Contacts of the helix formed by residues 65 - 76 (chain A) in PDB entry 1SNG
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 ASP 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ARG* 4.7 9.3 + - - +
59A THR* 4.1 12.2 - - - +
64A THR* 1.3 90.1 + - - +
66A PRO* 1.3 76.4 - - + +
67A ALA* 3.4 1.6 - - + +
68A PRO* 3.3 21.6 - - + +
69A LEU* 3.7 5.5 + - - +
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Residues in contact with PRO 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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44A GLY* 3.2 33.4 - - - +
47A ALA* 4.0 6.7 - - + -
48A ALA* 3.9 20.9 - - + +
55A ARG* 3.5 24.9 - - - +
59A THR* 3.9 14.4 - - + -
62A LEU* 5.5 1.6 - - + -
64A THR 3.8 1.1 - - - +
65A ASP* 1.3 87.4 - - + +
67A ALA* 1.3 66.4 + - + +
69A LEU* 3.0 9.4 + - + +
70A LEU* 2.8 31.2 + - + +
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Residues in contact with ALA 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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65A ASP* 3.4 1.3 - - + -
66A PRO* 1.3 84.6 - - + +
68A PRO* 1.3 69.9 - - + +
70A LEU* 4.0 6.7 - - - +
71A ALA* 3.3 21.1 + - - +
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Residues in contact with PRO 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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9A ARG* 4.2 11.4 + - - +
64A THR* 3.9 10.8 - - - +
65A ASP* 3.3 26.5 - - + +
67A ALA* 1.3 96.3 - - + +
69A LEU* 1.3 58.7 + - - +
71A ALA* 3.8 6.0 + - + +
72A ALA* 3.3 21.7 + - - +
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Residues in contact with LEU 69 (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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9A ARG* 3.8 32.0 - - - +
11A ASP* 3.8 11.2 - - - +
12A HIS* 5.1 8.1 - - + +
40A ALA* 4.5 6.3 - - + +
44A GLY* 5.2 3.8 - - - -
62A LEU* 3.9 36.3 - - + +
64A THR* 3.9 15.9 - - + -
65A ASP 3.8 9.6 - - - +
66A PRO* 3.0 9.3 + - + +
68A PRO* 1.3 79.9 - - - +
70A LEU* 1.3 61.5 + - + +
72A ALA* 3.2 4.3 + - - +
73A LEU* 2.9 56.7 + - + +
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Residues in contact with LEU 70 (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 ALA 4.7 0.2 - - - +
41A CAF 3.5 38.1 - - - +
44A GLY* 4.0 23.8 - - - +
45A VAL* 4.0 11.9 - - + +
48A ALA* 5.0 2.2 - - + -
66A PRO* 2.8 26.9 + - + +
67A ALA* 4.0 5.8 - - - +
69A LEU* 1.3 69.4 - - + +
71A ALA* 1.3 66.5 + - - +
73A LEU* 3.2 6.8 + - + +
74A ASP* 3.0 32.1 + - - +
104A THR* 4.4 8.5 - - + -
108A ARG* 3.6 40.6 - - - +
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Residues in contact with ALA 71 (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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67A ALA 3.3 14.6 + - - +
68A PRO* 3.8 7.9 - - + +
70A LEU* 1.3 80.1 - - - +
72A ALA* 1.3 62.3 + - - +
74A ASP* 3.7 18.8 + - - +
75A ARG* 4.1 10.2 + - - +
108A ARG* 4.7 3.5 - - - +
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Residues in contact with ALA 72 (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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9A ARG* 3.9 33.4 - - - +
68A PRO 3.3 11.0 + - - +
69A LEU 3.2 8.3 + - - +
71A ALA* 1.3 80.0 - - - +
73A LEU* 1.3 62.4 + - + +
74A ASP 3.5 0.2 + - - -
75A ARG* 3.6 19.7 + - - +
76A ALA* 4.0 3.1 + - - +
349A ARG 4.6 8.3 - - - +
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Residues in contact with LEU 73 (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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9A ARG* 6.1 2.5 - - - -
12A HIS* 4.1 21.1 - - + +
37A TYR* 3.2 27.3 - - + -
40A ALA* 3.8 10.5 - - + -
41A CAF 3.6 37.9 - - + +
69A LEU* 2.9 39.6 + - + +
70A LEU* 3.2 8.7 + - + +
72A ALA* 1.3 75.1 - - + +
74A ASP* 1.3 67.9 + - - +
76A ALA* 2.9 21.3 + - - +
351A ALA* 4.0 25.1 - - + -
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Residues in contact with ASP 74 (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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37A TYR* 4.9 2.4 + - - -
41A CAF 5.0 2.9 - - - -
70A LEU 3.0 18.4 + - - +
71A ALA* 3.9 9.0 - - - +
72A ALA 3.4 0.2 - - - -
73A LEU* 1.3 74.7 - - - +
75A ARG* 1.3 64.1 + - + +
76A ALA 3.1 1.0 + - - -
77A VAL* 3.2 13.7 + - - +
78A THR* 3.4 20.6 + - + +
107A ASP 3.6 7.6 - - - +
108A ARG* 2.9 45.0 + - - -
109A PRO* 3.5 26.7 - - + +
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Residues in contact with ARG 75 (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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71A ALA 4.1 11.4 + - - +
72A ALA* 3.6 11.1 + - - +
73A LEU 3.2 0.8 + - - -
74A ASP* 1.3 80.7 - - + +
76A ALA* 1.3 62.7 + - - +
77A VAL 3.1 1.2 + - - -
78A THR* 3.4 12.6 + - - +
218A GLU* 5.0 1.4 + - - -
348A ARG* 3.4 0.9 + - - -
349A ARG* 2.9 79.4 + - + +
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Residues in contact with ALA 76 (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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37A TYR* 4.2 3.4 - - + -
72A ALA 4.0 1.8 + - - +
73A LEU* 2.9 17.9 + - - +
75A ARG* 1.3 78.1 - - - +
77A VAL* 1.3 59.5 + - - +
348A ARG* 2.9 42.9 + - - +
349A ARG* 4.2 7.8 - - - +
351A ALA* 3.6 30.5 - - + -
353A LEU* 3.9 13.4 - - + +
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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