Contacts of the strand formed by residues 28 - 33 (chain B) in PDB entry 1SMN
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 TYR 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B ASN* 3.3 11.9 - - - +
23B ILE* 4.0 2.2 - - + +
24B VAL 3.8 0.2 - - - -
25B ARG* 2.8 65.4 + - - +
26B HIS 3.3 2.2 - - - -
27B ALA* 1.3 86.6 - - + +
29B THR* 1.3 57.1 + - - +
30B LEU* 3.5 37.2 - - + -
42B VAL* 3.7 14.4 - - + -
43B ALA 3.3 15.5 - - - +
44B TYR* 4.1 5.2 - - + -
91B ALA* 3.8 15.9 - - + -
104B SER* 2.7 45.9 + - - -
105B LEU* 3.9 3.8 - - + -
107B TYR* 4.3 0.2 - - - +
109B SER* 4.1 5.0 + - - -
110B ASN* 4.1 16.4 - - + +
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Residues in contact with THR 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE 4.8 1.0 + - - -
8B ASN* 2.9 32.7 + - - +
13B CYS* 4.4 12.3 - - - -
22B SER* 4.1 8.5 - - - -
23B ILE 3.1 11.0 - - - +
24B VAL* 4.0 23.5 - - + +
28B TYR* 1.3 71.9 + - - +
30B LEU* 1.3 65.0 + - - +
41B TRP* 3.6 26.6 - - + -
42B VAL* 3.4 3.5 - - - +
43B ALA* 2.8 35.6 + - - -
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B SER* 3.2 6.7 - - - -
23B ILE* 2.8 49.8 + - + +
25B ARG* 5.8 0.2 - - - +
28B TYR* 3.5 32.3 - - + -
29B THR* 1.3 76.8 - - - +
31B ASN* 1.3 61.8 + - - +
32B ASN* 3.8 25.5 + - + +
39B ALA* 3.7 12.6 - - + -
41B TRP* 3.6 6.3 - - - +
42B VAL* 4.1 13.0 - - + -
62B ASP* 5.3 1.3 - - - +
65B LEU* 5.1 1.3 - - + -
109B SER* 3.5 42.2 - - - +
110B ASN* 4.2 2.5 - - + +
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Residues in contact with ASN 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLY* 3.3 13.1 - - - -
19B SER* 2.9 30.3 + - - -
20B ASN 4.9 0.4 - - - -
21B VAL 3.7 8.3 + - - -
22B SER* 3.1 20.3 + - - +
30B LEU* 1.3 74.8 - - - +
32B ASN* 1.3 53.6 + - - +
39B ALA* 3.3 3.5 - - - +
40B ASN* 2.7 59.8 + - - -
41B TRP* 3.1 42.8 + - + +
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Residues in contact with ASN 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B SER* 3.2 6.4 + - - -
19B SER* 2.4 31.3 + - - +
21B VAL 5.0 1.6 + - - -
23B ILE* 6.0 0.4 - - + +
30B LEU* 3.8 14.0 + - + +
31B ASN* 1.3 73.5 - - - +
33B ASN* 1.3 73.7 + - - +
34B SER* 4.0 3.0 - - - +
37B LYS 4.3 5.2 - - - +
38B PHE 3.9 14.0 - - - -
39B ALA* 4.0 6.5 + - - +
40B ASN* 3.3 3.6 + - - -
65B LEU* 3.8 36.8 - - + +
69B ASP* 3.0 32.6 + - - +
70B THR* 4.8 1.0 + - - -
109B SER* 4.8 5.5 - - - -
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Residues in contact with ASN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B SER* 3.3 18.8 + - - -
32B ASN* 1.3 79.2 + - - +
34B SER* 1.3 56.4 + - - +
35B THR* 2.9 34.8 + - - -
36B THR* 3.1 26.5 + - - +
37B LYS* 2.9 28.2 + - - -
38B PHE 3.1 19.0 + - - +
40B ASN* 2.9 26.6 + - - +
150B TYR* 5.5 2.8 - - - -
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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