Contacts of the helix formed by residues 62 - 67 (chain N) 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 GLN 62 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9191 A 5.4 0.2 + - - -
10161 U 3.9 10.1 + - - +
10171 U 2.8 47.7 + - - +
10181 U 3.8 11.9 + - - -
16N LEU* 3.2 20.4 - - + +
60N VAL 4.3 0.4 + - - -
61N ALA* 1.3 77.2 - - - +
63N VAL* 1.3 56.9 + - - +
64N ARG* 3.0 40.0 - - + +
65N PHE* 2.6 73.1 + - + +
66N VAL 3.7 0.9 + - - -
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Residues in contact with VAL 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10181 U 4.9 7.5 + - - +
33N VAL* 4.3 11.4 - - + -
51N GLY* 6.0 4.7 - - - -
54N LEU* 4.6 21.5 - - + -
60N VAL* 4.5 15.3 - - + +
61N ALA 3.7 0.2 - - - -
62N GLN* 1.3 72.7 - - - +
64N ARG* 1.3 62.5 + - - +
65N PHE 3.1 0.3 + - - -
66N VAL* 3.1 9.4 + - + -
67N THR* 2.9 51.1 + - + +
69N ASN 4.3 3.4 - - - +
71N ILE* 3.8 32.1 - - + -
74N ILE* 4.9 3.6 - - + -
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Residues in contact with ARG 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9181 U 3.2 49.9 + - - +
9191 A 4.8 31.7 + - - +
10181 U 5.6 2.7 + - - +
10191 C 6.0 1.1 - - - -
62N GLN* 3.0 26.6 - - + +
63N VAL* 1.3 77.3 - - + +
65N PHE* 1.3 64.5 + - + +
68N GLY* 3.2 20.6 - - - +
69N ASN* 3.8 20.4 - - - +
70N LYS* 3.7 41.8 - - + +
71N ILE* 5.5 1.3 - - + +
73N ARG* 4.8 9.3 - - - +
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Residues in contact with PHE 65 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9181 U 6.3 0.4 - - - -
9191 A 4.2 14.1 - - - -
10161 U 4.3 7.2 - - - -
16N LEU* 3.8 14.4 - - + -
17N PRO* 4.2 24.5 - - + -
19N ARG 3.9 20.0 - - - -
20N ARG* 4.3 15.7 - - + -
21N SER* 3.2 51.8 - - - +
61N ALA 4.1 6.5 - - - +
62N GLN* 2.6 48.5 + - + +
64N ARG* 1.3 79.9 - - + +
66N VAL* 1.3 64.7 + - + +
68N GLY* 4.0 2.9 + - - -
56W HIS* 5.9 0.2 - - - -
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Residues in contact with VAL 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21N SER 5.5 0.2 - - - +
22N VAL* 4.1 28.3 - - + -
26N LEU 5.7 1.8 - - - +
28N LEU* 5.0 10.3 - - + +
29N THR 5.7 2.2 - - - +
30N SER* 6.4 0.9 - - - -
33N VAL* 4.9 13.9 - - + -
60N VAL* 3.7 30.3 - - + -
61N ALA 5.0 1.6 - - - +
62N GLN 4.4 1.3 - - - +
63N VAL* 3.4 16.4 - - + +
65N PHE* 1.3 79.9 - - + +
67N THR* 1.3 79.1 + - - +
68N GLY* 4.4 0.2 - - - -
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Residues in contact with THR 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30N SER* 4.7 11.5 + - - +
33N VAL* 3.9 18.9 - - - +
34N LYS* 5.0 12.9 - - + +
63N VAL* 2.9 32.4 + - - +
66N VAL* 1.3 77.9 - - - +
68N GLY* 1.3 59.5 + - - +
69N ASN* 4.0 14.9 - - + +
74N ILE* 4.0 21.4 - - + +
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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