Contacts of the strand formed by residues 47 - 53 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36F VAL* 6.3 2.5 - - + -
37F LEU* 3.8 31.8 - - + +
41F THR* 4.3 12.9 - - + +
45F SER 4.8 0.3 - - - -
46F VAL* 1.3 87.2 + - - +
48F GLU* 1.3 73.4 + - - +
49F ILE* 4.2 6.3 - - + -
120F TRP* 4.2 18.7 - - - -
308F ILE 3.4 0.9 - - - +
309F THR* 3.5 2.6 - - - -
310F LEU* 3.1 44.0 + - - +
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Residues in contact with GLU 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F VAL* 4.1 4.0 + - + +
47F THR* 1.3 83.2 - - - +
49F ILE* 1.3 64.1 + - - +
50F GLU* 4.4 7.4 + - - +
307F LYS* 3.3 38.9 + - + -
308F ILE 3.4 5.2 - - - +
309F THR* 4.2 21.1 - - + +
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Residues in contact with ILE 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F MET* 4.1 23.8 - - + -
37F LEU* 4.3 13.2 - - + -
47F THR* 4.2 11.4 - - + -
48F GLU* 1.3 79.9 - - - +
50F GLU* 1.3 70.7 + - - +
51F ALA* 5.0 3.6 - - + +
103F LEU* 4.5 21.3 - - + -
105F LEU* 4.2 23.3 - - + -
278F LEU* 5.1 4.3 - - + -
306F PHE 3.6 0.9 - - - +
307F LYS* 3.3 1.4 - - - +
308F ILE* 2.8 47.7 + - + +
310F LEU* 4.7 16.8 - - + -
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Residues in contact with GLU 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F GLU* 5.1 6.5 - - + +
49F ILE* 1.3 83.0 - - - +
51F ALA* 1.3 63.4 + - - +
305F TYR* 2.6 39.3 + - + +
306F PHE 2.8 7.9 - - - +
307F LYS* 3.7 26.0 + - + +
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Residues in contact with ALA 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ILE* 4.2 6.5 + - + -
50F GLU* 1.3 76.5 - - - +
52F PHE* 1.3 80.4 + - + +
53F LEU* 5.7 1.1 - - + -
103F LEU* 5.1 13.7 - - + -
280F LEU* 5.0 14.6 - - + -
305F TYR* 3.4 6.9 - - - -
306F PHE* 2.8 28.4 + - - +
308F ILE* 5.7 0.4 - - - +
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Residues in contact with PHE 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F ALA* 1.3 91.6 - - + +
53F LEU* 1.3 82.2 + - - +
54F ASN* 3.7 27.4 - - + -
303F PRO* 5.3 2.7 - - + -
304F ARG 2.8 23.3 - - - +
305F TYR* 3.9 5.2 - + + -
306F PHE* 4.2 3.8 - - - -
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Residues in contact with LEU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F ALA* 5.7 1.1 - - + -
52F PHE* 1.3 89.9 - - - +
54F ASN* 1.3 67.4 + - - +
56F ARG* 5.3 2.9 - - - +
99F SER* 3.7 20.4 - - - +
100F MET* 4.1 15.5 - - - +
101F ALA* 4.4 15.9 - - + -
103F LEU* 6.3 0.4 - - + -
280F LEU* 4.2 20.4 - - + -
281F SER* 4.1 5.4 - - - +
282F CYS* 3.6 36.7 - - - +
303F PRO* 3.5 2.3 - - - +
304F ARG 2.8 32.0 + - - +
306F PHE* 3.9 17.0 - - + -
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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