Contacts of the strand formed by residues 14 - 19 (chain F) in PDB entry 2E9X
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 LEU 14 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F LYS 4.3 9.0 - - - +
13F GLU* 1.3 79.0 + - - +
15F VAL* 1.3 65.2 + - - +
33F LEU* 5.4 4.5 - - + -
43F GLU* 3.9 34.1 - - + +
44F VAL* 3.4 24.0 - - - +
45F PRO* 4.1 9.4 - - + -
95F LEU* 5.6 1.4 - - - +
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Residues in contact with VAL 15 (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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13F GLU 4.3 4.9 - - - +
14F LEU* 1.3 80.4 - - - +
16F THR* 1.3 63.5 + - - +
17F ILE* 4.1 3.3 + - + -
43F GLU* 3.2 7.0 - - - -
44F VAL* 3.0 32.9 + - + +
46F LEU* 3.9 27.6 - - + -
49F ALA* 3.5 32.3 - - + -
60F LEU* 5.2 2.0 - - + -
61F LEU 5.1 6.5 - - - +
63F PRO* 5.2 9.9 - - + -
95F LEU* 4.9 15.0 - - + -
99F LEU* 5.0 7.9 - - + -
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Residues in contact with THR 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F VAL* 1.3 78.8 - - - +
17F ILE* 1.3 73.1 + - - +
41F PRO* 3.9 19.1 - - + -
42F VAL 3.6 9.2 - - - +
43F GLU* 4.0 16.6 + - + +
60F LEU* 4.2 0.2 - - - -
61F LEU* 3.0 57.7 + - + +
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Residues in contact with ILE 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F VAL* 4.5 1.1 - - + -
16F THR* 1.3 77.5 - - - +
18F ILE* 1.3 62.3 + - - +
19F PRO* 3.6 5.9 - - + +
36F PHE* 4.4 5.4 - - + -
41F PRO* 3.6 5.5 - - - +
42F VAL* 3.0 49.9 + - + +
44F VAL* 3.9 17.9 - - + -
49F ALA* 3.6 17.3 - - + -
52F LEU* 3.8 29.4 - - + -
58F CYS* 4.2 14.1 - - + -
59F ARG 3.2 8.5 - - - +
60F LEU* 3.3 31.4 - - + -
61F LEU* 4.7 0.4 - - - +
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Residues in contact with ILE 18 (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 ILE* 1.3 77.3 - - - +
19F PRO* 1.3 64.3 - - - +
20F ASN* 5.2 0.5 - - - +
39F GLY* 3.6 34.3 - - - +
40F LEU 4.1 0.9 - - - -
41F PRO* 4.9 12.3 - - + -
58F CYS* 3.2 2.1 - - - -
59F ARG* 2.8 50.8 + - + +
61F LEU* 3.7 35.9 - - + -
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Residues in contact with PRO 19 (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 ILE* 3.6 9.0 - - + +
18F ILE* 1.3 90.1 - - - +
20F ASN* 1.3 60.5 + - - +
21F PHE* 3.5 33.0 - - + +
36F PHE* 4.2 9.4 - - + -
37F ASN 3.5 29.4 - - - +
38F PRO* 3.3 0.7 - - - +
39F GLY 3.0 23.9 + - - -
40F LEU 3.2 17.7 - - - +
42F VAL* 4.0 10.8 - - + -
57F LYS 3.3 7.9 - - - +
58F CYS* 3.8 4.5 - - + -
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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