Contacts of the helix formed by residues 68 - 75 (chain H) 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 68 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42H GLU* 5.1 14.0 + - - +
43H LEU* 6.1 2.3 - - + -
44H ASN* 4.0 27.5 - - - +
65H PRO* 3.1 25.3 + - + +
67H PRO* 1.3 91.1 + - + +
69H LEU* 1.3 63.7 + - - +
70H LYS 3.2 2.9 - - - -
71H SER* 3.0 40.6 + - - -
72H PHE* 3.2 24.1 + - + -
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Residues in contact with LEU 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64H VAL* 3.7 30.1 - - + -
65H PRO 3.3 3.4 + - - -
66H VAL* 3.7 13.0 - - - +
67H PRO 3.3 2.2 - - - -
68H GLN* 1.3 76.3 - - - +
70H LYS* 1.3 63.9 + - + +
72H PHE* 3.0 6.4 + - + +
73H GLN* 2.9 40.4 + - + +
96H ALA* 4.5 9.9 - - + -
98H ARG* 5.4 2.2 - - - +
132H ASP* 4.3 22.7 - - - +
135H PHE* 5.2 7.8 - - + -
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Residues in contact with LYS 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H VAL 5.4 1.4 + - - -
67H PRO* 3.8 22.2 + - - +
68H GLN* 3.2 0.8 - - - +
69H LEU* 1.3 82.3 - - + +
71H SER* 1.3 57.8 + - - +
73H GLN* 3.2 15.2 + - - +
74H LYS* 2.9 27.5 + - - +
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Residues in contact with SER 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ALA* 5.2 2.4 - - - +
39H GLN* 3.4 22.7 + - - +
42H GLU* 5.5 2.4 + - - -
67H PRO 5.2 0.7 + - - -
68H GLN* 3.0 36.1 + - - -
70H LYS* 1.3 77.9 - - - +
72H PHE* 1.3 66.8 + - - +
74H LYS* 3.4 22.0 - - - +
75H ILE 4.2 1.0 + - - -
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Residues in contact with PHE 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H GLN* 3.1 23.7 + - + +
43H LEU* 3.5 32.5 - - + -
44H ASN 4.7 1.1 - - - -
45H ILE* 5.8 1.8 - - + -
62H ILE* 6.0 4.0 - - + -
63H PHE 4.1 5.2 - - - -
64H VAL* 3.5 48.0 - - + -
65H PRO* 3.6 23.8 - - + -
68H GLN* 3.2 17.2 + - + -
69H LEU* 3.0 8.3 + - + +
71H SER* 1.3 78.5 - - - +
73H GLN* 1.3 63.0 + - - +
74H LYS 3.1 1.6 - - - -
75H ILE 3.9 0.7 - - - -
76H GLN* 3.0 39.6 + - - +
94H PHE* 5.9 5.4 - + - -
135H PHE* 4.0 6.1 - - + -
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Residues in contact with GLN 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H LEU* 2.9 25.8 + - + +
70H LYS* 3.2 14.8 + - - +
72H PHE* 1.3 75.3 - - - +
74H LYS* 1.3 65.8 + - - +
75H ILE 3.5 0.2 - - - -
76H GLN* 4.3 2.3 + - - +
135H PHE* 3.1 30.3 - - + -
21N SER* 5.5 4.8 + - - -
22N VAL* 5.4 9.7 - - - +
27N LYS* 5.8 1.4 + - - -
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Residues in contact with LYS 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ALA* 3.6 31.1 + - + +
41H ARG* 5.6 5.1 - - - +
70H LYS 2.9 11.1 + - - +
71H SER* 3.4 17.5 - - - +
72H PHE 3.1 0.6 - - - -
73H GLN* 1.3 82.4 - - - +
75H ILE* 1.3 76.1 + - + +
76H GLN 3.7 0.2 - - - -
27N LYS* 5.1 8.1 + - - -
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Residues in contact with ILE 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H LEU* 4.5 28.3 - - + -
37H LYS 5.4 0.2 - - - -
38H ALA* 3.5 32.1 - - + +
39H GLN* 4.7 8.7 + - + +
71H SER 4.2 2.0 + - - -
72H PHE 3.9 3.0 + - - -
74H LYS* 1.3 99.0 - - + +
76H GLN* 1.3 66.1 + - - +
77H VAL* 2.7 33.0 - - + +
78H ARG* 4.7 2.5 - - + -
79H LEU* 3.9 16.8 - - + +
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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