Contacts of the strand formed by residues 47 - 53 (chain D) 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 THR 47 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D LEU* 4.7 15.7 - - + -
41D THR* 4.4 8.7 - - - +
45D SER 3.7 3.1 + - - -
46D VAL* 1.3 78.1 + - - +
48D GLU* 1.3 69.7 + - - +
49D ILE* 3.8 17.7 - - + -
105D LEU* 6.1 0.9 - - + -
120D TRP* 3.5 23.0 - - + -
309D THR* 3.5 2.6 - - - +
310D LEU* 2.9 58.8 + - + +
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Residues in contact with GLU 48 (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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46D VAL* 4.2 5.2 + - + +
47D THR* 1.3 76.3 - - - +
49D ILE* 1.3 66.7 + - - +
50D GLU* 4.1 12.5 + - - +
307D LYS* 3.3 39.3 + - + -
308D ILE 3.4 4.5 - - - +
309D THR* 3.8 26.8 - - + +
233E LYS 5.5 0.9 - - - +
266E GLU* 5.0 5.2 - - - +
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Residues in contact with ILE 49 (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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34D MET* 4.4 21.8 - - + -
37D LEU* 4.7 8.7 - - + -
47D THR* 3.8 15.0 - - + -
48D GLU* 1.3 80.5 - - - +
50D GLU* 1.3 73.0 + - - +
51D ALA* 4.9 3.1 - - + -
103D LEU* 4.2 22.7 - - + -
105D LEU* 4.4 18.2 - - + -
278D LEU* 4.8 4.3 - - + -
306D PHE 3.4 1.4 - - - +
307D LYS* 3.3 1.7 - - - -
308D ILE* 2.8 48.6 + - + +
310D LEU* 4.1 25.4 - - + -
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Residues in contact with GLU 50 (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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48D GLU* 4.5 11.6 - - - +
49D ILE* 1.3 80.2 - - - +
51D ALA* 1.3 66.5 + - - +
305D TYR* 2.9 36.2 + - + +
306D PHE 3.0 4.5 - - - +
307D LYS* 3.9 23.7 - - + +
233E LYS* 2.5 51.9 - - + +
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Residues in contact with ALA 51 (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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49D ILE* 4.9 8.7 - - + +
50D GLU* 1.3 80.5 - - - +
52D PHE* 1.3 77.1 + - - +
53D LEU* 6.1 0.7 - - + -
103D LEU* 5.3 10.1 - - + -
280D LEU* 5.1 10.8 - - + -
305D TYR* 3.3 7.6 - - - -
306D PHE* 2.7 37.6 + - + +
308D ILE* 5.7 0.7 - - + -
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Residues in contact with PHE 52 (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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51D ALA* 1.3 88.7 - - - +
53D LEU* 1.3 87.1 + - - +
54D ASN* 4.0 17.9 - - + -
304D ARG 2.9 20.6 - - - +
305D TYR* 4.1 4.0 - + + -
306D PHE* 3.8 4.0 - - - -
208E LEU* 3.3 44.6 - - + -
210E PRO* 4.0 16.4 - - + -
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Residues in contact with LEU 53 (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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51D ALA* 6.1 0.7 - - + -
52D PHE* 1.3 94.7 - - - +
54D ASN* 1.3 63.5 + - - +
55D PRO 3.7 0.4 - - - -
56D ARG* 5.5 2.9 - - - +
99D SER* 3.9 16.8 - - - +
100D MET* 4.1 17.3 - - - +
101D ALA* 4.2 22.4 - - + -
280D LEU* 4.2 17.9 - - + +
281D SER 4.2 2.5 - - - +
282D CYS* 3.4 34.1 - - - -
303D PRO* 3.3 8.3 - - - +
304D ARG 3.0 26.5 + - - +
306D PHE* 3.8 20.4 - - + -
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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