Contacts of the strand formed by residues 21 - 26 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20F GLU* 1.3 74.7 + - - +
22F VAL* 1.3 67.8 + - - +
33F ASN* 4.9 8.5 - - + +
34F GLY* 3.2 24.2 - - - +
35F ARG* 4.0 29.8 - - + +
90F PRO 4.1 0.2 - - - -
91F PRO* 3.2 32.8 - - + +
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Residues in contact with VAL 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F SER* 3.6 33.7 - - - +
20F GLU 3.6 2.0 + - - +
21F ILE* 1.3 79.6 - - - +
23F TYR* 1.3 62.7 + - - +
24F VAL* 3.9 20.0 + - + +
32F LEU 3.9 0.5 - - - +
33F ASN* 3.3 7.1 - - - +
34F GLY 2.8 34.6 + - - +
36F LEU* 4.2 21.3 - - + -
45F MSE 5.1 1.1 - - - -
47F LEU* 4.1 16.6 - - + -
88F ILE* 4.3 12.3 - - + -
89F ALA 3.4 10.5 - - - +
90F PRO* 4.4 1.8 - - + -
91F PRO* 4.8 0.2 - - + -
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Residues in contact with TYR 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLU* 4.7 2.3 + - - -
73A LYS* 3.8 12.8 + - - +
75A TYR* 3.3 41.1 + + - -
21F ILE 4.3 0.4 + - - -
22F VAL* 1.3 72.8 - - - +
24F VAL* 1.3 65.8 + - - +
25F LYS* 3.5 33.9 - - + +
31F GLU* 2.7 45.2 + - + +
32F LEU 3.5 9.9 - - - -
33F ASN* 3.8 17.7 - - - +
87F LEU* 4.7 5.8 - - + -
88F ILE* 3.3 6.3 - - - +
89F ALA* 2.8 45.4 + - + +
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Residues in contact with VAL 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F VAL* 3.9 21.5 - - + +
23F TYR* 1.3 84.0 - - - +
25F LYS* 1.3 63.1 + - - +
26F LEU* 3.7 25.9 + - + -
31F GLU* 3.3 5.7 - - - +
32F LEU* 2.8 45.7 + - + +
45F MSE 3.8 31.6 - - + -
47F LEU* 4.2 13.0 - - + -
85F VAL* 4.1 4.9 - - + -
87F LEU 3.3 10.1 - - - +
88F ILE* 4.5 4.3 - - + -
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Residues in contact with LYS 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ARG* 3.3 37.9 - - - +
52A GLU* 5.4 0.2 - - - +
23F TYR* 3.5 18.5 - - + +
24F VAL* 1.3 73.4 - - - +
26F LEU* 1.3 77.7 + - - +
28F GLY 4.3 0.8 - - - +
29F ASP* 3.1 34.4 + - - +
30F ARG 3.5 14.7 - - - +
31F GLU* 4.0 12.0 - - + +
85F VAL* 3.9 0.9 - - - -
86F ILE* 2.9 34.5 + - + -
87F LEU* 3.0 39.1 + - + +
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Residues in contact with LEU 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E ILE* 4.1 22.0 - - + -
87E LEU* 4.4 2.2 - - + -
24F VAL* 3.7 24.5 - - + -
25F LYS* 1.3 99.6 + - - +
27F ARG* 1.3 70.0 + - - +
30F ARG* 2.9 40.8 + - + +
32F LEU* 4.0 24.5 - - + -
80F VAL* 3.9 12.1 - - + -
84F SER* 3.1 20.2 - - - +
85F VAL* 3.8 15.5 - - + -
86F ILE* 3.6 4.1 - - - +
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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