Contacts of the strand formed by residues 23 - 28 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B LYS* 4.8 0.2 - - - +
22B GLY* 1.3 74.7 - - - +
24B THR* 1.3 62.5 + - - +
38B TRP* 3.3 4.2 - - - -
39B SER* 2.9 48.4 + - - +
40B ASN* 3.1 31.5 + - - +
41B ILE* 3.9 0.2 - - - +
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Residues in contact with THR 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B THR* 3.2 39.3 + - - +
17B LEU* 3.7 10.8 - - + +
19B LYS* 3.5 26.2 - - + +
22B GLY 3.9 0.8 + - - -
23B ASN* 1.3 80.6 - - - +
25B THR* 1.3 64.0 + - - +
37B GLN 3.7 4.9 - - - -
38B TRP* 4.3 0.9 - - + -
41B ILE* 3.8 19.3 - - + -
44B ALA* 3.9 17.9 - - + -
46B PHE* 3.8 17.7 - - + -
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Residues in contact with THR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ALA* 3.7 16.1 - - - +
2B LEU 3.1 10.5 + - - -
3B THR* 4.1 8.3 - - - +
17B LEU* 4.3 0.4 - - - -
24B THR* 1.3 76.3 - - - +
26B MET* 1.3 63.1 + - - +
27B THR* 5.0 0.7 + - - -
36B CYS* 3.2 7.2 - - - +
37B GLN* 3.1 60.2 + - + +
46B PHE* 3.7 2.8 - - - -
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Residues in contact with MET 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ALA* 3.3 3.3 - - - -
2B LEU* 2.7 48.1 + - + +
16B GLU 3.6 20.0 - - - +
17B LEU* 3.8 16.4 - - + -
25B THR* 1.3 77.4 + - - +
27B THR* 1.3 68.1 + - - +
28B VAL* 4.3 8.7 - - + -
34B PHE* 3.7 29.2 - - + -
35B SER 3.3 13.0 - - - +
46B PHE* 3.8 21.3 - - + -
47B ARG 3.5 34.8 - - - +
48B THR* 3.8 7.6 - - + -
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Residues in contact with THR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ALA* 3.4 26.0 - - + +
25B THR* 5.0 0.9 + - - -
26B MET* 1.3 70.3 - - - +
28B VAL* 1.3 67.0 + - - +
29B TYR* 3.6 30.6 - - + +
34B PHE* 3.2 6.3 - - - +
35B SER* 3.0 42.2 + - - -
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU* 4.7 7.4 - - + +
10B PHE* 3.8 32.8 - - + +
13B TYR* 6.0 2.2 - - + +
15B TYR* 4.0 34.8 - - + -
26B MET* 4.3 18.4 - - + -
27B THR* 1.3 80.6 - - - +
29B TYR* 1.3 79.5 + - - +
32B GLY* 5.5 1.8 - - - -
33B ARG 3.7 7.4 - - - +
34B PHE* 4.1 0.4 - - - -
48B THR* 4.4 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