Contacts of the strand formed by residues 23 - 31 (chain D) in PDB entry 1SZU
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 HIS 23 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C VAL* 3.2 23.2 + - + +
81C LEU* 3.6 15.0 - - + -
21D GLN* 2.9 22.5 + - - -
22D ILE* 1.3 85.9 - - + +
24D PRO* 1.3 59.6 - - + +
25D ILE* 2.6 25.1 + - + +
377D VAL* 4.0 11.2 - - + -
381D ARG* 3.7 15.4 - - + +
386D ILE* 3.7 24.6 - - + +
387D LEU 2.9 35.7 + - - -
388D LEU* 5.1 0.2 - - + -
1027D EDO 3.0 31.0 + - - -
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Residues in contact with PRO 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ASN* 3.7 16.8 - - - +
5D LYS* 6.1 0.7 - - - +
8D MET* 3.8 45.3 - - + +
21D GLN* 4.1 2.4 - - + +
22D ILE 3.9 7.0 - - - +
23D HIS* 1.3 78.9 - - + +
25D ILE* 1.3 59.6 + - - +
381D ARG* 3.4 36.0 + - - +
1006D SO4 4.2 11.7 - - - +
1027D EDO 3.9 7.4 - - - +
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Residues in contact with ILE 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C LEU* 3.7 20.7 - - + -
82C ALA* 3.0 24.4 + - - +
4D ASN* 3.8 8.3 - - - +
8D MET* 4.9 0.6 - - - -
21D GLN* 5.0 0.2 - - - +
23D HIS* 2.6 18.2 + - + +
24D PRO* 1.3 82.4 - - - +
26D PHE* 1.3 68.5 + - - +
27D ALA* 3.8 0.6 + - - +
35D VAL* 6.4 0.4 - - + -
37D ASP* 3.6 29.4 - - + +
43D TYR* 3.5 30.3 - - + +
381D ARG* 3.3 44.2 - - + +
386D ILE* 4.3 5.4 - - + -
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Residues in contact with PHE 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C PHE* 4.4 3.6 - + - -
82C ALA* 3.3 24.5 - - + -
83C TYR* 3.4 36.3 - - - -
84C GLU* 3.6 3.8 - - - +
87C LEU* 3.9 19.1 - - + -
4D ASN* 2.8 20.0 + - - +
7D LEU* 3.4 65.7 - - + -
8D MET* 3.7 18.4 - - - -
11D ARG* 4.3 10.1 - - + -
25D ILE* 1.3 77.3 - - - +
27D ALA* 1.3 59.8 + - - +
37D ASP* 3.1 5.8 - - - +
38D VAL* 3.0 28.7 + - + +
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LEU* 3.8 18.2 - - + -
76C THR* 4.1 11.9 - - + -
81C LEU* 4.2 7.6 - - + +
82C ALA 2.8 14.5 + - - +
83C TYR* 3.8 9.6 - - + +
84C GLU 4.7 0.3 + - - -
1031C EDO 3.5 16.1 - - - -
25D ILE* 3.8 2.8 + - - +
26D PHE* 1.3 74.7 - - - +
28D ASP* 1.3 60.7 + - - +
35D VAL* 3.7 25.6 - - + -
36D TRP 3.8 4.9 - - - -
37D ASP* 4.0 2.5 - - - +
38D VAL* 4.4 4.0 - - - +
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Residues in contact with ASP 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C LYS* 3.4 19.7 + - - +
73C LEU* 3.8 4.0 - - - +
1031C EDO 2.8 35.7 + - - -
26D PHE 3.8 0.4 + - - -
27D ALA* 1.3 75.2 - - - +
29D ARG* 1.3 79.4 + - - +
36D TRP* 2.8 16.0 + - + +
37D ASP 3.9 15.7 - - - +
38D VAL* 4.1 13.4 - - + +
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Residues in contact with ARG 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ALA 5.5 0.2 + - - -
71C LYS* 3.2 23.6 + - - +
72C LYS* 3.3 40.2 - - + +
73C LEU* 4.2 2.7 - - - -
1011C SO4 3.1 35.5 + - - -
28D ASP* 1.3 98.5 + - - +
30D ALA* 1.3 62.8 + - - +
35D VAL* 3.4 2.9 - - - +
36D TRP* 2.8 49.7 + - + +
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Residues in contact with ALA 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C LYS 5.1 1.0 - - - +
72C LYS 2.8 15.0 + - - +
73C LEU* 4.1 11.4 - - + -
29D ARG* 1.3 77.8 - - - +
31D GLU* 1.3 65.0 + - - +
34D ARG 3.1 13.9 - - - +
35D VAL* 4.0 7.4 - - + -
36D TRP* 4.0 4.5 - - - -
57D HIS* 3.4 35.8 - - + +
58D LEU* 3.9 13.9 - - - +
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Residues in contact with GLU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ALA* 1.3 77.7 - - - +
32D ASN* 1.3 79.0 + - + +
33D CYS 2.9 4.9 + - - -
34D ARG* 2.9 22.3 + - - +
36D TRP* 3.9 19.5 - - + -
57D HIS 3.8 7.4 - - - +
58D LEU* 5.4 4.5 - - + +
60D PRO* 6.5 0.7 - - + -
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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