Contacts of the strand formed by residues 38 - 44 (chain F) in PDB entry 1ZWS
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 GLU 38 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29F LYS* 2.7 41.5 + - - -
30F CYS 3.4 8.1 - - - +
31F ARG* 3.8 29.1 + - - +
36F GLY 4.0 0.6 + - - +
37F LEU* 1.3 75.7 - - - +
39F TYR* 1.3 72.9 + - - +
95F LEU* 3.8 23.1 + - + +
97F SER* 5.5 0.5 + - - -
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Residues in contact with TYR 39 (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 TYR* 3.9 15.0 - + - -
29F LYS* 3.7 3.8 - - - +
30F CYS* 2.9 40.5 + - - -
32F GLU* 3.4 36.3 + - + -
37F LEU* 3.3 38.5 - - + +
38F GLU* 1.3 77.1 - - - +
40F ALA* 1.3 61.6 + - - +
80F HIS* 3.0 47.5 - + + -
92F ILE* 3.9 9.9 - - + -
93F LEU 3.7 14.6 - - - +
94F GLU* 4.9 4.9 - - - -
95F LEU* 3.8 14.4 - - - +
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Residues in contact with ALA 40 (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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19F LEU* 5.0 0.2 - - + -
27F VAL* 4.5 14.8 - - + -
28F LYS 4.1 3.6 - - - -
29F LYS* 4.6 0.4 - - - +
30F CYS* 4.2 1.1 - - - -
39F TYR* 1.3 73.6 - - - +
41F ALA* 1.3 59.6 + - - +
42F LYS 4.1 0.4 - - - -
91F LEU 3.5 0.7 - - - +
92F ILE* 3.6 2.4 - - - -
93F LEU* 2.7 45.0 + - + +
94F GLU 3.8 14.8 - - - +
95F LEU* 3.4 23.0 - - + +
96F VAL 5.4 0.2 - - - +
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Residues in contact with ALA 41 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9F VAL* 5.6 2.0 - - + -
15F ILE* 5.3 2.2 - - + -
27F VAL* 3.2 5.5 - - - -
28F LYS 2.9 44.8 + - - +
30F CYS* 4.1 17.7 - - + -
39F TYR 4.1 0.4 - - - -
40F ALA* 1.3 72.5 - - - +
42F LYS* 1.3 60.7 + - - +
43F PHE* 3.4 26.1 - - + -
90F VAL* 4.2 7.4 - - + -
91F LEU 3.3 6.5 - - - +
92F ILE* 4.7 6.5 - - + +
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Residues in contact with LYS 42 (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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25F ALA* 3.8 23.6 - - + -
26F ILE 3.7 2.2 - - - -
27F VAL* 3.8 21.5 - - + -
40F ALA 4.0 0.8 + - - -
41F ALA* 1.3 71.9 - - - +
43F PHE* 1.3 62.7 + - - +
44F ILE* 4.0 13.2 - - + -
64F GLU* 2.7 36.1 + - - +
89F VAL 3.3 2.6 - - - +
90F VAL* 3.3 5.2 - - - -
91F LEU* 2.8 57.0 + - + +
93F LEU* 4.6 18.1 - - + +
161F ASP* 5.5 5.3 + - - +
162F PHE 5.0 4.0 - - - +
163F GLY* 4.8 7.5 - - - +
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Residues in contact with PHE 43 (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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9F VAL* 5.2 4.3 - - + -
10F GLU* 6.0 2.7 - - - -
15F ILE* 3.8 30.7 - - + -
24F PHE 3.5 0.2 - - - +
25F ALA* 2.7 11.0 - - - -
26F ILE* 2.6 63.1 + - + +
28F LYS* 4.1 24.5 - - + -
41F ALA* 3.4 24.7 - - + -
42F LYS* 1.3 71.7 - - - +
44F ILE* 1.3 55.7 + - - +
45F LYS 3.5 2.9 + - - -
88F ASP* 3.5 22.0 - - + +
89F VAL 3.7 2.9 - - - -
90F VAL* 3.4 39.3 - - + -
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Residues in contact with ILE 44 (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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24F PHE 3.4 3.1 - - - +
25F ALA* 3.7 17.9 - - + -
42F LYS* 4.0 11.9 - - + -
43F PHE* 1.3 70.3 - - - +
45F LYS* 1.3 63.4 + - - +
46F LYS* 3.0 4.2 + - - -
56F VAL* 3.5 25.1 - - + -
61F ILE* 3.1 38.8 - - + -
64F GLU* 3.9 21.3 - - + +
65F VAL* 6.0 1.1 - - + -
88F ASP* 3.6 2.7 + - - -
89F VAL* 3.0 36.2 + - + +
91F LEU* 3.7 31.0 - - + -
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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