Contacts of the strand formed by residues 78 - 83 (chain E) in PDB entry 4M75
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 ILE 78 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E ILE* 3.6 28.9 - - + -
23E VAL 4.1 2.9 - - - -
24E LEU* 4.2 7.8 - - + +
41E VAL* 3.7 9.6 - - + +
43E VAL* 3.3 38.1 - - + +
73E LEU* 4.4 6.7 - - + +
74E SER 3.8 4.9 - - - +
75E GLY* 3.2 25.6 + - - +
77E ASN* 1.3 75.6 - - - +
79E ALA* 1.3 61.0 + - - +
80E ILE 4.5 3.8 - - - +
81E LEU* 4.0 27.8 - - + -
95F ARG* 3.7 18.0 - - - +
98F ILE* 3.4 17.9 - - - +
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Residues in contact with ALA 79 (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 VAL* 2.8 17.4 + - + +
24E LEU 4.3 1.1 - - - -
25E GLN* 4.0 19.7 - - + +
77E ASN 3.2 1.5 + - - +
78E ILE* 1.3 73.9 - - - +
80E ILE* 1.3 68.0 + - + +
42F LEU* 4.7 10.1 - - + -
43F MSE 5.6 0.2 - - - +
46F LYS* 5.7 2.7 - - - +
94F ILE* 3.4 6.7 - - - +
95F ARG* 2.9 32.5 + - - +
98F ILE* 4.0 22.0 - - + -
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Residues in contact with ILE 80 (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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22E ILE* 4.0 1.4 - - - -
23E VAL* 3.0 46.0 + - + +
78E ILE* 4.5 1.5 - - - +
79E ALA* 1.3 84.1 - - + +
81E LEU* 1.3 62.3 + - - +
82E VAL* 4.1 7.0 + - + -
42F LEU* 4.8 6.1 - - + -
46F LYS* 5.4 2.5 - - - -
48F VAL* 4.5 21.3 - - + -
66F THR* 5.2 3.1 - - + -
68F GLU* 4.0 22.4 - - + +
89F LEU* 4.7 13.2 - - + -
92F THR* 4.1 15.7 - - + +
93F VAL 3.2 13.5 - - - +
94F ILE* 3.5 28.5 - - + -
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Residues in contact with LEU 81 (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 ILE* 3.9 41.1 - - + -
20E VAL* 4.8 10.5 - - + -
21E LEU 3.8 3.6 - - - +
22E ILE* 4.7 11.9 - - + +
34E LEU* 4.9 3.1 - - + -
41E VAL* 4.2 7.6 - - + -
43E VAL* 4.4 20.0 - - + -
78E ILE* 4.0 21.8 - - + -
80E ILE* 1.3 73.1 - - - +
82E VAL* 1.3 61.3 + - - +
83E PRO* 3.7 3.7 - - + +
92F THR* 3.2 8.1 - - - -
93F VAL* 2.7 48.9 + - + +
95F ARG* 4.1 17.7 - - + -
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Residues in contact with VAL 82 (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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20E VAL* 3.3 4.8 - - - +
21E LEU* 2.7 68.4 + - + +
23E VAL* 4.8 2.2 - - + -
80E ILE* 4.5 10.3 - - + +
81E LEU* 1.3 78.5 - - - +
83E PRO* 1.3 77.0 - - + +
84E GLY 5.2 2.0 - - - +
89F LEU* 4.5 25.8 - - + -
90F GLY 4.8 4.7 - - - +
91F LEU 4.3 6.5 - - - +
92F THR* 3.6 17.7 - - + -
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Residues in contact with PRO 83 (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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11E VAL* 4.8 16.2 - - + -
15E THR* 4.2 26.0 - - + +
18E GLN* 5.1 6.1 - - - +
19E LYS 4.3 0.4 - - - +
20E VAL* 4.4 0.2 - - - -
81E LEU* 3.7 7.4 - - + +
82E VAL* 1.3 93.0 - - - +
84E GLY* 1.3 60.0 + - - +
91F LEU* 3.1 34.5 - - + +
92F THR* 4.4 1.6 - - - -
93F VAL* 6.1 0.9 - - + -
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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