Contacts of the strand formed by residues 25 - 30 (chain E) in PDB entry 1MGQ
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 PRO 25 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E ASN 4.8 0.9 - - - +
24E SER* 1.3 89.4 - - - +
26E VAL* 1.3 57.9 + - - +
38E GLY* 3.4 13.0 - - - +
39E VAL* 4.3 8.9 - - + -
81E PRO 3.2 19.2 - - - +
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Residues in contact with VAL 26 (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 SER* 4.0 12.3 - - - -
24E SER 3.8 8.7 - - - +
25E PRO* 1.3 79.8 - - - +
27E ILE* 1.3 66.0 + - - +
28E ILE* 3.8 16.4 - - + -
36E PHE 3.9 0.2 - - - +
37E ARG* 3.4 6.2 - - - +
38E GLY 2.9 38.1 + - - +
40E LEU* 4.1 15.5 - - + -
51E LEU* 3.6 24.5 - - + -
79E ILE* 4.5 7.6 - - + -
80E SER 3.5 8.5 - - - +
81E PRO* 3.6 23.3 - - + +
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Residues in contact with ILE 27 (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 VAL* 1.3 78.8 - - - +
28E ILE* 1.3 66.6 + - - +
29E LYS 4.2 0.2 + - - -
35E GLU* 3.8 31.0 - - + +
36E PHE 3.4 4.5 - - - +
37E ARG* 4.0 34.1 - - + +
78E TYR* 4.0 10.3 - - + +
79E ILE* 3.3 4.2 - - - +
80E SER* 2.8 55.8 + - - +
64F ARG* 4.6 9.2 - - - +
66F LEU* 5.5 6.3 - - + -
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Residues in contact with ILE 28 (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 VAL* 3.8 17.0 - - + -
27E ILE* 1.3 74.4 - - - +
29E LYS* 1.3 62.1 + - - +
30E LEU* 3.7 24.4 + - + -
35E GLU* 3.3 5.9 - - - +
36E PHE* 2.7 46.5 + - + +
40E LEU* 5.7 0.7 - - + -
49E LEU* 4.0 19.3 - - + -
51E LEU* 4.1 25.4 - - + -
71E ILE* 4.5 7.2 - - + -
76E ILE* 4.0 20.4 - - + -
78E TYR 3.7 5.4 - - - +
79E ILE* 3.5 31.9 - - + -
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Residues in contact with LYS 29 (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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27E ILE* 4.2 0.8 - - + -
28E ILE* 1.3 73.7 - - - +
30E LEU* 1.3 58.9 + - - +
33E ASP* 3.7 44.7 + - - +
34E ARG 3.4 13.3 + - - +
35E GLU* 3.7 27.4 + - + +
76E ILE* 3.7 3.3 - - - +
77E VAL* 2.7 36.7 + - + -
78E TYR* 2.8 59.9 + - + +
34F ARG* 5.3 9.0 - - - +
56F GLU* 6.1 0.7 - - - -
64F ARG* 5.8 0.4 - - - +
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Residues in contact with LEU 30 (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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77D VAL* 3.5 32.3 - - + -
28E ILE* 3.7 25.4 - - + -
29E LYS* 1.3 79.5 - - - +
31E LYS* 1.3 72.0 + - - +
33E ASP* 3.2 13.7 + - - +
34E ARG* 2.8 24.9 + - + +
36E PHE* 3.5 31.0 - - + -
71E ILE* 4.1 14.1 - - + -
75E ASN* 3.3 19.7 - - + +
76E ILE* 3.9 11.4 - - + -
77E VAL* 3.6 8.9 - - - +
34F ARG* 5.2 1.0 + - - -
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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