Contacts of the strand formed by residues 21 - 26 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H GLU* 1.3 74.8 + - - +
22H VAL* 1.3 64.9 + - - +
23H TYR 4.2 0.2 + - - -
33H ASN* 4.9 8.7 - - + +
34H GLY* 3.3 18.2 - - - +
35H ARG* 3.7 40.2 - - + +
90H PRO 4.3 0.2 - - - -
91H PRO* 3.3 30.4 - - + +
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Residues in contact with VAL 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H SER* 3.6 32.8 - - - +
20H GLU 4.1 7.6 - - - +
21H ILE* 1.3 78.2 - - - +
23H TYR* 1.3 60.1 + - - +
24H VAL* 3.9 20.0 + - + +
33H ASN* 3.3 7.6 - - - +
34H GLY 2.8 37.6 + - - +
36H LEU* 4.2 16.2 - - + -
45H MSE 5.1 1.1 - - - -
47H LEU* 4.2 15.3 - - + -
88H ILE* 4.2 14.4 - - + -
89H ALA 3.4 11.4 - - - +
90H PRO* 4.4 3.4 - - + -
91H PRO* 4.7 0.2 - - + -
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Residues in contact with TYR 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H ILE 4.2 0.4 + - - -
22H VAL* 1.3 73.2 - - - +
24H VAL* 1.3 66.2 + - - +
25H LYS* 3.5 33.7 - - + +
31H GLU* 2.7 43.1 + - + +
32H LEU 3.5 10.1 - - - -
33H ASN* 3.8 18.4 - - - +
87H LEU* 4.8 6.9 - - + +
88H ILE* 3.3 5.8 - - - +
89H ALA* 2.8 44.3 + - + +
30N ARG* 5.7 0.2 + - - -
52N GLU* 4.7 3.8 + - - -
73N LYS* 4.0 15.5 + - - +
75N TYR* 3.3 40.2 + + + -
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Residues in contact with VAL 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H VAL* 3.9 20.9 - - + +
23H TYR* 1.3 84.8 - - - +
25H LYS* 1.3 61.5 + - - +
26H LEU* 3.7 25.7 + - + -
31H GLU* 3.3 5.4 - - - +
32H LEU* 2.8 43.8 + - + +
45H MSE 3.7 31.9 - - + -
47H LEU* 4.2 15.5 - - + -
85H VAL* 4.1 6.3 - - + -
87H LEU 3.3 11.4 - - - +
88H ILE* 4.5 3.1 - - + -
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Residues in contact with LYS 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H TYR* 3.5 20.3 - - + +
24H VAL* 1.3 72.9 - - - +
26H LEU* 1.3 77.2 + - - +
28H GLY 4.3 1.5 - - - +
29H ASP* 3.1 33.9 - - - +
30H ARG 3.4 15.9 + - - +
31H GLU* 4.0 11.5 - - + +
85H VAL* 3.8 0.7 - - - -
86H ILE* 2.8 37.1 + - + +
87H LEU* 3.0 37.4 + - + +
30N ARG* 3.1 38.8 - - - +
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Residues in contact with LEU 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H VAL* 3.7 25.4 - - + +
25H LYS* 1.3 99.0 + - - +
27H ARG* 1.3 71.6 + - - +
30H ARG* 3.0 40.9 + - + +
32H LEU* 3.9 24.7 - - + -
80H VAL* 4.0 12.6 - - + -
84H SER* 3.1 19.5 - - - +
85H VAL* 3.9 15.0 - - + -
86H ILE* 3.6 4.1 - - - +
86M ILE* 4.2 20.2 - - + -
87M LEU* 4.5 3.1 - - + -
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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