Contacts of the strand formed by residues 43 - 47 (chain B) in PDB entry 1SIW
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 ASN 43 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B SER* 3.5 6.1 - - - -
40B TRP* 3.9 18.6 - - + +
42B ASN* 1.3 76.2 - - - +
44B VAL* 1.3 64.6 + - - +
45B GLU* 3.2 38.1 + - - +
52B PHE* 3.7 23.1 - - + +
142B PRO* 4.8 6.1 + - + +
181B PRO* 3.6 0.2 - - - +
182B ARG* 2.8 45.5 + - - +
231B LYS* 2.8 25.8 + - - -
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Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLY* 4.6 4.5 - - - -
20B HIS* 3.2 38.4 + - + +
22B CYS* 3.7 29.6 - - - -
23B SER* 3.7 8.4 + - - +
42B ASN* 4.2 0.2 - - - +
43B ASN* 1.3 79.7 + - - +
45B GLU* 1.3 72.6 + - - +
46B THR* 5.8 0.2 - - - +
142B PRO 5.2 1.2 - - - +
143B ASN* 3.5 10.4 - - - +
179B TYR* 4.2 18.2 - - + -
180B LEU 3.7 2.9 - - - -
181B PRO* 3.8 23.1 - - + -
802B SF4 3.9 15.5 - - - -
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Residues in contact with GLU 45 (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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43B ASN* 3.2 22.4 + - - +
44B VAL* 1.3 76.8 - - - +
46B THR* 1.3 65.7 + - - +
47B LYS* 4.3 14.0 - - + -
51B GLY* 3.4 24.4 - - - -
52B PHE* 2.8 21.8 + - + +
56B TRP* 3.0 20.8 + - - -
142B PRO 5.7 1.3 - - - +
143B ASN* 5.0 1.3 - - - -
179B TYR* 3.5 2.1 - - - -
180B LEU* 2.8 47.7 + - + +
182B ARG* 3.0 29.4 + - - -
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Residues in contact with THR 46 (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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20B HIS* 5.6 0.9 + - - -
44B VAL 4.3 0.6 + - - -
45B GLU* 1.3 75.8 - - - +
47B LYS* 1.3 72.3 + - - +
48B PRO 3.3 13.1 - - - +
49B GLY* 3.8 7.1 + - - -
143B ASN* 4.9 3.5 + - - -
145B GLU* 4.0 15.6 - - - +
146B ASP* 3.7 9.3 + - - +
147B ASP* 3.1 35.0 + - - +
148B LEU* 3.9 13.5 - - + +
177B MET* 4.3 9.9 - - + -
178B MET 3.5 10.5 - - - +
179B TYR* 3.3 23.5 - - + -
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Residues in contact with LYS 47 (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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45B GLU* 4.3 12.4 + - + +
46B THR* 1.3 79.0 - - - +
48B PRO* 1.3 62.6 - - - +
49B GLY* 3.1 25.9 + - - +
50B GLN 4.8 2.2 - - - -
51B GLY 5.6 0.4 - - - +
57B GLU* 2.6 30.7 + - - -
158B ASP* 3.3 14.7 + - - +
159B LYS 5.5 0.2 - - - +
160B ASN* 3.9 6.3 - - - +
176B PHE* 4.6 1.1 - - - -
177B MET* 3.2 7.1 - - - +
178B MET* 2.8 52.6 + - + +
180B LEU* 4.1 36.8 - - + -
389B TYR* 3.2 26.0 - - + +
393B LEU* 5.0 2.7 - - + -
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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
------------------------------------------------------------
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