Contacts of the strand formed by residues 47 - 54 (chain W) 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 ILE 47 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148H LEU* 3.3 15.2 - - - +
14W ILE* 5.5 2.7 - - + -
38W LEU* 3.7 33.4 - - + +
41W MET* 3.7 37.9 - - + +
42W MET* 4.5 1.8 - - - +
45W GLY* 4.0 7.6 - - - +
46W TYR* 1.3 85.1 - - - +
48W GLY* 1.3 64.9 + - - +
50W PHE* 3.7 31.2 - - + -
63W VAL* 3.7 15.0 - - + -
64W ASN 3.7 8.5 - - - +
65W LEU* 4.6 6.1 - - + -
66W THR* 3.5 9.3 + - - +
69W LEU* 4.0 10.8 - - + -
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Residues in contact with GLY 48 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H LEU* 3.3 16.6 - - - +
47W ILE* 1.3 77.7 - - - +
49W GLU* 1.3 67.6 + - - -
50W PHE* 3.3 10.6 + - - +
64W ASN* 2.7 29.0 + - - +
65W LEU 4.7 1.3 - - - -
66W THR* 3.5 12.4 + - - +
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Residues in contact with GLU 49 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H ARG* 4.1 18.6 - - + +
146H VAL 3.2 19.5 - - - +
147H LYS* 3.5 32.4 + - - +
148H LEU* 3.6 19.8 - - + +
153H LEU* 6.0 0.3 - - - +
48W GLY* 1.3 69.4 - - - -
50W PHE* 1.3 57.6 + - - +
64W ASN* 2.3 42.3 + - - +
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Residues in contact with PHE 50 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H VAL* 3.0 30.7 + - + +
148H LEU* 4.6 0.2 - - + -
35W VAL* 5.0 2.7 - - + -
38W LEU* 3.3 43.1 - - + -
39W THR* 4.5 6.1 - - - -
42W MET* 3.4 29.8 - - + -
47W ILE* 3.7 22.9 - - + -
48W GLY 3.3 5.6 + - - +
49W GLU* 1.3 78.2 - - - +
51W GLU* 1.3 57.8 + - - +
52W ILE* 4.0 31.6 - - + -
61W ILE* 4.2 9.2 - - + -
62W VAL 3.1 18.6 - - - +
63W VAL* 3.5 18.6 - - + -
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Residues in contact with GLU 51 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H ARG* 3.3 15.1 - - + +
144H ILE 3.2 17.0 - - - +
145H ARG* 3.6 30.0 + - + +
155H LYS* 3.0 37.1 + - - -
49W GLU* 4.4 0.4 + - + -
50W PHE* 1.3 73.6 - - - +
52W ILE* 1.3 66.6 + - - +
53W ILE* 3.5 7.3 + - + +
62W VAL* 3.2 28.8 + - - +
64W ASN* 5.4 0.4 - - - +
8b LEU* 3.3 40.3 - - + +
9b HIS* 5.6 0.9 - - - -
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Residues in contact with ILE 52 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H ARG* 3.6 0.9 - - - -
144H ILE* 2.5 67.7 + - + +
146H VAL* 4.8 7.2 - - + -
152H ARG* 6.3 1.1 - - - -
30W CYS* 5.0 4.3 - - - -
35W VAL* 3.9 36.1 - - + -
50W PHE* 4.0 24.5 - - + -
51W GLU* 1.3 70.9 - - - +
53W ILE* 1.3 67.0 + - - +
54W ASP* 5.4 0.9 - - - -
59W GLY* 6.0 0.2 - - - -
60W LYS 3.6 10.1 - - - +
61W ILE* 3.9 20.6 - - + -
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Residues in contact with ILE 53 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H LYS 4.9 0.2 - - - +
143H ARG* 3.3 38.6 - - + +
26W LEU* 6.0 0.2 - - + -
51W GLU* 3.5 9.2 + - + +
52W ILE* 1.3 77.3 - - - +
54W ASP* 1.3 68.0 + - - +
55W ASP* 4.8 4.5 - - + +
59W GLY* 3.2 5.5 - - - -
60W LYS* 2.5 65.5 + - + +
62W VAL* 3.7 26.7 - - + -
8b LEU* 4.5 6.5 - - + -
24b LEU* 3.9 26.0 - - + +
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Residues in contact with ASP 54 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H ASP* 5.7 1.2 - - - +
141H GLY* 5.7 0.5 - - - -
142H LYS* 3.0 61.2 + - + +
143H ARG 4.3 0.9 - - - +
144H ILE* 4.4 19.4 - - + +
18N TYR* 4.9 8.6 + - - -
52W ILE* 3.6 3.5 + - - -
53W ILE* 1.3 74.7 - - - +
55W ASP* 1.3 71.4 + - - +
59W GLY* 4.7 0.8 - - - -
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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