Contacts of the strand formed by residues 47 - 53 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C LEU* 3.7 28.1 - - + +
41C THR* 4.5 8.1 - - - +
45C SER 3.9 3.8 + - - -
46C VAL* 1.3 79.6 + - - +
48C GLU* 1.3 67.3 + - - +
49C ILE* 3.8 21.8 - - + -
105C LEU* 6.0 0.9 - - + -
120C TRP* 3.7 24.0 - - + -
309C THR* 3.5 2.9 - - - -
310C LEU* 3.0 43.2 + - - +
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Residues in contact with GLU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C VAL* 4.1 7.2 + - + +
47C THR* 1.3 76.8 - - - +
49C ILE* 1.3 63.0 + - - +
50C GLU* 4.3 5.9 + - - +
307C LYS* 3.3 37.2 + - - -
308C ILE 3.4 5.4 - - - +
309C THR* 3.7 26.9 - - + +
233D LYS 5.5 0.7 - - - +
266D GLU* 5.6 1.6 - - - +
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Residues in contact with ILE 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C MET* 4.6 14.4 - - + -
37C LEU* 4.4 18.6 - - + -
47C THR* 3.8 18.2 - - + -
48C GLU* 1.3 78.9 - - - +
50C GLU* 1.3 71.7 + - - +
51C ALA* 4.9 3.1 - - + +
103C LEU* 4.6 21.3 - - + -
105C LEU* 4.5 19.3 - - + -
278C LEU* 4.8 5.6 - - + -
307C LYS* 3.3 1.6 - - - +
308C ILE* 2.8 49.9 + - + +
310C LEU* 3.9 21.1 - - + -
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Residues in contact with GLU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C GLU* 4.3 5.0 + - - +
49C ILE* 1.3 80.3 - - - +
51C ALA* 1.3 61.8 + - - +
305C TYR* 2.7 32.0 + - + +
306C PHE 3.1 6.7 - - - +
307C LYS* 3.4 28.7 - - + -
232D ALA 3.1 1.9 - - - +
233D LYS* 2.6 58.4 + - + +
234D ASN* 4.2 1.9 + - - -
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Residues in contact with ALA 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ILE* 4.1 8.0 - - + +
50C GLU* 1.3 75.7 - - - +
52C PHE* 1.3 68.4 + - + +
53C LEU* 5.5 1.8 - - + -
103C LEU* 5.2 12.6 - - + -
280C LEU* 5.1 13.7 - - + -
305C TYR* 3.4 6.3 - - - -
306C PHE* 2.6 38.5 + - - +
308C ILE* 5.3 1.5 - - + +
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Residues in contact with PHE 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ALA* 1.3 86.5 - - + +
53C LEU* 1.3 88.2 + - - +
54C ASN* 3.6 20.4 - - + -
303C PRO* 5.7 0.4 - - + -
304C ARG 3.0 15.9 - - - +
305C TYR* 3.8 11.0 - - + -
306C PHE* 4.3 2.0 - - - -
208D LEU* 3.0 35.0 - - + -
210D PRO* 4.0 24.2 - - + -
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ALA* 5.5 2.0 - - + -
52C PHE* 1.3 103.7 - - - +
54C ASN* 1.3 64.2 + - - +
55C PRO 3.7 0.6 - - - -
56C ARG* 6.1 1.3 - - - +
99C SER* 4.5 4.0 - - - +
100C MET* 4.3 16.4 - - - +
101C ALA* 4.4 19.3 - - + -
280C LEU* 4.1 31.9 - - + +
281C SER 4.4 0.2 - - - +
282C CYS* 3.9 18.6 - - - -
303C PRO* 3.2 7.3 - - - +
304C ARG 2.7 32.5 + - - +
306C PHE* 3.4 32.8 - - + -
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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