Contacts of the strand formed by residues 21 - 26 (chain N) in PDB entry 4EMG
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 21 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20N GLU* 1.3 74.2 + - - +
22N VAL* 1.3 65.0 + - - +
33N ASN* 5.0 8.3 - - + +
34N GLY* 3.3 22.7 - - - +
35N ARG* 3.8 35.6 - - + +
90N PRO 4.1 0.2 - - - -
91N PRO* 3.2 31.5 - - + +
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Residues in contact with VAL 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N SER* 3.6 32.8 - - - +
20N GLU 3.6 2.7 + - - +
21N ILE* 1.3 78.4 - - - +
23N TYR* 1.3 59.9 + - - +
24N VAL* 3.9 20.3 + - + +
32N LEU 3.9 0.5 - - - +
33N ASN* 3.3 8.1 - - - +
34N GLY 2.8 34.4 + - - +
36N LEU* 4.2 20.2 - - + -
45N MSE 5.0 1.6 - - - -
47N LEU* 4.1 15.7 - - + -
88N ILE* 4.2 14.1 - - + -
89N ALA 3.4 11.2 - - - +
90N PRO* 4.4 2.7 - - + -
91N PRO* 4.8 0.2 - - + -
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Residues in contact with TYR 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52K GLU* 4.6 2.6 + - - -
73K LYS* 3.7 15.5 + - - +
75K TYR* 3.1 41.9 + + - -
21N ILE 4.3 0.4 + - - -
22N VAL* 1.3 73.0 - - - +
24N VAL* 1.3 65.6 + - - +
25N LYS* 3.6 30.3 - - + +
31N GLU* 2.6 47.5 + - + +
32N LEU 3.5 9.9 - - - -
33N ASN* 3.8 19.1 - - - +
87N LEU* 4.8 6.3 - - + -
88N ILE* 3.3 5.8 - - - +
89N ALA* 2.8 45.2 + - + +
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Residues in contact with VAL 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N VAL* 3.9 21.8 - - + +
23N TYR* 1.3 84.3 - - - +
25N LYS* 1.3 61.8 + - - +
26N LEU* 3.7 25.4 + - + -
31N GLU* 3.3 5.4 - - - +
32N LEU* 2.8 47.5 + - + +
45N MSE 3.8 30.3 - - + -
47N LEU* 4.2 13.7 - - + -
85N VAL* 4.1 4.9 - - + -
87N LEU 3.4 11.0 - - - +
88N ILE* 4.5 3.6 - - + -
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Residues in contact with LYS 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ARG* 3.1 39.6 - - - +
23N TYR* 3.6 20.0 - - - +
24N VAL* 1.3 73.4 - - - +
26N LEU* 1.3 77.5 + - - +
28N GLY 4.3 0.6 - - - +
29N ASP* 3.1 34.1 + - - +
30N ARG 3.4 15.2 + - - +
31N GLU* 4.0 12.4 - - + +
85N VAL* 3.9 0.5 - - - -
86N ILE* 2.9 31.4 + - + -
87N LEU* 3.0 41.6 + - + +
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Residues in contact with LEU 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86H ILE* 4.2 21.5 - - + -
87H LEU* 4.2 5.8 - - + -
24N VAL* 3.7 24.2 - - + +
25N LYS* 1.3 98.9 + - - +
27N ARG* 1.3 70.2 + - - +
30N ARG* 3.0 41.9 + - + +
32N LEU* 4.0 25.1 - - + -
80N VAL* 3.9 9.6 - - + -
84N SER* 3.1 19.3 - - - +
85N VAL* 3.9 15.9 - - + -
86N ILE* 3.6 4.7 - - - +
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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