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62E SER 4.9 1.2 + - - +
63E SER* 3.5 24.7 + - - +
64E THR 3.4 0.4 - - - -
65E TYR* 1.3 84.0 - - + +
67E ASN* 1.3 80.6 + - - +
98E ARG* 3.6 9.0 + - - -
143E DUD 5.4 4.9 + - - -
39F PHE* 5.6 9.1 - - + -
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Residues in contact with ASN 67 (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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61E ARG* 5.0 4.9 - - - +
63E SER* 3.0 36.8 + - - +
66E LYS* 1.3 96.2 + - - +
68E PHE* 1.4 93.9 + - + +
98E ARG* 3.2 10.1 + - - -
100E THR* 4.9 0.3 + - - -
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Residues in contact with PHE 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E THR* 2.8 25.9 + - + +
67E ASN* 1.4 109.5 - - + +
69E GLY* 1.3 61.6 + - - +
70E VAL* 3.4 14.3 + - + +
98E ARG* 3.4 6.5 - - - +
100E THR* 2.5 36.1 + - - +
101E LYS 3.7 22.4 - - - -
102E ILE* 3.9 16.4 - - + -
106E ASP* 3.2 37.9 - - + -
107E ARG 4.6 8.3 - - - -
108E ILE* 3.8 23.3 - - + -
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Residues in contact with GLY 69 (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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64E THR 3.6 0.4 + - - -
65E TYR* 2.8 40.8 + - - -
68E PHE* 1.3 72.8 - - - +
70E VAL* 1.4 52.8 + - - +
96E ALA* 3.7 1.4 - - - +
97E LEU* 2.7 37.6 + - - +
98E ARG* 3.4 22.7 + - - +
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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