Contacts of the strand formed by residues 54 - 60 (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 TYR 54 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1E MET* 3.7 29.0 - - + +
50E LEU* 4.5 3.6 - - + +
51E PRO* 3.1 31.5 + - + +
52E GLU 3.7 13.5 - - - -
53E GLY* 1.3 81.7 - - - +
55E GLU* 1.3 62.5 + - - +
81E GLU* 3.5 24.4 + - - +
113E ILE* 3.8 27.6 - - + -
114E MET* 3.3 22.9 - - - -
115E LYS* 3.4 39.2 - - + +
116E LYS* 3.6 8.7 - - - +
118F PRO* 4.0 18.2 - - + +
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Residues in contact with GLU 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D GLY 4.6 2.3 - - - +
23D TRP* 3.0 35.2 + - - -
112D ARG* 3.0 21.7 + - - -
50E LEU* 3.9 5.8 - - - -
54E TYR* 1.3 74.4 - - - +
56E ALA* 1.3 60.6 + - - +
57E HIS* 2.8 30.1 + - + +
78E VAL* 4.2 5.0 - - + +
79E ILE 3.3 16.2 - - - +
80E ASP* 4.4 7.2 - - - +
113E ILE* 3.1 6.6 - - - +
114E MET 2.8 40.8 + - - +
116E LYS* 3.6 20.3 - - + +
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Residues in contact with ALA 56 (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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50E LEU* 3.5 15.4 - - + +
55E GLU* 1.3 75.7 - - - +
57E HIS* 1.3 65.0 + - - +
77E GLY 3.7 0.2 - - - +
78E VAL* 3.4 6.8 - - - +
79E ILE* 2.7 37.8 + - + -
90E TRP* 3.4 33.7 - - + -
111E PHE* 4.1 8.3 - - + -
112E ARG 3.2 9.9 - - - +
113E ILE* 4.2 0.9 - - + +
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Residues in contact with HIS 57 (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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23D TRP* 4.2 5.3 - + - -
112D ARG* 4.9 0.9 - - - -
114D MET* 5.0 4.9 - - + -
23E TRP* 3.5 16.6 - - + -
55E GLU* 2.8 33.9 + - + +
56E ALA* 1.3 80.9 - - - +
58E VAL* 1.3 63.4 + - - +
76E MET* 3.4 43.3 - - + +
77E GLY 3.3 2.7 - - - -
78E VAL* 4.1 7.6 - - + -
111E PHE* 3.0 24.9 - - - -
112E ARG* 2.8 19.4 + - + +
114E MET* 3.7 38.7 - - + +
57F HIS* 6.1 1.6 - - - -
76F MET* 5.9 0.8 - - - +
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Residues in contact with VAL 58 (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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26E LEU* 5.2 1.1 - - + -
44E LEU* 5.1 5.4 - - + -
57E HIS* 1.3 78.2 - - - +
59E VAL* 1.3 65.4 + - - +
72E GLN* 3.2 13.7 + - - +
76E MET* 3.3 4.9 - - - -
77E GLY* 2.9 44.2 + - - +
79E ILE* 4.3 13.7 - - + -
90E TRP* 3.9 32.1 - - + -
91E PHE 5.5 3.6 - - - +
92E PHE* 4.9 2.9 - - + -
109E CYS* 3.7 33.0 - - + -
110E GLN 3.4 7.4 - - - +
111E PHE* 4.0 3.6 - - + -
144E DUD 5.0 5.4 - - - +
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Residues in contact with VAL 59 (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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23E TRP* 3.7 24.7 - - + -
57E HIS 4.2 0.4 - - - -
58E VAL* 1.3 78.2 - - - +
60E PRO* 1.3 86.1 - - + +
72E GLN* 3.3 5.6 - - - -
75E SER 4.1 4.3 - - - +
76E MET* 3.6 30.3 - - + -
109E CYS* 3.3 3.8 - - - +
110E GLN* 2.9 39.5 + - + +
74F ASN 4.5 0.4 - - - +
76F MET* 4.1 32.5 - - + +
78F VAL* 4.6 3.8 - - + -
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Residues in contact with PRO 60 (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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59E VAL* 1.3 100.6 - - + +
61E ARG* 1.3 71.4 + - - +
62E SER 3.9 0.3 + - - -
64E THR* 4.4 11.2 - - + -
65E TYR 6.0 0.2 - - - +
70E VAL 6.0 1.1 - - - +
71E ILE* 5.4 0.7 - - - -
72E GLN* 3.1 30.2 - - + +
75E SER 4.1 1.1 - - - +
92E PHE* 4.1 9.2 - - + -
108E ILE 4.0 7.0 - - - +
109E CYS* 4.2 0.4 - - - -
110E GLN* 4.0 3.9 - - - +
73F THR 4.4 4.9 - - - +
74F ASN* 3.3 41.5 + - - +
75F SER* 3.9 10.1 - - - +
76F MET 4.9 1.4 - - - +
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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