Contacts of the strand formed by residues 43 - 48 (chain I) in PDB entry 3NFP
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 TYR 43 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H TRP* 5.6 0.5 - - - -
59H GLU* 2.5 27.3 + - - +
60H TYR 4.5 8.8 + - - -
25I MET* 3.6 39.7 - - + -
26I LEU 3.6 4.7 - - - +
27I ASN* 2.7 43.7 + - - -
28I CYS* 4.0 7.4 - - - -
41I SER* 3.8 12.5 + - - +
42I LEU* 1.3 98.5 + - + +
44I MET* 1.3 62.9 + - - +
45I LEU* 4.1 1.2 + - + +
57I ASN* 3.8 18.9 + - - +
59I CYS* 4.6 0.3 - - - -
120I HIS* 4.3 7.2 - + - -
93L TYR* 3.8 37.7 - + + +
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Residues in contact with MET 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I THR 3.7 0.9 - - - +
25I MET* 3.2 8.1 - - - -
26I LEU* 2.9 41.1 + - + +
28I CYS* 4.0 14.8 - - - -
43I TYR* 1.3 72.4 - - - +
45I LEU* 1.3 58.9 + - - +
55I TRP* 3.9 27.9 - - + -
57I ASN* 3.3 34.3 - - - +
58I GLN* 4.3 3.8 - - + -
59I CYS* 4.0 18.4 - - - -
107I PRO* 3.8 27.1 - - + -
108I PRO* 6.1 0.7 - - + -
110I TRP* 4.4 23.1 - - - -
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Residues in contact with LEU 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I GLY* 3.9 13.0 - - - +
24I THR 3.7 5.6 - - - +
25I MET* 3.6 41.3 - - + -
43I TYR* 4.1 2.1 + - + +
44I MET* 1.3 71.0 - - - +
46I CYS* 1.3 72.9 + - - +
47I THR* 3.5 27.8 + - + -
55I TRP* 3.4 7.2 - - - -
56I ASP* 2.6 51.9 + - + +
57I ASN* 5.1 1.1 - - - +
92L THR* 4.1 13.2 - - + -
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Residues in contact with CYS 46 (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 TYR 4.0 2.9 - - - -
22I GLU* 3.6 18.6 - - - +
23I GLY* 3.0 23.6 + - - +
24I THR* 3.2 21.6 + - - +
45I LEU* 1.3 76.7 - - - +
47I THR* 1.3 60.2 + - - +
53I SER* 4.3 7.6 - - - -
54I SER 4.1 2.7 - - - -
55I TRP* 3.5 13.2 - - + -
104I CYS* 2.0 54.7 - - - -
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Residues in contact with THR 47 (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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22I GLU* 4.9 1.6 - - - -
45I LEU* 3.5 22.7 - - + -
46I CYS* 1.3 74.3 - - - +
48I GLY* 1.3 59.7 + - - +
49I ASN* 5.7 1.0 + - - -
53I SER* 3.2 5.7 + - - -
54I SER* 2.9 37.6 + - - +
55I TRP 5.2 0.2 - - - -
56I ASP* 3.8 32.6 + - + +
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Residues in contact with GLY 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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22I GLU* 3.8 20.9 + - - +
47I THR* 1.3 78.1 - - - +
49I ASN* 1.3 71.2 + - - +
52I HIS 3.9 4.7 - - - -
53I SER* 3.7 13.0 - - - -
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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