Contacts of the strand formed by residues 25 - 31 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21G SER 3.5 0.7 - - - -
22G GLY* 3.0 26.0 + - - +
23G GLN 3.5 3.5 + - - +
24G PHE* 1.3 78.3 - - - +
26G ILE* 1.3 67.9 + - - +
27G VAL* 5.7 0.9 - - + -
42G LYS* 3.8 19.3 - - + -
43G PHE 2.8 13.2 - - - +
44G ILE* 3.6 23.6 - - + -
56G VAL* 5.9 0.9 - - + -
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Residues in contact with ILE 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G GLU* 3.7 19.1 - - + +
20G GLY 3.7 5.8 - - - +
21G SER* 3.3 23.3 - - - +
23G GLN 4.8 9.0 - - - +
24G PHE 5.7 1.6 - - - -
25G ALA* 1.3 83.1 - - - +
27G VAL* 1.3 64.1 + - - +
28G LYS* 4.2 16.6 - - - -
43G PHE* 2.7 53.9 + - + +
45G LYS* 6.4 2.0 - - - -
88G ASP* 5.8 3.4 - - - +
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Residues in contact with VAL 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G GLU* 3.3 7.1 - - - +
19G LEU* 2.7 39.9 + - + -
20G GLY* 2.5 32.2 + - - +
21G SER* 5.8 0.2 - - - -
25G ALA* 5.7 0.7 - - + -
26G ILE* 1.3 75.3 - - - +
28G LYS* 1.3 62.4 + - - +
40G ALA* 4.4 15.9 - - + -
41G ALA 3.1 9.9 - - - +
42G LYS* 3.7 35.9 - - + -
93G LEU* 6.1 1.1 - - + -
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Residues in contact with LYS 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G ILE* 3.8 17.4 - - + +
16G GLY 3.6 15.7 - - - +
17G GLU 2.9 11.2 - - - +
18G GLU* 3.4 20.6 - - + +
19G LEU* 3.7 3.8 - - - +
26G ILE* 4.2 17.7 - - + -
27G VAL* 1.3 81.4 - - - +
29G LYS* 1.3 66.2 + - - +
41G ALA* 2.8 35.5 + - - +
43G PHE* 4.0 19.5 - - + -
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Residues in contact with LYS 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G GLY* 2.7 25.8 + - - -
17G GLU* 2.8 30.9 + - + +
19G LEU* 3.1 37.1 - - + +
28G LYS* 1.3 77.6 - - - +
30G CYS* 1.3 63.8 + - - +
31G ARG* 6.0 0.2 - - - +
38G GLU* 2.8 47.5 + - - -
39G TYR 3.7 9.6 - - - +
40G ALA* 4.6 0.4 - - - +
95G LEU* 4.1 11.6 - - + +
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Residues in contact with CYS 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G TYR* 4.4 19.7 - - + -
14G ASP 3.5 15.5 - - - +
15G ILE* 4.1 10.5 - - + -
16G GLY* 4.0 1.1 - - - +
28G LYS 4.1 2.9 - - - +
29G LYS* 1.3 80.7 - - - +
31G ARG* 1.3 65.6 + - - +
38G GLU* 3.4 12.6 - - - +
39G TYR* 2.8 52.8 + - - +
41G ALA* 4.0 21.3 - - + -
92G ILE* 5.0 3.6 - - - -
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Residues in contact with ARG 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G TYR* 2.9 13.4 - - - -
14G ASP* 2.9 53.2 + - + +
30G CYS* 1.3 80.6 - - - +
32G GLU* 1.3 70.3 + - - +
33G LYS* 5.3 1.1 - - - +
36G GLY* 2.5 46.5 + - - -
37G LEU 3.3 10.8 - - - +
38G GLU* 3.9 24.7 + - - +
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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