Contacts of the helix formed by residues 59 - 68 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A THR* 4.8 0.4 - - - -
40A ASN* 3.5 5.1 + - - +
58A GLY* 1.3 73.4 - - - -
60A ALA* 1.3 62.7 + - - -
61A THR 3.6 1.6 - - - -
62A ILE 4.2 1.7 + - - -
63A GLU* 3.4 24.9 + - - +
415A HIS* 5.2 3.2 - - - -
421A GLY* 3.0 33.8 + - - -
422A ALA* 3.9 9.6 - - - -
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Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLY* 1.3 71.0 - - - -
61A THR* 1.3 56.7 + - - +
63A GLU* 4.4 7.9 - - - +
64A ASN* 2.8 55.3 + - - +
420A ASN* 5.8 2.2 + - - +
421A GLY* 5.0 1.4 - - - -
422A ALA* 5.0 4.0 - - - +
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Residues in contact with THR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLY 3.6 0.4 - - - -
60A ALA* 1.3 77.3 - - - +
62A ILE* 1.3 62.9 + - + +
64A ASN* 4.0 7.0 - - - +
65A ALA* 3.3 21.1 + - - +
108A GLU* 4.4 25.5 + - + +
110A ARG* 3.8 40.8 - - + +
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASN* 3.5 19.3 - - - +
56A ALA* 4.2 10.1 - - + -
57A PRO* 3.6 24.7 - - + +
58A GLY 4.0 9.0 - - - +
59A GLY 4.2 1.4 + - - +
60A ALA 3.4 0.2 - - - -
61A THR* 1.3 77.5 - - + +
63A GLU* 1.3 66.3 + - - +
65A ALA* 3.1 15.6 + - - +
66A LEU* 3.1 28.4 + - + +
107A PHE 3.4 26.9 - - - +
108A GLU* 4.6 6.3 - - - +
109A LEU 3.6 25.4 - - - +
110A ARG* 4.8 4.0 - - - +
112A ASN* 3.8 9.0 - - + -
113A ALA* 4.0 11.0 - - + +
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.7 21.6 - - + +
18A PRO* 3.0 39.1 - - + +
40A ASN* 3.3 23.0 - - - +
59A GLY 3.4 14.5 + - - +
60A ALA* 3.3 9.3 + - - +
62A ILE* 1.3 77.4 - - - +
64A ASN* 1.3 66.0 + - - +
66A LEU* 3.0 8.7 + - - +
67A THR* 2.9 28.0 + - - +
415A HIS* 5.1 2.8 + - - -
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Residues in contact with ASN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ALA* 2.8 42.6 + - - +
61A THR* 4.0 6.2 - - - +
63A GLU* 1.3 78.7 - - - +
65A ALA* 1.3 57.7 + - - +
67A THR* 3.3 15.8 + - + +
68A GLU* 2.8 32.0 + - - +
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A THR 3.3 11.6 + - - +
62A ILE* 3.1 10.1 + - - +
64A ASN* 1.3 75.8 - - - +
66A LEU* 1.3 61.7 + - - +
68A GLU* 3.1 6.6 + - - +
69A ALA* 3.0 27.0 + - - +
88A MSE 3.9 5.6 - - - +
92A TYR* 3.6 35.2 + - + +
110A ARG* 4.8 7.9 - - + -
113A ALA* 4.4 10.5 - - + -
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A MSE 3.3 30.5 - - + +
16A VAL* 3.8 17.7 - - + -
40A ASN* 4.2 18.2 - - + +
42A VAL* 3.7 31.0 - - + -
56A ALA* 5.2 0.4 - - + -
62A ILE* 3.1 31.3 + - + +
63A GLU* 3.0 9.1 + - - +
65A ALA* 1.3 75.2 - - - +
67A THR* 1.3 62.9 + - - +
69A ALA* 3.2 10.0 + - - +
70A ILE* 3.3 6.2 + - - +
88A MSE 4.4 4.9 - - + -
113A ALA* 3.4 35.9 - - + +
116A ALA* 5.0 2.7 - - + -
117A LEU* 4.6 4.0 - - + -
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Residues in contact with THR 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.9 14.4 - - - +
63A GLU* 2.9 14.7 + - - +
64A ASN* 3.3 18.2 - - + +
66A LEU* 1.3 77.0 - - - +
68A GLU* 1.3 62.0 + - + +
69A ALA 3.1 0.9 + - - -
70A ILE* 3.4 30.7 + - + +
71A PRO* 4.0 4.2 - - - +
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Residues in contact with GLU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ASN* 2.8 22.2 + - - +
65A ALA* 3.1 11.1 + - - +
67A THR* 1.3 75.5 - - + +
69A ALA* 1.3 57.7 + - - +
71A PRO* 4.1 8.0 - - - +
72A HIS* 3.5 20.0 + - + -
92A TYR* 3.3 23.2 + - - +
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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