Contacts of the strand formed by residues 23 - 28 (chain A) in PDB entry 1F5J
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 ASN 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LYS* 4.7 0.4 - - - +
22A GLY* 1.3 74.2 - - - +
24A THR* 1.3 61.5 + - - +
38A TRP* 3.3 4.7 - - - -
39A SER* 3.0 45.0 + - - +
40A ASN* 3.2 32.3 + - - +
41A ILE* 3.9 0.4 - - - +
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Residues in contact with THR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A THR* 3.1 38.3 + - - +
17A LEU* 3.7 9.0 - - + +
19A LYS* 3.3 28.7 - - + +
22A GLY 3.8 1.0 + - - -
23A ASN* 1.3 79.5 - - - +
25A THR* 1.3 62.2 + - - +
37A GLN 3.6 4.9 - - - -
38A TRP* 4.2 0.7 - - + -
41A ILE* 3.9 17.7 - - + -
44A ALA* 3.9 9.9 - - + -
46A PHE* 3.8 27.1 - - + -
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Residues in contact with THR 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ALA* 3.7 19.1 - - - +
2A LEU 3.1 7.0 + - - -
3A THR* 4.2 7.8 - - - +
24A THR* 1.3 76.7 - - - +
26A MET* 1.3 62.6 + - - +
27A THR* 5.1 0.5 + - - -
36A CYS* 3.2 6.0 - - - +
37A GLN* 3.1 58.4 + - + +
46A PHE* 3.8 3.0 - - - -
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Residues in contact with MET 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ALA* 3.3 3.0 - - - +
2A LEU* 2.7 50.8 + - + +
16A GLU 3.7 20.2 - - - +
17A LEU* 3.7 22.2 - - + -
25A THR* 1.3 78.4 + - - +
27A THR* 1.3 69.9 + - - +
28A VAL* 4.0 11.7 - - + -
34A PHE* 3.7 33.4 - - + -
35A SER 3.3 11.7 - - - +
46A PHE* 3.8 19.1 - - + -
47A ARG 3.7 28.3 - - - +
48A THR* 4.0 5.4 - - + -
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Residues in contact with THR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ALA* 3.4 24.4 - - + +
25A THR* 5.1 0.5 + - - -
26A MET* 1.3 71.5 - - - +
28A VAL* 1.3 68.3 + - - +
29A TYR* 3.5 33.0 - - + +
34A PHE* 3.1 6.0 - - - +
35A SER* 2.9 46.2 + - - -
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Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 4.5 10.5 - - + +
10A PHE* 3.9 34.0 - - + +
13A TYR* 6.0 2.0 - - + +
15A TYR* 3.8 41.3 - - + -
26A MET* 4.0 17.7 - - + -
27A THR* 1.3 79.2 - - - +
29A TYR* 1.3 79.5 + - - +
32A GLY* 5.7 1.8 - - - -
33A ARG 3.8 6.7 - - - +
34A PHE* 4.1 0.9 - - + -
48A THR* 4.7 5.8 - - + -
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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