Contacts of the strand formed by residues 46 - 53 (chain A) in PDB entry 1SID
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 VAL 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A THR* 5.9 0.7 - - - +
44A ASP 3.4 9.9 - - - +
45A SER* 1.3 85.0 - - - +
47A THR* 1.3 75.8 + - - +
48A GLU* 4.1 4.8 + - + +
120A TRP* 6.1 0.2 - - - -
309A THR* 4.8 11.2 - - + -
310A LEU 3.5 20.4 - - - +
311A ARG* 4.8 5.2 - - + +
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Residues in contact with THR 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 6.6 0.7 - - + -
37A LEU* 4.6 20.6 - - + -
41A THR* 4.8 10.3 - - + +
45A SER* 4.8 0.5 + - - -
46A VAL* 1.3 86.0 + - - +
48A GLU* 1.3 67.2 + - - +
49A ILE* 3.8 23.6 - - + -
105A LEU* 6.2 0.7 - - + -
120A TRP* 3.8 22.5 - - + -
308A ILE 3.3 0.5 - - - +
309A THR* 3.6 1.6 - - - -
310A LEU* 3.0 47.8 + - + +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A VAL* 4.1 4.8 + - + +
47A THR* 1.3 78.9 - - - +
49A ILE* 1.3 66.6 + - - +
50A GLU* 3.8 16.0 - - - +
307A LYS* 3.0 39.5 + - + -
308A ILE 3.5 3.8 - - - +
309A THR* 4.5 20.6 - - + +
233B LYS 5.2 0.7 - - - +
266B GLU* 5.4 3.1 - - - +
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Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A MET* 4.5 28.3 - - + -
37A LEU* 4.9 5.6 - - + -
47A THR* 3.8 22.0 - - + -
48A GLU* 1.3 79.7 - - - +
50A GLU* 1.3 72.9 + - - +
51A ALA* 5.0 4.0 - - + -
103A LEU* 4.8 14.8 - - + -
105A LEU* 4.8 20.4 - - + -
278A LEU* 5.1 7.4 - - + -
306A PHE 3.1 2.9 - - - +
307A LYS* 4.2 0.6 - - - +
308A ILE* 2.8 48.0 + - + +
310A LEU* 4.2 12.8 - - + -
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Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLU* 3.8 16.5 - - - +
49A ILE* 1.3 81.0 - - - +
51A ALA* 1.3 64.2 + - - +
305A TYR* 2.8 38.8 + - + +
306A PHE 2.8 4.3 - - - -
307A LYS* 3.8 24.1 - - + -
233B LYS* 2.5 47.6 - - + +
234B ASN* 4.5 0.5 + - - -
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Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 5.0 8.5 - - + +
50A GLU* 1.3 76.2 - - - +
52A PHE* 1.3 71.1 + - - +
53A LEU* 5.3 2.9 - - + -
103A LEU* 5.0 13.7 - - + -
280A LEU* 4.8 11.4 - - + -
305A TYR* 3.4 5.1 - - - -
306A PHE* 2.7 39.9 + - + +
308A ILE* 6.0 0.2 - - + -
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Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ALA* 1.3 85.7 - - - +
53A LEU* 1.3 79.0 + - - +
54A ASN* 3.1 27.8 - - - -
304A ARG 2.9 18.8 - - - +
305A TYR* 4.2 4.7 - - + -
306A PHE* 4.2 0.7 - - - -
208B LEU* 3.2 45.8 - - + -
210B PRO* 3.7 20.0 - - + -
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ALA* 5.3 2.7 - - + -
52A PHE* 1.3 92.9 - - - +
54A ASN* 1.3 66.5 + - - +
56A ARG* 5.2 3.6 - - - +
99A SER* 4.3 7.2 - - - +
100A MET* 4.3 7.4 - - - +
101A ALA* 4.2 22.4 - - + -
103A LEU* 6.4 0.7 - - + -
280A LEU* 4.0 35.2 - - + +
281A SER* 4.1 3.4 - - - +
282A CYS* 4.0 29.9 - - - -
303A PRO* 3.3 6.9 - - - +
304A ARG 2.9 30.8 + - - +
306A PHE* 4.0 20.0 - - + -
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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