Contacts of the strand formed by residues 91 - 98 (chain E) in PDB entry 5X6E
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 91 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E GLN* 4.3 21.6 - - + +
22E PHE 3.5 5.8 - - - +
23E HIS* 3.6 31.2 + - + +
43E ASP* 4.3 5.5 - - - +
44E GLY* 3.8 5.5 - - - -
89E SER* 2.3 28.3 + - - -
90E GLU* 1.3 83.1 - - + +
92E ALA* 1.3 58.9 + - - +
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Residues in contact with ALA 92 (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 GLN* 3.5 6.3 - - - -
22E PHE* 2.9 36.6 + - + +
28E ILE* 5.9 1.6 - - + -
41E LEU* 4.5 11.0 - - + -
43E ASP* 3.2 13.5 - - - +
44E GLY* 4.2 3.8 - - - -
45E ILE 4.7 1.3 - - - +
46E THR* 5.9 0.9 - - - -
87E VAL* 3.8 27.6 - - + -
89E SER* 3.8 3.8 - - - +
91E GLN* 1.3 78.4 - - - +
93E THR* 1.3 64.1 + - - +
94E ALA* 3.9 2.2 + - + -
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Residues in contact with THR 93 (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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19E PRO* 3.9 24.7 - - + -
20E LYS 4.6 1.6 - - - -
21E GLN* 4.2 22.7 + - - +
41E LEU* 3.6 1.6 - - - +
42E TYR* 2.8 38.8 + - + -
43E ASP* 2.7 37.1 + - - +
92E ALA* 1.3 72.3 - - - +
94E ALA* 1.3 63.2 + - - +
95E TYR* 4.7 7.0 - - + +
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Residues in contact with ALA 94 (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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19E PRO* 3.8 0.8 - - - +
20E LYS 3.3 31.3 + - - +
22E PHE* 4.3 14.5 - - + -
28E ILE* 4.0 27.4 - - + -
39E ILE* 4.2 8.1 - - + -
40E PHE 3.5 7.4 - - - +
41E LEU* 4.1 12.3 - - + -
92E ALA* 3.9 1.5 + - + +
93E THR* 1.3 77.0 - - - +
95E TYR* 1.3 66.6 + - - +
96E VAL* 3.7 2.9 + - + +
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Residues in contact with TYR 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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9E LYS* 3.5 27.1 - - + +
10E LYS* 3.0 38.1 - - - +
12E LEU* 3.6 20.0 - - + -
13E GLU* 5.8 0.2 - - + -
17E ILE* 6.4 0.9 - - + -
18E LYS 4.0 3.6 - - - -
19E PRO* 3.3 39.6 - - + +
39E ILE* 3.5 6.7 - - - -
40E PHE* 2.7 68.4 + + + +
42E TYR* 3.9 19.2 - - + +
93E THR* 4.7 6.3 - - + +
94E ALA* 1.3 71.4 - - - +
96E VAL* 1.3 63.5 + - - +
97E ILE* 3.8 5.0 + - + +
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Residues in contact with VAL 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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17E ILE* 3.8 23.7 - - + +
18E LYS 5.1 4.2 + - - -
20E LYS* 5.2 9.5 - - + +
22E PHE* 4.0 31.6 - - + -
28E ILE* 4.1 17.9 - - + +
37E TYR* 4.1 33.2 - - + -
38E CYS 4.1 2.5 - - - +
39E ILE* 4.9 5.6 - - + -
94E ALA* 3.7 3.7 + - + +
95E TYR* 1.3 73.8 - - - +
97E ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 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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12E LEU* 6.3 1.8 - - + -
17E ILE* 6.0 5.2 - - + -
37E TYR* 3.5 6.2 - - - +
38E CYS* 2.8 71.5 + - + +
39E ILE* 4.7 0.2 - - - -
40E PHE* 5.0 3.1 - - + +
95E TYR* 4.2 7.6 - - + +
96E VAL* 1.3 78.0 - - - +
98E LYS* 1.3 75.5 + - - +
101E GLU* 3.2 43.5 - - + +
102E LEU* 4.6 16.2 - - + +
105E LEU* 5.2 9.4 - - + -
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Residues in contact with LYS 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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35E GLN* 3.9 28.0 - - + +
37E TYR* 4.3 12.8 - - + -
97E ILE* 1.3 91.4 - - - +
99E ILE* 1.3 65.2 + - - +
100E ASN* 3.4 23.9 + - - +
101E GLU* 3.4 19.5 + - - +
102E LEU* 3.5 1.6 + - - +
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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