Contacts of the helix formed by residues 48 - 67 (chain Q) in PDB entry 6CNF
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 THR 48 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46Q PRO 5.3 0.4 - - - -
47Q ILE* 1.3 74.4 - - - +
49Q ASN* 1.3 63.7 + - - +
50Q LYS* 4.2 7.4 + - + +
51Q GLU* 2.7 36.2 + - + +
52Q ARG* 2.7 38.0 + - - +
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Residues in contact with ASN 49 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48Q THR* 1.3 82.0 + - - +
50Q LYS* 1.3 53.3 + - - +
52Q ARG* 2.7 26.6 + - + +
53Q SER* 2.4 44.2 + - - +
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Residues in contact with LYS 50 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138O ASP* 4.9 12.4 + - - -
141O ILE* 5.8 7.2 - - - +
294O LYS* 5.2 9.8 - - - +
48Q THR* 3.6 7.4 + - + +
49Q ASN* 1.3 76.7 - - - +
51Q GLU* 1.3 54.0 + - - +
53Q SER* 3.5 9.9 - - - -
54Q LEU* 2.7 35.0 + - - +
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Residues in contact with GLU 51 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639O ALA* 3.4 25.7 - - + +
643O ARG* 4.1 22.8 - - + +
45Q GLY 4.5 4.3 - - - +
46Q PRO 3.6 6.3 - - - +
47Q ILE* 3.1 25.5 - - + -
48Q THR* 2.7 40.5 + - + +
50Q LYS* 1.3 79.8 - - - +
52Q ARG* 1.3 54.5 + - - -
54Q LEU* 3.3 16.2 - - + +
55Q ALA* 2.9 23.9 + - - +
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Residues in contact with ARG 52 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632O GLU* 4.6 17.7 + - - +
635O LEU* 3.3 32.2 - - + +
47Q ILE* 3.4 38.8 + - + +
48Q THR 2.7 19.1 + - - +
49Q ASN* 2.7 30.5 + - + +
51Q GLU* 1.3 68.4 - - - +
53Q SER* 1.3 59.9 + - - +
54Q LEU 3.1 1.8 - - - -
55Q ALA* 2.5 25.1 + - - -
56Q VAL* 2.9 18.8 + - + +
57Q LYS 4.3 0.2 + - - -
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Residues in contact with SER 53 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153O LYS* 5.9 2.7 - - - -
49Q ASN* 2.4 35.8 + - - +
50Q LYS* 3.5 12.3 - - - -
52Q ARG* 1.3 64.8 - - - +
54Q LEU* 1.3 61.8 + - - +
57Q LYS* 3.0 44.6 + - - +
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Residues in contact with LEU 54 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134O GLY* 3.4 39.3 - - - +
135O LEU* 3.8 11.4 - - + +
137O ILE* 6.5 0.4 - - - -
138O ASP* 5.6 3.1 - - + -
639O ALA* 5.4 2.9 - - - -
642O SER* 3.7 32.5 - - - +
50Q LYS* 2.7 17.1 + - + +
51Q GLU* 3.3 20.4 - - + +
53Q SER* 1.3 74.7 - - - +
55Q ALA* 1.3 56.9 + - - +
57Q LYS* 3.6 1.7 - - - +
58Q TYR* 2.8 41.1 + - + +
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Residues in contact with ALA 55 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635O LEU* 3.6 24.2 - - + -
638O PHE* 4.8 7.6 - - + -
639O ALA* 4.7 10.3 - - + +
47Q ILE* 4.6 4.5 - - + -
51Q GLU 2.9 19.3 + - - +
52Q ARG* 2.5 17.1 + - - +
54Q LEU* 1.3 76.5 - - - +
56Q VAL* 1.3 58.4 + - - +
58Q TYR* 3.1 6.6 - - - +
59Q ILE* 2.9 31.4 + - + +
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Residues in contact with VAL 56 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635O LEU* 3.9 24.0 - - + -
52Q ARG* 2.9 11.8 + - + +
55Q ALA* 1.3 77.5 - - - +
57Q LYS* 1.3 52.0 + - - +
59Q ILE* 2.8 20.1 + - + +
60Q ASN* 2.3 42.1 + - + +
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Residues in contact with LYS 57 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137O ILE* 3.6 36.9 - - + +
153O LYS* 3.8 29.7 - - - +
157O ALA* 5.6 9.9 - - + -
161O GLN* 4.6 4.1 - - - +
52Q ARG 4.3 0.2 + - - -
53Q SER* 3.0 34.7 + - - +
54Q LEU* 3.5 1.5 + - - +
55Q ALA 3.3 0.2 - - - -
56Q VAL* 1.3 77.8 - - - +
58Q TYR* 1.3 61.2 + - - +
60Q ASN* 3.1 11.5 + - + +
61Q PHE* 2.9 23.9 + - - +
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Residues in contact with TYR 58 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130O LEU 3.9 9.2 + - - -
131O LEU* 4.2 10.8 + - - -
132O TYR 3.2 18.2 - - - -
133O SER* 3.4 14.4 - - - -
134O GLY* 3.0 35.9 - - - +
135O LEU 4.8 0.2 - - - -
137O ILE* 4.4 3.9 - - - +
638O PHE* 3.1 46.2 - + + -
641O LEU* 4.4 15.7 - - + +
642O SER* 5.6 8.7 - - - -
54Q LEU* 2.8 23.5 + - + +
55Q ALA* 3.1 9.9 - - - +
57Q LYS* 1.3 73.0 - - - +
59Q ILE* 1.3 56.2 + - - +
61Q PHE* 3.3 6.8 + + - +
62Q GLY* 2.9 24.1 + - - -
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Residues in contact with ILE 59 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634O GLU* 4.3 14.8 - - + +
635O LEU* 5.2 0.9 - - + +
638O PHE* 3.4 52.9 - - + -
55Q ALA* 2.9 23.3 + - + +
56Q VAL* 2.8 31.5 + - + +
58Q TYR* 1.3 69.9 - - - +
60Q ASN* 1.3 59.6 + - - +
62Q GLY* 2.6 23.1 + - - +
63Q LYS* 3.0 19.7 + - + +
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Residues in contact with ASN 60 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161O GLN* 4.4 12.9 + - - +
56Q VAL* 2.3 31.6 + - + +
57Q LYS* 3.2 16.0 - - + +
59Q ILE* 1.3 67.1 - - - +
61Q PHE* 1.3 57.3 + - - +
63Q LYS* 3.7 2.3 + - - +
64Q THR* 2.2 43.3 + - - -
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Residues in contact with PHE 61 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130O LEU* 4.6 15.0 - - + -
133O SER* 3.1 34.8 - - - -
137O ILE* 4.5 9.4 - - + -
161O GLN* 3.4 54.6 + - + +
164O ILE* 3.4 35.9 - - + -
165O SER 3.8 1.3 - - - -
57Q LYS 2.9 10.2 + - - +
58Q TYR* 3.4 9.9 - + - +
60Q ASN* 1.3 77.0 - - - +
62Q GLY* 1.3 67.6 + - - +
64Q THR* 3.1 6.5 + - + -
65Q VAL* 2.9 55.1 + - + +
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Residues in contact with GLY 62 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56O HIS* 5.9 0.7 - - - -
638O PHE* 6.5 0.2 - - - -
58Q TYR* 2.9 12.3 + - - -
59Q ILE* 2.6 17.1 + - - -
61Q PHE* 1.3 79.8 - - - +
63Q LYS* 1.3 60.1 + - - -
65Q VAL* 3.3 15.5 + - - +
66Q LYS* 3.5 5.7 + - - +
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Residues in contact with LYS 63 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596O LYS* 6.1 2.5 - - - +
607O ASN* 2.8 45.2 + - - +
59Q ILE* 3.0 17.0 + - + +
60Q ASN* 4.6 2.0 - - - +
62Q GLY* 1.3 68.1 - - - -
64Q THR* 1.3 67.0 + - - +
65Q VAL 3.1 2.0 - - - -
66Q LYS* 3.0 27.5 + - + +
67Q ASP* 3.2 28.4 + - - +
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Residues in contact with THR 64 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158O GLU* 5.3 3.8 - - - +
161O GLN* 4.4 20.1 + - + +
162O ASN* 6.4 0.9 - - - -
165O SER* 4.7 8.1 + - - -
60Q ASN* 2.2 39.5 + - - -
61Q PHE* 3.1 11.2 + - + +
63Q LYS* 1.3 76.7 - - - +
65Q VAL* 1.3 62.3 + - + +
67Q ASP* 3.3 16.9 + - - +
68Q GLY* 3.4 8.1 + - - -
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Residues in contact with VAL 65 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56O HIS* 3.2 36.3 + - + +
101O LEU* 5.5 1.8 - - + -
130O LEU* 5.2 6.1 - - + -
165O SER* 4.0 29.2 - - - +
61Q PHE* 2.9 50.5 + - + +
62Q GLY* 3.5 7.9 - - - +
63Q LYS 3.1 0.4 - - - -
64Q THR* 1.3 72.4 - - - +
66Q LYS* 1.3 57.1 + - - +
67Q ASP 3.0 2.2 - - - -
68Q GLY* 2.6 26.7 + - - -
69Q PRO* 4.8 2.2 - - + +
70Q PHE 4.4 3.8 + - - -
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Residues in contact with LYS 66 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56O HIS* 4.6 17.8 - - - +
57O LEU* 5.2 0.9 - - - -
596O LYS* 6.2 1.6 - - - +
62Q GLY 3.5 4.6 + - - +
63Q LYS* 3.0 26.2 + - + +
65Q VAL* 1.3 78.4 - - - +
67Q ASP* 1.3 63.0 + - - +
68Q GLY 3.2 0.7 - - - +
70Q PHE 3.1 33.8 - - - +
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Residues in contact with ASP 67 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63Q LYS* 3.2 28.7 + - - +
64Q THR* 3.7 13.6 - - - +
65Q VAL 3.0 1.2 - - - -
66Q LYS* 1.3 81.3 - - - +
68Q GLY* 1.3 64.3 + - - +
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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