Contacts of the strand formed by residues 43 - 49 (chain B) in PDB entry 5FLX
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 43 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B ASP* 4.0 8.4 - - - +
33B VAL 3.0 15.0 - - - +
34B LYS* 3.4 23.8 + - - +
41B ILE* 3.4 16.1 - - - +
42B ARG* 1.3 78.9 - - - +
44B ILE* 1.3 64.6 + - - +
45B GLY* 3.8 14.8 + - - +
46B LYS* 5.9 3.6 - - - +
25O GLU* 3.1 30.3 + - - -
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Residues in contact with ILE 44 (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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33B VAL* 2.9 26.3 + - + -
35B ALA* 3.5 37.9 - - + +
41B ILE* 5.0 2.7 - - + +
42B ARG 3.9 0.2 + - - -
43B ASN* 1.3 77.9 - - - +
45B GLY* 1.3 61.9 + - - +
67B PHE* 5.1 13.7 - - + -
69B VAL* 4.8 22.2 - - + -
74B LEU* 3.9 34.8 - - + -
86B LEU* 5.5 4.7 - - + -
98B THR* 5.5 0.2 - - + -
28O PHE* 5.3 7.6 - - - -
47O LEU* 4.0 16.5 - - + +
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Residues in contact with GLY 45 (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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32B ASP* 3.3 5.9 - - - +
33B VAL* 2.4 40.0 + - - +
43B ASN* 3.6 9.3 + - - +
44B ILE* 1.3 82.3 - - - +
46B LYS* 1.3 61.8 + - - -
25O GLU* 5.9 0.9 - - - -
28O PHE* 6.3 0.9 - - - -
47O LEU* 3.6 12.6 - - - -
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Residues in contact with LYS 46 (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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30B TRP* 3.9 22.2 - - + -
31B TYR 3.9 5.8 - - - +
32B ASP* 4.4 15.0 - - + -
43B ASN* 5.9 3.6 - - - +
45B GLY* 1.3 79.5 - - - +
47B THR* 1.3 69.8 + - - +
19O PRO* 3.6 22.9 - - + +
20O GLN 2.3 33.2 + - - +
21O VAL* 3.5 16.8 + - - +
22O ALA* 5.0 1.0 - - - +
25O GLU* 5.0 13.6 + - - -
27O VAL* 3.9 28.1 - - + +
28O PHE 5.0 4.0 + - - +
46O ASP* 4.4 1.4 - - - +
47O LEU* 3.9 19.7 + - - +
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Residues in contact with THR 47 (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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30B TRP* 3.1 19.1 - - - -
31B TYR 3.4 28.4 + - - -
33B VAL* 3.8 7.9 - - + +
46B LYS* 1.3 79.4 - - - +
48B LEU* 1.3 70.4 + - - +
62B LEU* 5.1 4.7 - - - +
65B ARG* 4.7 4.9 + - - -
67B PHE* 3.5 32.4 - - + -
96B CYS* 4.4 6.6 - - - -
46O ASP* 3.6 13.5 - - - +
47O LEU* 4.3 2.5 - - + +
48O SER* 3.7 21.5 - - - +
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Residues in contact with LEU 48 (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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25B PHE* 4.8 12.6 - - + -
28B LYS* 3.8 34.1 - - + +
29B ASP 3.5 5.6 - - - +
30B TRP* 3.4 34.1 - - + -
47B THR* 1.3 82.2 + - - +
49B VAL* 1.3 64.6 + - - +
62B LEU* 4.4 4.3 - - - +
65B ARG* 3.9 17.5 + - - -
46O ASP* 3.8 7.8 + - + -
51O GLU* 3.6 43.1 - - + +
52O THR 4.6 10.8 - - - +
53O ILE* 4.0 16.8 - - + -
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Residues in contact with VAL 49 (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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28B LYS* 3.1 11.3 - - - +
29B ASP* 2.7 48.6 + - + +
30B TRP 3.6 2.9 - - - -
31B TYR* 3.3 69.5 - - + +
47B THR 4.1 0.4 - - - +
48B LEU* 1.3 79.8 - - - +
50B THR* 1.3 62.8 + - - +
51B ARG* 3.7 11.7 - - - +
58B ALA* 4.4 11.9 - - + -
62B LEU* 4.1 9.0 - - + -
65B ARG* 5.5 0.4 - - - +
51O GLU* 6.5 0.4 - - - -
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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