Contacts of the strand formed by residues 44 - 50 (chain E) in PDB entry 2CHS
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 GLN 44 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D GLN* 5.1 4.7 - - - +
42E VAL* 3.4 9.2 - - - +
43E VAL* 1.3 85.6 - - + +
45E MET* 1.3 66.2 + - - +
46E LEU* 4.4 14.8 - - + +
72E PRO* 3.4 18.6 - - + +
94E THR* 3.1 38.0 + - - +
5F GLY* 3.8 10.1 - - - -
44F GLN* 5.1 4.7 - - - +
46F LEU* 4.9 4.7 - - - +
92F MET* 3.6 33.5 - - + +
94F THR* 2.7 36.4 + - - +
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Residues in contact with MET 45 (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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28E LEU* 3.6 31.9 - - + -
42E VAL* 4.7 2.7 - - + -
44E GLN* 1.3 79.4 - - - +
46E LEU* 1.3 68.2 + - - +
47E LEU* 4.3 13.9 - - + -
62E VAL* 4.5 6.5 - - - -
68E TRP* 3.8 17.0 - - + -
71E VAL* 4.8 0.7 - - + -
72E PRO 3.0 6.2 + - - +
73E VAL* 3.1 29.9 - - + +
74E THR 2.9 25.1 + - - +
91E VAL* 4.0 13.0 - - + -
92E MET 3.5 11.2 - - - +
93E MET* 3.3 39.5 - - + -
92F MET* 5.0 0.9 - - - +
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Residues in contact with LEU 46 (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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44D GLN* 5.5 3.4 - - - +
46D LEU* 4.2 21.5 - - + -
44E GLN* 4.4 16.4 - - + +
45E MET* 1.3 77.2 - - - +
47E LEU* 1.3 62.4 + - - +
48E SER 4.3 0.2 + - - -
74E THR* 3.2 33.9 - - + +
76E MET* 4.2 28.0 - - + +
91E VAL* 3.5 2.4 - - - +
92E MET* 2.8 46.3 + - + +
46F LEU* 3.8 31.2 - - + -
76F MET* 4.7 2.2 - - + -
92F MET* 4.6 5.4 - - + -
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Residues in contact with LEU 47 (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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24E THR* 4.2 22.9 - - + -
27E LEU* 6.1 0.9 - - + -
28E LEU* 4.5 8.5 - - + -
45E MET* 4.3 19.1 - - - -
46E LEU* 1.3 77.0 - - - +
48E SER* 1.3 60.9 + - - +
58E PRO* 4.4 9.4 - - + +
59E ALA* 3.7 35.2 - - + +
62E VAL* 4.4 7.0 - - + -
73E VAL* 4.6 8.1 - - + -
74E THR 2.9 8.6 + - - +
75E CYS* 3.1 34.6 - - - +
76E MET* 3.1 6.1 + - - +
89E ILE* 4.7 7.6 - - + -
90E ARG 3.4 6.5 - - - +
91E VAL* 3.9 23.8 - - + -
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Residues in contact with SER 48 (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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74D THR* 4.7 4.0 + - - +
75D CYS 4.7 2.6 + - - -
46E LEU 4.2 0.2 - - - -
47E LEU* 1.3 75.1 - - - +
49E ALA* 1.3 60.1 + - - +
58E PRO* 5.3 0.9 - - - -
76E MET* 3.3 33.8 - - - +
78E GLU* 4.2 17.9 - - - +
88E CYS 4.5 0.4 - - - -
89E ILE* 3.2 12.0 - - - +
90E ARG* 2.8 58.8 + - - +
79F MET* 5.3 1.1 - - - -
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Residues in contact with ALA 49 (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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48E SER* 1.3 75.4 - - - +
50E THR* 1.3 70.2 + - - +
53E LEU* 4.5 14.4 - - + -
58E PRO* 4.5 8.5 - - + -
76E MET 3.4 4.9 + - - -
77E GLN* 3.6 5.9 - - - +
78E GLU* 2.9 24.8 + - - -
88E CYS 3.5 7.6 - - - +
89E ILE* 4.6 0.7 - - + +
79F MET* 3.6 36.0 - - + +
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Residues in contact with THR 50 (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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57D PHE* 6.1 0.7 - - + -
49E ALA* 1.3 82.7 - - - +
51E PRO* 1.3 68.8 - - + +
52E ASP* 2.7 32.2 + - - -
53E LEU* 3.3 15.1 + - - +
77E GLN* 4.7 1.0 - - - +
78E GLU* 4.1 11.4 - - + -
79E MET 5.4 1.1 - - - +
85E LEU 3.6 20.6 - - - +
86E LYS* 5.2 0.7 - - - -
87E LYS* 3.2 2.6 + - - -
88E CYS* 3.0 24.3 + - + +
90E ARG* 3.6 24.2 - - - +
79F MET* 6.1 0.3 - - - +
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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