Contacts of the strand formed by residues 21 - 26 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M GLU* 1.3 75.0 + - - +
22M VAL* 1.3 64.1 + - - +
23M TYR 4.2 0.2 + - - -
33M ASN* 4.9 7.6 - - + +
34M GLY* 3.2 23.1 - - - +
35M ARG* 3.7 35.9 - - - +
90M PRO 4.2 0.2 - - - -
91M PRO* 3.3 31.6 - - + +
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Residues in contact with VAL 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M SER* 3.6 32.8 - - - +
20M GLU 4.2 7.9 - - - +
21M ILE* 1.3 79.6 - - - +
23M TYR* 1.3 62.7 + - - +
24M VAL* 3.9 19.9 - - + +
32M LEU 3.9 0.3 - - - +
33M ASN* 3.3 7.1 - - - +
34M GLY 2.8 36.1 + - - +
36M LEU* 4.3 16.4 - - + -
45M MSE 5.2 0.9 - - - -
47M LEU* 4.1 17.0 - - + -
88M ILE* 4.3 11.9 - - + -
89M ALA 3.4 10.8 - - - +
90M PRO* 4.3 3.1 - - + -
91M PRO* 4.7 0.2 - - + -
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Residues in contact with TYR 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52H GLU* 4.7 2.1 + - - -
73H LYS* 3.7 15.3 + - - +
75H TYR* 3.2 43.8 + + + -
21M ILE 4.2 0.2 + - - -
22M VAL* 1.3 73.9 - - - +
24M VAL* 1.3 66.1 + - - +
25M LYS* 3.5 31.5 - - + +
31M GLU* 2.6 44.7 + - + +
32M LEU 3.5 9.6 - - - -
33M ASN* 3.8 19.7 - - - +
87M LEU* 4.8 5.4 - - + -
88M ILE* 3.3 5.5 - - - +
89M ALA* 2.8 46.3 + - + +
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Residues in contact with VAL 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M VAL* 3.9 21.8 - - + -
23M TYR* 1.3 84.3 - - - +
25M LYS* 1.3 62.0 + - - +
26M LEU* 3.6 27.1 + - + -
31M GLU* 3.3 4.2 - - - +
32M LEU* 2.8 46.9 + - + +
45M MSE 3.8 33.0 - - + -
47M LEU* 4.3 12.8 - - + -
85M VAL* 4.0 6.3 - - + -
87M LEU 3.3 11.0 - - - +
88M ILE* 4.6 4.0 - - + -
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Residues in contact with LYS 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H ARG* 3.3 39.7 - - - +
52H GLU* 5.1 0.2 - - - +
23M TYR* 3.5 20.7 - - + +
24M VAL* 1.3 72.1 - - - +
26M LEU* 1.3 77.2 + - - +
28M GLY 4.3 0.6 - - - +
29M ASP* 3.1 34.4 + - - +
30M ARG 3.5 14.6 + - - +
31M GLU* 4.0 11.5 - - + +
85M VAL 3.9 0.3 - - - -
86M ILE* 2.9 33.6 + - + -
87M LEU* 3.0 37.2 + - + +
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Residues in contact with LEU 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86L ILE* 4.1 21.5 - - + -
87L LEU* 4.3 2.7 - - + -
24M VAL* 3.6 26.4 + - + +
25M LYS* 1.3 97.8 + - - +
27M ARG* 1.3 69.6 - - - +
30M ARG* 3.0 42.2 + - + +
32M LEU* 4.0 24.2 - - + -
80M VAL* 3.9 12.8 - - + -
84M SER* 3.1 20.2 - - - +
85M VAL* 3.8 14.4 - - + -
86M ILE* 3.8 4.4 - - - +
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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