Contacts of the helix formed by residues 66 - 73 (chain A) in PDB entry 3IOT
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 ARG 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A GLU* 3.9 14.4 + - + +
45A GLU* 2.6 44.3 + - - -
48A PRO* 4.9 3.4 - - - +
62A TRP* 3.5 34.1 - - + +
63A ALA 3.3 0.9 + - - +
65A ASP* 1.3 87.9 - - - +
67A PHE* 1.3 64.0 + - + +
68A GLY 3.3 0.9 + - - -
69A GLY* 3.4 11.7 + - - -
70A TYR* 3.6 47.4 + - + +
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Residues in contact with PHE 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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60A ILE* 3.4 31.2 - - + -
62A TRP* 3.8 28.3 - - + -
63A ALA 3.8 7.2 - - - -
64A HIS* 3.4 14.1 - - - +
65A ASP 3.2 0.6 - - - -
66A ARG* 1.3 74.5 - - - +
68A GLY* 1.3 56.3 + - - +
70A TYR* 3.0 26.9 + + - +
71A ALA* 2.7 37.7 + - - +
76A LEU* 3.9 15.7 - - + +
97A VAL* 5.7 0.7 - - + -
104A ILE* 4.2 11.0 - - + -
105A ALA* 3.5 34.5 - - + -
263A SER* 3.6 19.3 - - - -
265A GLY* 3.7 14.1 - - - -
332A ASN* 4.9 0.4 - - - +
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Residues in contact with GLY 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 HIS 4.0 0.2 + - - -
65A ASP 3.5 4.2 + - - -
66A ARG 3.2 2.0 - - - -
67A PHE* 1.3 77.7 - - - +
69A GLY* 1.3 60.2 + - - +
71A ALA 3.5 0.2 + - - -
72A GLN* 3.1 20.7 + - - +
99A TYR* 3.4 18.3 - - - -
332A ASN* 3.3 43.5 - - - +
334A PRO* 6.3 1.3 - - - -
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Residues in contact with GLY 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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65A ASP 4.7 0.8 + - - -
66A ARG* 3.4 8.8 + - - -
67A PHE 3.2 0.6 - - - -
68A GLY* 1.3 73.0 - - - +
70A TYR* 1.3 67.3 + - - +
72A GLN* 3.5 12.1 + - - +
73A SER* 3.0 28.1 + - - -
332A ASN 4.4 2.0 + - - -
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Residues in contact with TYR 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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44A GLU* 2.6 39.6 + - - +
47A PHE* 4.2 23.3 - + - -
48A PRO* 3.6 27.3 - - + +
60A ILE* 4.7 8.5 - - + -
62A TRP* 5.4 2.0 - - + -
66A ARG* 3.6 31.8 - - + +
67A PHE* 3.0 42.5 + + - +
69A GLY* 1.3 75.6 - - - +
71A ALA* 1.3 65.4 + - - +
73A SER* 3.0 8.1 + - - -
74A GLY 3.2 0.2 + - - -
75A LEU* 3.0 39.4 + - + +
76A LEU* 3.7 17.9 - - + -
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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 PHE 2.7 19.5 + - - +
68A GLY 3.9 0.2 - - - +
70A TYR* 1.3 73.7 - - - +
72A GLN* 1.3 56.7 + - - +
74A GLY* 3.0 17.5 + - - -
76A LEU* 4.0 13.9 - - + +
99A TYR* 3.8 36.6 - - + -
104A ILE* 4.3 20.9 - - + -
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Residues in contact with GLN 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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68A GLY 3.1 13.9 + - - +
69A GLY* 3.8 11.0 + - - +
70A TYR 3.2 0.2 - - - -
71A ALA* 1.3 77.6 - - - +
73A SER* 1.3 63.4 + - - +
74A GLY 3.1 1.4 + - - -
99A TYR* 3.3 33.9 + - + +
334A PRO* 4.2 20.7 - - - +
379A LYS* 5.3 8.3 - - - +
184B ASP* 5.5 0.5 - - - +
362B ALA* 3.6 21.3 - - - +
366B THR* 4.2 25.2 - - + +
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Residues in contact with SER 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 GLY 3.0 17.0 + - - -
70A TYR 3.0 6.6 + - - -
72A GLN* 1.3 80.3 + - - +
74A GLY* 1.3 61.7 + - - +
75A LEU* 3.4 19.3 + - - +
359B ALA* 3.4 27.3 - - - +
362B ALA* 3.8 8.7 - - - -
363B ALA* 5.5 1.6 - - - +
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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