Contacts of the strand formed by residues 25 - 31 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H SER 3.5 0.9 - - - -
22H GLY* 3.1 25.2 + - - +
23H GLN 3.1 5.2 + - - +
24H PHE* 1.3 81.9 - - - +
26H ILE* 1.3 69.6 + - - +
27H VAL* 5.7 0.7 - - - -
42H LYS* 3.9 18.8 - - + -
43H PHE 2.8 11.0 - - - +
44H ILE* 3.7 23.8 - - + -
56H VAL* 5.8 0.7 - - + -
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Residues in contact with ILE 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H GLU* 3.8 17.7 - - + +
20H GLY 3.6 5.4 - - - +
21H SER* 3.4 24.0 - - - +
23H GLN 4.9 8.1 - - - +
24H PHE 5.8 1.3 - - - -
25H ALA* 1.3 81.8 - - - +
27H VAL* 1.3 66.1 + - - +
28H LYS* 4.3 15.7 - - - -
43H PHE* 2.8 53.0 + - + +
45H LYS* 6.5 1.8 - - - -
88H ASP* 5.9 1.8 - - - +
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Residues in contact with VAL 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H GLU* 3.1 7.1 - - - +
19H LEU* 2.7 40.7 + - + -
20H GLY* 2.5 29.9 + - - +
21H SER* 5.8 0.4 - - - -
25H ALA* 5.7 0.4 - - + -
26H ILE* 1.3 76.5 - - - +
28H LYS* 1.3 67.6 + - - +
40H ALA* 4.4 12.8 - - + -
41H ALA 3.3 13.0 - - - +
42H LYS* 3.8 33.9 - - + -
93H LEU* 6.2 0.7 - - + -
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Residues in contact with LYS 28 (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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15H ILE* 3.7 23.4 - - + +
16H GLY 3.6 11.4 - - - +
17H GLU 2.9 10.3 - - - +
18H GLU* 3.4 21.8 - - + +
19H LEU* 3.8 2.9 - - - +
26H ILE* 4.3 14.8 - - + -
27H VAL* 1.3 83.3 - - - +
29H LYS* 1.3 66.9 + - - +
41H ALA* 2.9 32.4 + - - +
43H PHE* 4.1 19.3 - - + -
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Residues in contact with LYS 29 (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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15H ILE 3.8 0.2 - - - -
16H GLY* 2.7 31.2 + - - -
17H GLU* 2.7 30.9 + - + +
19H LEU* 3.3 36.5 - - + +
28H LYS* 1.3 78.0 - - - +
30H CYS* 1.3 59.8 + - - +
31H ARG* 5.9 0.2 - - - +
38H GLU* 2.7 49.6 + - - -
39H TYR 3.7 9.9 - - - +
40H ALA* 4.6 0.2 - - - +
95H LEU* 4.1 10.1 - - + +
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Residues in contact with CYS 30 (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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13H TYR* 4.4 19.7 - - + -
14H ASP 3.2 15.9 - - - +
15H ILE* 4.0 10.1 - - + -
16H GLY* 3.9 1.6 - - - +
28H LYS 4.1 2.5 - - - +
29H LYS* 1.3 79.3 - - - +
31H ARG* 1.3 64.8 + - - +
38H GLU* 3.4 12.5 - - - +
39H TYR* 2.9 52.4 + - - -
40H ALA 4.3 0.4 - - - -
41H ALA* 3.8 24.0 - - + -
92H ILE* 5.2 2.9 - - - -
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Residues in contact with ARG 31 (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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13H TYR* 3.0 13.0 - - - -
14H ASP* 2.8 53.8 + - + +
29H LYS* 5.9 0.4 - - - +
30H CYS* 1.3 79.4 - - - +
32H GLU* 1.3 72.4 + - - +
33H LYS* 3.4 1.6 + - - +
36H GLY* 2.7 42.0 + - - -
37H LEU 3.3 11.0 - - - +
38H GLU* 4.0 24.1 + - - +
39H TYR 4.9 0.2 - - - +
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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