Contacts of the strand formed by residues 43 - 49 (chain C) in PDB entry 3GB9
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 43 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LYS 4.3 7.0 - - - +
42C LEU* 1.3 74.0 - - - +
44C GLN* 1.3 84.8 + - - +
45C ALA 3.0 2.9 + - - -
71C GLY* 3.5 1.4 - - - -
72C PHE* 3.0 44.8 + - - +
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Residues in contact with GLN 44 (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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22C LYS* 5.1 8.8 - - - +
23C HIS* 2.8 42.7 + - + -
43C THR* 1.3 90.3 + - - +
45C ALA* 1.3 63.8 + - - +
72C PHE* 4.1 19.9 - - + -
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Residues in contact with ALA 45 (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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39C THR 5.4 1.8 - - - +
42C LEU* 3.8 19.3 - - + +
43C THR 3.0 3.4 - - - -
44C GLN* 1.3 81.9 - - - +
46C GLN* 1.3 62.4 + - - +
47C ILE* 5.2 7.2 - - + -
69C VAL* 4.3 15.5 - - + -
70C PHE 3.1 9.9 - - - +
71C GLY* 4.4 0.2 - - - -
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Residues in contact with GLN 46 (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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20C HIS 2.7 30.5 + - - -
21C THR* 3.2 22.5 + - - +
22C LYS* 3.8 6.9 + - - +
23C HIS* 3.5 21.6 + - + +
45C ALA* 1.3 75.8 - - - +
47C ILE* 1.3 66.3 + - - +
48C PHE* 3.6 16.5 - - + -
68C LEU 3.9 0.7 - - - +
69C VAL* 3.5 1.4 - - - -
70C PHE* 2.8 37.3 + - + -
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Residues in contact with ILE 47 (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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45C ALA* 5.2 6.5 - - + -
46C GLN* 1.3 82.7 - - - +
48C PHE* 1.3 80.6 + - - +
49C ASP* 4.6 8.1 - - - +
52C GLU* 4.4 5.2 - - - +
67C ARG* 3.7 40.6 - - + +
68C LEU 3.5 7.0 - - - +
69C VAL* 4.3 14.8 - - + -
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Residues in contact with PHE 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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16C TRP* 3.7 31.9 - + - -
17C LEU* 4.1 9.2 - - + -
20C HIS* 3.6 21.3 - + + -
21C THR* 4.4 5.4 - - - -
46C GLN* 3.6 33.0 - - + -
47C ILE* 1.3 81.0 - - - +
49C ASP* 1.3 61.3 + - - +
52C GLU* 3.6 22.9 - - + +
53C ILE* 3.8 20.6 - - + -
67C ARG* 3.5 1.2 - - - +
68C LEU* 2.8 43.3 + - + +
70C PHE* 3.8 35.7 - + - -
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Residues in contact with ASP 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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47C ILE* 4.3 7.9 - - - +
48C PHE* 1.3 75.7 - - - +
50C TYR* 1.3 65.7 + - - +
51C GLY* 3.2 4.7 - - - +
52C GLU* 2.9 36.5 + - + +
53C ILE* 3.7 4.4 - - - +
65C ALA 6.0 0.3 - - - -
66C GLY 3.9 14.9 + - - +
67C ARG* 4.3 10.2 - - - +
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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