Contacts of the strand formed by residues 47 - 52 (chain I) in PDB entry 1ZUM
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 47 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E ASN* 3.2 34.9 + - - +
14E GLN* 4.6 20.0 - - + +
38I PRO* 3.6 33.9 - - + -
39I THR 3.6 5.6 - - - +
40I VAL* 4.3 10.3 - - + +
45I GLY 5.5 0.9 - - - +
46I GLU* 1.3 79.0 + - - +
48I ILE* 1.3 61.9 + - - +
49I CYS* 3.6 19.1 - - - +
50I GLN* 4.6 4.3 - - - +
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Residues in contact with ILE 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ALA 5.3 0.7 - - - +
11E PRO 4.5 0.3 - - - -
12E ASN* 3.8 19.2 + - - +
17I VAL* 4.0 16.3 - - + +
39I THR* 2.8 15.2 + - + +
40I VAL 3.8 1.8 - - - -
41I ASN* 3.7 28.5 - - + +
47I VAL* 1.3 75.2 - - - +
49I CYS* 1.3 61.4 + - - +
108I LEU* 3.6 43.7 - - + +
109I ASP* 3.5 29.6 - - + +
199I LEU* 3.9 18.8 - - + -
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Residues in contact with CYS 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ALA* 4.2 15.7 - - + +
11E PRO 3.7 16.8 - - - +
12E ASN* 4.9 2.0 - - - +
13E GLN 5.8 0.2 - - - +
17I VAL* 3.9 20.6 - - + -
20I ASN* 4.5 0.2 - - - -
38I PRO* 3.5 3.5 - - - +
39I THR* 3.1 31.1 + - - +
47I VAL* 3.6 9.6 - - - +
48I ILE* 1.3 84.3 - - + +
50I GLN* 1.3 73.5 + - - +
199I LEU* 3.8 28.7 - - - -
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Residues in contact with GLN 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E PRO 4.4 3.4 + - - +
13E GLN* 3.5 36.0 + - - +
20I ASN* 2.7 32.6 + - - +
36I THR* 2.7 36.3 + - + +
37I PHE* 2.9 33.7 - - - +
38I PRO* 3.0 18.9 - - - +
47I VAL* 4.6 4.0 - - - +
49I CYS* 1.3 78.7 - - - +
51I VAL* 1.3 60.2 + - - +
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Residues in contact with VAL 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I ASN* 3.3 16.6 - - + +
36I THR* 3.0 6.0 - - - -
37I PHE* 2.8 62.0 + - + +
39I THR* 4.3 11.7 - - + -
49I CYS* 4.3 0.2 - - - -
50I GLN* 1.3 80.8 - - - +
52I ALA* 1.3 75.8 + - - +
198I PRO* 4.0 20.2 - - + -
199I LEU* 4.0 19.5 - - + -
202I LEU* 4.3 6.1 - - + -
222I PRO* 3.8 17.3 - - + -
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Residues in contact with ALA 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I ASN 2.9 8.5 + - - -
21I GLN* 3.7 28.0 - - + -
22I ILE* 3.7 19.7 - - + +
29I HIS 4.2 1.8 - - - +
30I ASP* 4.6 2.7 - - - +
31I ALA 4.1 14.4 - - - +
35I LYS 3.9 6.3 - - - -
36I THR* 4.3 5.9 - - + +
37I PHE* 3.4 6.6 - - - -
51I VAL* 1.3 72.3 - - - +
53I GLU* 1.3 59.3 + - - +
54I GLY 3.4 5.2 + - - -
222I PRO* 3.4 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