Contacts of the helix formed by residues 59 - 68 (chain C) in PDB entry 3N6J
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 GLY 59 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C PRO* 6.0 1.6 - - - +
38C THR* 3.6 7.9 + - - -
40C ASN* 3.6 5.4 + - - +
58C GLY* 1.3 74.0 - - - -
60C ALA* 1.3 66.0 + - - -
61C THR* 3.2 4.5 + - - -
62C ILE 3.5 2.0 + - - -
63C GLU* 3.4 21.4 + - - +
109C LEU* 6.5 0.2 - - - -
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Residues in contact with ALA 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C GLY* 1.3 71.7 - - - +
61C THR* 1.3 61.9 + - - +
63C GLU* 3.6 9.5 - - - +
64C ASN* 2.7 43.6 + - - +
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Residues in contact with THR 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C GLY 3.2 1.2 + - - -
60C ALA* 1.3 78.7 - - - +
62C ILE* 1.3 61.5 + - + +
64C ASN* 3.3 5.3 + - - +
65C ALA* 3.0 28.5 + - - +
109C LEU* 3.9 32.1 - - + +
110C ARG* 3.5 46.2 - - + +
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Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ASN* 3.6 11.9 - - - +
56C ALA* 4.1 7.4 - - + -
57C PRO* 3.1 34.5 - - + +
58C GLY 3.7 10.8 - - - +
59C GLY 3.5 2.3 + - - +
61C THR* 1.3 74.2 - - + +
63C GLU* 1.3 68.9 + - - +
65C ALA* 3.4 6.5 + - - +
66C LEU* 3.1 21.9 + - + +
107C PHE* 4.5 3.6 - - + -
109C LEU* 3.6 39.9 - - + +
110C ARG* 5.4 1.1 - - - +
112C ASN* 3.9 14.8 - - + +
113C ALA* 3.6 33.2 - - + +
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Residues in contact with GLU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C VAL* 3.9 20.4 - - + +
18C PRO* 3.8 27.7 - - + +
40C ASN* 3.2 24.1 - - - +
59C GLY 3.4 9.9 + - - +
60C ALA* 3.6 13.3 - - - +
61C THR 3.3 0.2 - - - -
62C ILE* 1.3 74.5 - - - +
64C ASN* 1.3 66.3 + - - +
66C LEU* 2.8 26.9 + - - +
67C THR* 3.2 16.8 + - + +
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Residues in contact with ASN 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ALA* 2.7 33.2 + - - +
61C THR* 3.9 5.0 + - - +
63C GLU* 1.3 89.0 - - - +
65C ALA* 1.3 61.6 + - - +
67C THR* 2.7 23.1 + - - +
68C GLU* 3.1 27.6 + - - +
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Residues in contact with ALA 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C THR 3.0 17.4 + - - +
62C ILE* 3.6 10.1 - - - +
63C GLU 3.2 0.2 - - - -
64C ASN* 1.3 76.3 - - - +
66C LEU* 1.3 60.8 + - - +
68C GLU* 4.0 8.1 + - - +
69C ALA 3.6 8.3 + - - -
88C MSE 3.7 8.8 - - - +
92C TYR* 3.4 39.7 + - + -
110C ARG* 5.0 13.0 - - + +
113C ALA* 4.3 9.0 - - + -
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C MSE 3.4 20.5 - - + +
16C VAL* 3.7 25.6 - - + -
40C ASN* 4.1 21.5 - - + -
41C ILE 4.8 0.2 - - - +
42C VAL* 3.6 32.5 - - + -
56C ALA* 5.2 0.2 - - + -
62C ILE* 3.1 21.1 + - + +
63C GLU 2.8 9.8 + - - +
65C ALA* 1.3 76.9 - - - +
67C THR* 1.3 61.2 + - - -
69C ALA* 3.1 18.5 + - - +
70C ILE* 3.3 5.7 + - - +
88C MSE 4.7 4.3 - - + -
113C ALA* 3.5 37.5 - - + +
116C ALA* 5.0 2.2 - - + -
117C LEU* 4.7 3.6 - - + -
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Residues in contact with THR 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C VAL* 3.6 22.2 - - + +
63C GLU* 3.2 13.6 + - + +
64C ASN* 2.7 33.2 + - - +
66C LEU* 1.3 69.9 - - - +
68C GLU* 1.3 57.4 + - - +
69C ALA 2.9 4.5 - - - -
70C ILE* 2.9 42.5 + - + +
71C PRO* 3.5 4.5 - - - +
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Residues in contact with GLU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ASN* 3.1 29.0 + - - +
65C ALA* 4.1 9.9 - - - +
67C THR* 1.3 74.1 - - - +
69C ALA* 1.3 56.7 + - - +
71C PRO* 3.6 7.0 - - - +
72C HIS* 3.3 24.8 + - - -
92C TYR* 4.3 17.1 + - - +
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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