Contacts of the helix formed by residues 94 - 103 (chain U) 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 PRO 94 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93U SER* 1.3 95.6 - - - +
95U SER* 1.3 62.7 + - - +
96U GLU* 3.1 16.5 + - + +
97U ILE* 3.3 26.7 + - + +
98U VAL* 3.7 11.4 + - - +
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Residues in contact with SER 95 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20U ILE* 5.1 5.3 - - - +
93U SER 3.8 0.4 + - - -
94U PRO* 1.3 72.6 - - - +
96U GLU* 1.3 73.5 + - - +
98U VAL* 3.7 11.2 + - - +
99U LYS* 3.4 34.8 + - - +
116U ILE* 5.2 14.6 - - - -
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Residues in contact with GLU 96 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94U PRO* 3.1 8.8 - - + -
95U SER* 1.3 90.4 + - - +
97U ILE* 1.3 67.6 + - + +
99U LYS* 3.4 25.0 + - - +
100U GLN* 3.3 18.6 + - - +
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Residues in contact with ILE 97 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46U LYS* 5.3 6.7 - - + +
48U LEU* 4.5 16.4 - - + -
93U SER* 4.0 15.5 - - - +
94U PRO* 3.3 33.9 + - + +
96U GLU* 1.3 78.2 - - + +
98U VAL* 1.3 61.7 + - + +
100U GLN* 2.9 17.7 + - - +
101U ILE* 2.9 47.3 + - + +
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Residues in contact with VAL 98 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20U ILE* 3.7 45.8 - - + -
22U ILE* 5.1 9.2 - - + -
91U LEU* 4.9 7.2 - - + +
93U SER* 5.0 6.1 - - - +
94U PRO 3.7 14.6 + - - +
95U SER* 4.0 9.9 - - - +
96U GLU 3.3 0.6 - - - -
97U ILE* 1.3 77.2 - - + +
99U LYS* 1.3 51.7 + - + +
101U ILE* 3.4 8.9 + - + +
102U THR* 2.3 40.9 + - - +
114U VAL* 4.7 15.3 - - + -
116U ILE* 6.4 0.2 - - + -
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Residues in contact with LYS 99 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95U SER* 3.4 22.9 + - - +
96U GLU* 3.4 27.5 + - - +
97U ILE 3.2 0.6 - - - -
98U VAL* 1.3 78.9 - - + +
100U GLN* 1.3 61.1 + - - +
102U THR* 3.3 20.1 + - - +
103U SER* 4.0 7.4 + - - -
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Residues in contact with GLN 100 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46U LYS* 3.6 29.5 + - - +
96U GLU 3.3 9.8 + - - +
97U ILE* 2.9 21.0 + - - +
99U LYS* 1.3 81.2 - - - +
101U ILE* 1.3 60.6 + - - +
102U THR 3.4 0.2 + - - -
103U SER* 4.1 12.1 + - - +
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Residues in contact with ILE 101 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22U ILE* 5.5 7.0 - - + -
39U LEU* 4.4 21.3 - - + -
42U GLY 6.0 4.5 - - - +
43U ALA* 6.2 6.5 - - + -
46U LYS* 3.9 25.1 - - + +
48U LEU* 4.6 11.4 - - + -
91U LEU* 4.2 28.0 - - + -
97U ILE* 2.9 32.5 + - + +
98U VAL* 4.0 7.6 - - + +
100U GLN* 1.3 76.0 - - - +
102U THR* 1.3 65.8 + - - +
103U SER 3.4 1.3 - - - +
104U ILE* 3.3 21.0 - - + +
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Residues in contact with THR 102 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98U VAL* 2.3 34.3 + - - +
99U LYS* 3.3 15.4 - - - +
100U GLN 3.2 0.8 - - - -
101U ILE* 1.3 79.1 - - - +
103U SER* 1.3 64.5 + - - +
104U ILE* 3.2 10.4 + - - +
112U VAL* 5.7 10.5 - - + +
114U VAL* 5.1 12.0 - - + +
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Residues in contact with SER 103 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99U LYS 4.0 7.4 + - - -
100U GLN 4.1 8.8 + - - +
101U ILE 3.4 3.9 - - - +
102U THR* 1.3 77.4 - - - +
104U ILE* 1.3 64.8 + - - +
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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