Contacts of the strand formed by residues 25 - 31 (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 ALA 25 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21F SER 3.5 0.7 - - - -
22F GLY* 3.1 26.0 + - - +
23F GLN 3.1 5.0 + - - +
24F PHE* 1.3 78.9 - - - +
26F ILE* 1.3 70.3 + - - +
27F VAL* 5.6 0.7 - - - -
42F LYS* 3.8 19.1 - - + -
43F PHE 2.7 13.0 - - - +
44F ILE* 3.7 24.0 - - + -
56F VAL* 5.8 0.9 - - + -
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Residues in contact with ILE 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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18F GLU* 3.7 18.4 - - + -
20F GLY 3.7 2.5 - - - +
21F SER* 3.3 26.7 - - - +
23F GLN 5.0 8.7 - - - +
24F PHE 5.7 1.6 - - - -
25F ALA* 1.3 83.6 - - - +
27F VAL* 1.3 63.8 + - - +
28F LYS* 4.2 16.4 - - - -
43F PHE* 2.6 54.8 + - + +
45F LYS* 6.4 2.5 - - + -
88F ASP* 5.8 2.5 - - - +
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Residues in contact with VAL 27 (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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18F GLU* 3.1 6.6 - - - +
19F LEU* 2.6 42.3 + - + -
20F GLY* 2.5 33.3 + - - +
21F SER* 5.6 0.4 - - - -
22F GLY 6.2 0.4 - - - +
25F ALA 5.6 0.4 - - - -
26F ILE* 1.3 75.6 - - - +
28F LYS* 1.3 67.4 + - - +
40F ALA* 4.5 11.7 - - + -
41F ALA 3.2 13.9 - - - +
42F LYS* 3.8 29.8 - - + -
93F LEU* 6.4 0.7 - - + -
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Residues in contact with LYS 28 (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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15F ILE* 3.8 22.9 - - + +
16F GLY 3.7 10.5 - - - +
17F GLU 2.8 11.7 - - - +
18F GLU* 3.3 22.9 - - + +
19F LEU* 3.7 3.4 - - - +
26F ILE* 4.2 15.7 - - + -
27F VAL* 1.3 83.7 - - - +
29F LYS* 1.3 67.3 + - - +
30F CYS* 4.2 0.2 - - - +
41F ALA* 2.9 32.1 + - - +
43F PHE* 4.1 19.5 - - + -
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Residues in contact with LYS 29 (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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15F ILE 3.8 0.2 - - - -
16F GLY* 2.7 26.1 + - - -
17F GLU* 2.6 30.9 + - + +
19F LEU* 3.2 37.1 - - + +
28F LYS* 1.3 77.9 - - - +
30F CYS* 1.3 64.9 + - - +
31F ARG* 5.8 0.2 - - - +
38F GLU* 2.7 48.0 + - - -
39F TYR 3.7 10.1 - - - +
40F ALA* 4.6 0.2 - - - +
95F LEU* 4.2 11.2 - - + -
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Residues in contact with CYS 30 (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* 6.4 0.2 - - - -
13F TYR* 4.5 17.9 - - + -
14F ASP 3.4 19.3 - - - +
15F ILE* 4.2 6.1 - - + -
16F GLY* 3.9 0.9 - - - +
28F LYS 4.2 2.9 - - - +
29F LYS* 1.3 80.2 - - - +
31F ARG* 1.3 65.6 + - - +
38F GLU* 3.4 12.3 - - - +
39F TYR* 2.9 59.7 + - - +
40F ALA 4.1 0.7 - - - -
41F ALA* 4.1 22.0 - - + -
92F ILE* 5.0 3.4 - - - -
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Residues in contact with ARG 31 (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* 3.0 12.7 - - - -
14F ASP* 2.8 55.9 + - + +
29F LYS* 5.8 0.2 - - - +
30F CYS* 1.3 80.3 - - - +
32F GLU* 1.3 72.8 + - - +
33F LYS* 5.3 1.3 - - - +
36F GLY* 2.6 43.6 + - - -
37F LEU 3.2 11.9 - - - +
38F GLU* 3.8 25.8 + - - +
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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