Contacts of the helix formed by residues 61 - 72 (chain B) in PDB entry 3G9C
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 GLU 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B HIS* 4.2 4.0 + - - -
59B PHE* 3.5 13.4 - - - +
60B LYS* 1.3 107.8 - - + +
62B VAL* 1.3 63.8 + - - +
63B SER* 3.3 11.2 - - - +
64B SER* 3.4 16.8 + - - +
65B ALA* 3.4 14.7 + - - +
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PRO* 3.9 17.3 - - + -
9B ASN* 3.5 30.5 - - - +
10B HIS* 3.5 37.2 - - + +
61B GLU* 1.3 71.7 + - - +
63B SER* 1.3 55.8 + - - +
65B ALA* 3.1 6.1 + - + +
66B THR* 2.7 42.0 + - - +
86B TYR* 5.2 0.2 - - + -
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Residues in contact with SER 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLU* 3.3 8.2 - - - +
62B VAL* 1.3 79.8 - - - +
64B SER* 1.3 58.4 + - - +
66B THR* 3.7 5.3 + - - -
67B ASN* 3.1 41.7 + - - +
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Residues in contact with SER 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 2.9 34.4 + - - +
38B GLY* 3.4 18.0 - - - -
59B PHE* 3.9 13.8 - - - -
61B GLU* 3.4 22.8 + - - +
62B VAL 3.2 0.4 - - - -
63B SER* 1.3 76.4 - - - +
65B ALA* 1.3 62.6 + - - +
67B ASN* 3.8 2.9 + - - +
68B ALA* 3.3 23.0 + - - +
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ASN 3.3 26.5 - - - +
10B HIS 3.9 15.3 - - - +
12B ILE* 3.5 24.5 - - + +
59B PHE* 3.8 12.1 - - + -
61B GLU 3.4 7.6 + - - +
62B VAL* 3.1 7.3 + - + +
64B SER* 1.3 78.5 - - - +
66B THR* 1.3 63.8 + - - +
68B ALA* 3.6 1.4 + - - +
69B LEU* 3.2 17.3 + - - +
86B TYR* 4.6 2.6 - - + -
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Residues in contact with THR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PRO* 5.1 2.3 - - + +
62B VAL* 2.7 30.5 + - - +
63B SER* 4.0 6.6 - - - -
64B SER 3.4 0.2 - - - -
65B ALA* 1.3 74.5 - - - +
67B ASN* 1.3 64.4 + - - +
69B LEU* 3.1 5.5 + - + +
70B ARG* 3.1 66.7 + - + +
86B TYR* 2.9 28.6 + - - +
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Residues in contact with ASN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PHE* 3.3 21.4 + - + +
63B SER* 3.1 27.5 + - - +
64B SER* 4.1 5.7 - - - +
66B THR* 1.3 74.4 - - - +
68B ALA* 1.3 59.6 + - - +
70B ARG* 3.3 25.7 + - - +
71B SER* 2.9 32.5 + - - +
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ILE* 4.4 1.8 - - + -
34B PHE* 3.6 30.0 - - + -
37B PHE* 3.7 19.7 - - + -
59B PHE* 3.9 10.1 - - + -
64B SER 3.3 16.6 + - - +
65B ALA 3.7 5.6 - - - +
66B THR 3.2 0.4 - - - -
67B ASN* 1.3 75.8 - - - +
69B LEU* 1.3 63.5 + - - +
72B MET* 3.2 28.6 + - - +
84B ILE* 3.7 3.9 - - - +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ILE* 4.6 2.7 - - + +
65B ALA 3.2 8.7 + - - +
66B THR* 3.1 11.3 + - - +
68B ALA* 1.3 81.0 - - - +
70B ARG* 1.3 63.6 - - + +
73B GLN* 3.2 41.1 + - - +
84B ILE* 3.8 24.4 - - + +
85B GLN* 3.7 30.1 - - - +
86B TYR* 3.7 38.6 - - + +
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B THR* 3.1 43.5 + - + +
67B ASN* 3.3 27.9 + - - +
68B ALA 3.4 0.2 - - - -
69B LEU* 1.3 87.2 - - + +
71B SER* 1.3 63.9 + - - +
73B GLN* 4.1 9.5 - - - +
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Residues in contact with SER 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ARG* 4.2 7.6 + - - -
37B PHE* 3.6 23.6 - - - -
67B ASN* 2.9 19.7 + - - +
70B ARG* 1.3 81.2 - - - +
72B MET* 1.3 68.1 + - - +
73B GLN 3.4 4.2 + - - +
75B PHE* 5.2 1.7 - - - +
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Residues in contact with MET 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PHE* 4.0 10.3 - - + -
33B ILE* 3.5 24.0 - - + -
34B PHE* 4.0 16.2 - - + -
36B ARG* 3.4 26.7 - - - -
37B PHE* 3.6 25.4 - - + -
68B ALA 3.2 14.8 + - - +
71B SER* 1.3 79.5 - - - +
73B GLN* 1.3 64.5 + - - +
74B GLY 3.2 0.7 + - - -
75B PHE* 3.1 56.0 + - + +
82B MET* 4.1 7.4 - - + +
84B ILE* 3.6 18.6 - - + +
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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