Contacts of the strand formed by residues 22 - 28 (chain D) in PDB entry 1SL0
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 22 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D GLY* 1.3 72.1 - - - -
23D ILE* 1.3 65.7 + - - +
24D LEU 4.1 0.2 - - - -
52D LYS 4.5 13.1 + - - +
53D LEU* 3.5 16.3 - - + +
54D THR* 2.9 27.5 + - - -
80D LEU* 6.1 2.7 - - + -
81D PHE 3.2 10.8 - - - +
82D LYS* 4.9 6.5 - - + +
107D LEU* 6.1 4.0 - - + -
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Residues in contact with ILE 23 (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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5D ILE* 5.0 1.1 - - + -
15D ASP 4.7 3.8 - - - +
16D VAL* 3.4 29.2 - - + +
19D ALA* 3.5 33.7 - - + -
21D GLY* 4.6 1.8 - - - +
22D ALA* 1.3 77.5 - - - +
24D LEU* 1.3 57.2 + - - +
25D VAL* 3.3 6.5 + - + -
53D LEU* 4.9 0.7 - - - -
54D THR* 2.9 49.8 - - + +
56D ALA* 3.6 29.8 - - + -
80D LEU* 4.4 0.9 - - - -
81D PHE* 2.6 40.5 + - + +
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Residues in contact with LEU 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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22D ALA 4.1 1.2 + - - -
23D ILE* 1.3 68.8 - - - +
25D VAL* 1.3 60.3 + - - +
26D ASP* 3.5 1.4 + - - +
42D LEU* 3.3 29.2 - - + -
45D ILE* 4.7 6.7 - - + -
53D LEU* 4.3 28.4 - - + +
54D THR 3.0 9.7 + - - +
55D VAL* 4.1 12.4 - - + +
56D ALA 3.5 17.4 + - - +
78D LEU* 4.0 32.5 - - + -
79D LEU 3.1 18.8 - - - +
80D LEU* 4.0 11.9 - - + +
99D LEU* 6.5 0.7 - - + -
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Residues in contact with VAL 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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7D LEU* 3.8 15.0 - - + -
12D PHE* 3.6 19.5 - - + -
16D VAL* 3.1 35.4 - - + -
23D ILE* 3.9 2.9 - - + +
24D LEU* 1.3 70.8 - - - +
26D ASP* 1.3 62.8 + - - +
27D PHE* 3.5 24.4 + - + -
56D ALA 3.3 5.4 - - - +
58D LEU* 4.6 4.7 - - + -
77D THR 3.9 1.4 - - - +
78D LEU* 3.7 4.3 - - - +
79D LEU 2.7 30.0 + - - +
81D PHE* 3.1 29.6 - - + -
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Residues in contact with ASP 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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24D LEU 4.5 3.6 - - - +
25D VAL* 1.3 74.8 - - - +
27D PHE* 1.3 71.8 + - - +
28D TRP* 3.0 24.7 - - - +
35D CYS 5.4 0.9 - - - +
38D ILE* 4.8 2.8 - - - +
39D ALA* 5.9 0.2 - - - -
42D LEU* 3.6 23.0 - - + +
55D VAL* 5.9 0.4 - - + -
56D ALA 3.0 10.6 + - - +
57D LYS* 3.1 36.7 - - + +
58D LEU 3.0 11.4 + - - -
76D PRO* 3.5 11.3 - - - +
77D THR 4.0 2.2 - - - -
78D LEU* 3.5 22.0 - - + +
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Residues in contact with PHE 27 (chain D).
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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12D PHE* 4.3 4.5 - + - -
25D VAL* 3.5 31.6 - - + -
26D ASP* 1.3 85.9 + - - +
28D TRP* 1.3 58.5 + - - +
35D CYS* 3.9 0.2 - - - -
58D LEU* 3.2 28.0 - - + -
60D ILE* 3.7 9.4 - - + -
66D THR* 3.8 2.7 - - + -
67D ALA* 3.3 43.5 - - + -
70D TYR* 3.6 26.9 - + - -
72D ILE* 4.2 13.0 - - + -
75D ILE* 4.3 5.2 - - + +
76D PRO* 3.6 16.3 - - - +
77D THR* 3.4 23.6 + - - +
79D LEU* 4.0 19.3 - - + -
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Residues in contact with TRP 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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6D HIS* 5.8 3.8 - + - -
26D ASP* 3.0 33.0 - - - +
27D PHE* 1.3 74.0 - - - +
29D ALA* 1.3 89.7 + - - +
30D GLU* 3.4 37.0 - - + -
35D CYS* 3.2 30.5 - - + +
57D LYS* 3.5 39.2 - - + +
58D LEU 3.0 22.3 + - - +
59D ASN* 3.1 32.6 - - + +
60D ILE* 2.9 30.9 + - - +
62D GLN* 5.0 5.6 - - - -
75D ILE* 4.7 4.0 - - - -
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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