Contacts of the helix formed by residues 61 - 73 (chain A) in PDB entry 3G8T
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A HIS* 4.4 3.2 + - - -
39A GLN* 6.2 1.8 - - + -
59A PHE* 3.4 8.7 - - - +
60A LYS* 1.3 103.8 - - + +
62A VAL* 1.3 66.1 + - - +
63A SER* 3.2 11.4 - - - +
64A SER* 3.1 31.6 + - - +
65A ALA* 3.4 4.5 + - - +
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Residues in contact with VAL 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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8A PRO* 4.1 26.2 - - + -
9A ASN* 4.0 13.9 - - - +
10A HIS* 3.6 44.6 - - + +
61A GLU* 1.3 70.3 + - - +
63A SER* 1.3 66.2 + - - +
65A ALA* 2.9 8.8 + - + +
66A THR* 2.9 32.6 + - - +
86A TYR* 5.3 0.2 - - + -
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Residues in contact with SER 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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61A GLU* 4.4 10.5 - - - -
62A VAL* 1.3 77.5 - - - +
64A SER* 1.3 61.8 + - - +
66A THR* 3.4 6.6 + - - -
67A ASN* 3.2 35.7 + - - -
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Residues in contact with SER 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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37A PHE* 2.7 33.1 + - - +
38A GLY* 3.3 9.2 - - - -
59A PHE* 3.5 25.6 - - - -
61A GLU* 3.1 22.7 + - - +
62A VAL 3.1 0.4 - - - -
63A SER* 1.3 76.2 + - - +
65A ALA* 1.3 60.1 + - - +
67A ASN* 3.6 2.6 + - - +
68A ALA* 3.0 31.2 + - - +
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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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9A ASN 3.2 27.1 - - - +
10A HIS 3.6 16.2 - - - +
12A ILE* 3.6 19.6 - - + +
59A PHE* 4.0 11.4 - - + -
61A GLU 3.4 2.4 + - - +
62A VAL* 2.9 11.3 + - - +
64A SER* 1.3 76.0 - - - +
66A THR* 1.3 59.7 + - - +
68A ALA* 3.9 0.3 - - - +
69A LEU* 3.1 28.8 + - - +
86A TYR* 4.2 3.5 - - + -
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Residues in contact with THR 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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8A PRO* 5.1 1.7 - - - +
62A VAL* 2.9 23.7 + - - +
63A SER* 3.8 8.6 - - - -
65A ALA* 1.3 74.3 - - - +
67A ASN* 1.3 60.3 + - - +
69A LEU* 3.3 3.1 + - - +
70A ARG* 3.0 64.7 + - + +
86A TYR* 3.3 24.2 + - - +
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Residues in contact with ASN 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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37A PHE* 3.6 20.9 + - + -
63A SER* 3.2 27.2 + - - +
64A SER* 4.0 4.9 - - - +
66A THR* 1.3 76.5 - - - +
68A ALA* 1.3 62.3 + - - +
70A ARG* 3.5 23.4 + - - +
71A SER* 3.0 32.5 + - - +
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Residues in contact with ALA 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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12A ILE* 4.2 2.9 - - + -
34A PHE* 3.7 30.3 - - + -
37A PHE* 3.5 20.1 - - + -
59A PHE* 4.0 10.8 - - + -
64A SER 3.0 19.5 + - - +
65A ALA 3.9 3.6 - - - +
67A ASN* 1.3 76.3 - - - +
69A LEU* 1.3 57.9 + - - +
72A MET* 3.0 34.3 + - - +
84A ILE* 4.2 1.8 - - - +
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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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12A ILE* 4.7 1.1 - - + -
65A ALA 3.1 17.2 + - - +
66A THR* 3.3 6.5 + - - +
68A ALA* 1.3 74.1 - - - +
70A ARG* 1.3 70.3 + - + +
73A GLN* 3.3 44.4 + - + +
84A ILE* 3.8 24.6 - - + +
85A GLN* 3.8 22.4 - - - +
86A TYR* 3.6 42.0 - - + +
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Residues in contact with ARG 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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66A THR* 3.0 48.5 + - + +
67A ASN* 3.6 24.4 + - - +
69A LEU* 1.3 84.1 - - + +
71A SER* 1.3 64.4 + - - +
73A GLN* 4.1 8.4 + - - +
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Residues in contact with SER 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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36A ARG* 4.5 9.8 + - - -
37A PHE* 3.6 23.6 - - - -
67A ASN* 3.0 19.1 + - - +
70A ARG* 1.3 80.2 - - - +
72A MET* 1.3 67.1 + - - +
73A GLN 3.4 4.0 + - - +
75A PHE* 5.2 2.4 - - - +
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Residues in contact with MET 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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33A ILE* 3.5 25.4 - - + -
34A PHE* 3.9 18.4 - - + -
36A ARG* 4.0 11.9 - - - -
37A PHE* 3.6 33.9 - - + -
68A ALA 3.0 18.6 + - - +
71A SER* 1.3 80.6 - - - +
73A GLN* 1.3 63.8 + - - +
74A GLY 3.2 0.7 + - - -
75A PHE* 3.0 60.9 + - + +
82A MET* 4.2 5.9 - - - +
84A ILE* 3.6 20.2 - - + +
75B PHE* 4.5 3.6 - - + -
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Residues in contact with GLN 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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69A LEU* 3.3 27.6 + - + +
70A ARG 4.2 7.7 - - - +
71A SER 3.4 5.9 - - - +
72A MET* 1.3 75.9 - - - +
74A GLY* 1.3 61.8 + - - +
75A PHE 3.2 1.3 + - - -
82A MET 3.7 3.7 - - - +
83A ARG* 3.6 16.3 - - - +
84A ILE* 2.8 52.5 + - - +
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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