Contacts of the strand formed by residues 94 - 101 (chain E) in PDB entry 1A4Y
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 TYR 94 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E ASP* 3.3 20.1 - - - +
26E CYS* 3.7 19.5 - - + -
27E GLU* 3.1 21.2 + - - +
30E MET* 3.7 41.7 - - + +
35E LEU 4.0 2.9 + - - -
36E THR* 4.7 1.3 - - - -
39E CYS* 3.8 1.7 - - - +
40E LYS 2.7 41.1 + - - -
41E ASP 4.1 1.6 - - - -
81E CYS* 4.0 6.3 - - + -
82E LYS* 3.1 33.4 - - - +
83E LEU* 3.2 22.7 - - + -
92E CYS* 3.6 31.2 - - + +
93E GLN* 1.3 71.5 - - - +
95E ARG* 1.3 75.9 + - - +
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Residues in contact with ARG 95 (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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150D TYR* 3.2 15.0 + - - -
178D ASN* 4.5 3.8 + - - -
207D SER* 5.6 1.0 + - - -
23E ASP* 3.3 20.7 + - - +
27E GLU* 3.4 7.1 + - - -
80E THR 3.6 2.3 - - - +
82E LYS* 2.8 38.5 + - + +
84E HIS* 3.2 48.0 + - + +
93E GLN* 3.2 26.5 + - - -
94E TYR* 1.3 116.6 + - - +
96E ALA* 1.3 65.2 + - - +
97E THR* 4.4 3.3 + - - +
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Residues in contact with ALA 96 (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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21E ARG 3.7 9.0 - - - +
22E ASP* 3.1 43.1 - - - +
23E ASP* 2.9 10.3 + - - +
26E CYS* 3.5 16.1 - - - -
79E THR* 4.3 2.0 - - + -
80E THR 3.5 5.2 - - - -
94E TYR 3.9 1.2 + - - -
95E ARG* 1.3 74.4 - - - +
97E THR* 1.3 65.2 + - - +
98E ALA 4.3 0.2 - - - -
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Residues in contact with THR 97 (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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78E VAL* 4.0 1.2 - - - +
79E THR* 3.5 2.9 - - - +
80E THR* 2.8 49.7 + - - +
82E LYS* 6.0 0.7 - - - +
95E ARG* 4.4 4.0 + - - +
96E ALA* 1.3 77.1 + - - +
98E ALA* 1.3 70.1 + - - +
120E PHE 6.2 0.4 - - - +
123E PRO* 4.6 32.2 - - + +
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Residues in contact with ALA 98 (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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21E ARG* 4.0 39.6 + - + +
78E VAL 3.4 9.2 - - - +
79E THR* 4.3 2.4 - - - +
96E ALA 4.3 0.2 - - - -
97E THR* 1.3 84.8 - - - +
99E GLY* 1.3 59.0 + - - +
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Residues in contact with GLY 99 (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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21E ARG* 3.4 7.0 + - - +
77E GLN* 3.6 4.6 - - - +
78E VAL* 2.9 37.2 + - - +
98E ALA* 1.3 78.0 - - - +
100E PHE* 1.3 61.1 + - - -
101E ARG* 4.0 7.9 - - - -
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Residues in contact with PHE 100 (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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75E SER* 3.1 46.1 + - - -
76E PHE 3.2 20.2 - - - -
77E GLN* 3.6 30.1 - - + +
99E GLY* 1.3 74.3 - - - +
101E ARG* 1.3 65.7 - - - +
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Residues in contact with ARG 101 (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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75E SER* 3.6 9.6 - - - -
76E PHE* 2.7 38.7 + - - +
78E VAL* 4.3 15.8 - - + +
99E GLY* 4.0 4.5 - - - -
100E PHE* 1.3 86.1 - - - +
102E ASN* 1.3 73.2 + - - +
103E VAL* 4.0 2.7 - - - +
119E ILE* 2.7 41.2 + - - +
120E PHE* 3.8 23.0 - - + +
122E ARG 4.1 9.7 + - - -
123E PRO 3.6 19.2 + - - -
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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