Contacts of the strand formed by residues 124 - 130 (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 LYS 124 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8021 A 5.7 3.1 - - + -
8031 C 4.8 5.4 - - - +
8621 A 4.4 9.4 - - + +
8631 U 2.6 55.8 + - + +
8641 A 4.3 6.3 + - - -
78W ARG* 3.9 34.4 - - + +
79W PHE 3.8 7.0 - - - +
80W ASP* 3.1 25.8 - - - +
104W LEU* 3.2 6.9 - - - +
105W THR* 2.9 42.6 + - - +
123W GLY* 1.3 75.7 - - - +
125W ILE* 1.3 61.8 + - - +
126W LEU* 4.0 1.6 - - + -
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Residues in contact with ILE 125 (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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75W ILE* 3.6 29.8 - - + +
78W ARG* 3.6 23.2 - - - +
79W PHE* 3.5 14.6 + - + +
81W VAL* 3.6 31.2 - - + -
86W LEU* 5.0 4.5 - - + -
89W TRP* 3.9 29.4 - - + +
93W LEU* 4.8 1.3 - - + -
102W ILE* 3.9 22.9 - - + -
103W VAL 3.8 2.9 - - - -
104W LEU* 3.5 20.9 - - + -
123W GLY 4.4 3.4 - - - +
124W LYS* 1.3 73.1 - - - +
126W LEU* 1.3 65.1 + - - +
127W GLY 4.0 4.9 - - - +
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Residues in contact with LEU 126 (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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8631 U 5.5 2.5 - - - +
7W LEU* 4.0 16.4 - - + -
33W VAL* 3.6 29.8 - - + +
37W PHE* 5.3 1.8 - - + -
74W VAL* 3.2 14.8 - - - +
75W ILE 3.0 23.1 + - - +
78W ARG* 3.5 43.1 - - - +
103W VAL* 3.1 36.6 + - + +
105W THR* 3.2 28.0 - - + +
110W ILE* 4.0 7.0 - - + -
124W LYS* 4.0 2.4 + - + -
125W ILE* 1.3 73.4 - - - +
127W GLY* 1.3 59.9 + - - +
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Residues in contact with GLY 127 (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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7W LEU* 5.9 0.2 - - - -
37W PHE* 5.6 4.7 - - - -
73W GLY 3.6 11.7 - - - -
74W VAL* 4.0 1.1 - - - -
75W ILE* 3.9 12.8 - - - -
102W ILE* 3.5 10.1 - - - +
103W VAL* 3.3 26.7 + - - +
125W ILE* 3.6 4.7 - - - +
126W LEU* 1.3 81.3 - - - +
128W PHE* 1.3 67.0 + - - +
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Residues in contact with PHE 128 (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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11561 U 3.5 35.7 - - - -
11571 G 5.4 7.6 - + + -
11W LEU* 5.4 1.2 - - - +
37W PHE* 5.6 1.5 - - - -
71W LYS* 4.8 3.8 - - + -
72W CYS* 3.7 0.3 - - - +
73W GLY* 3.0 50.9 + - - +
74W VAL 5.1 1.6 - - - -
75W ILE* 4.5 10.5 - - + -
93W LEU* 3.6 44.4 - - + -
94W LEU* 5.1 2.5 - - + -
101W PHE 3.8 16.4 - - - +
102W ILE* 4.4 8.1 - - + +
127W GLY* 1.3 79.5 - - - +
129W PHE* 1.3 69.5 + - - +
130W PHE* 3.8 30.5 - + - -
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Residues in contact with PHE 129 (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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37W PHE* 3.7 22.4 - + + -
40W VAL* 4.2 4.5 - - + -
41W MET* 3.6 32.3 - - + -
44W HIS* 3.3 32.3 - + - -
46W TYR* 3.4 35.2 - + - -
69W LEU* 4.8 2.0 - - + -
71W LYS 3.9 6.3 - - - -
72W CYS* 4.0 16.6 - - + -
100W GLY 4.7 0.5 - - - -
101W PHE* 4.0 29.8 + - + +
103W VAL* 3.4 27.8 - - + -
112W ASP* 5.1 0.2 - - - -
128W PHE* 1.3 78.9 - - - +
130W PHE* 1.3 69.3 + - - +
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Residues in contact with PHE 130 (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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11551 U 3.3 35.0 - + - -
250C TYR* 3.7 31.4 + + - +
46W TYR* 4.9 12.8 - - - +
68W ARG* 3.1 37.2 + - - +
69W LEU* 3.9 11.4 - - - +
70W ASN* 3.2 23.4 + - + -
71W LYS* 3.0 41.1 + - + +
93W LEU 4.5 10.1 - - - -
94W LEU* 5.4 3.8 - - + -
95W PRO* 4.3 23.3 - - + -
99W PHE* 5.3 0.9 - - + -
100W GLY* 4.4 17.7 - - - +
128W PHE* 3.8 32.1 - + + -
129W PHE* 1.3 83.2 - - - +
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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