Contacts of the helix formed by residues 79 - 85 (chain D) in PDB entry 1I0E
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 79 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78D ASP* 1.3 73.6 - - - +
80D GLU* 1.3 74.2 + - - +
81D SER 3.2 0.7 + - - -
82D TYR* 3.4 19.8 + - - +
83D GLU* 4.3 1.7 + - - +
138D LYS* 2.6 32.7 + - - +
140D TYR 5.5 0.6 + - - -
142D LEU* 4.7 1.2 - - - +
272D MET* 3.4 47.1 - - + +
273D TRP 4.5 9.4 + - - +
274D ASN* 5.5 3.6 + - - +
280D VAL* 4.5 17.1 - - + +
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Residues in contact with GLU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D THR* 4.2 3.1 - - - -
48D PRO* 3.3 43.4 - - + +
78D ASP* 3.5 18.6 - - - +
79D GLU* 1.3 85.2 + - - +
81D SER* 1.3 58.9 + - - +
82D TYR 3.0 4.3 + - - -
83D GLU* 3.0 9.5 + - + +
84D VAL* 2.8 36.4 + - + +
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Residues in contact with SER 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D THR* 3.6 11.0 - - - +
51D PHE* 3.2 13.9 - - - -
56D VAL* 5.3 0.2 - - - -
76D ALA* 3.8 20.6 - - - -
77D GLY 3.2 12.3 + - - -
78D ASP* 2.3 39.0 + - - -
80D GLU* 1.3 76.1 - - - +
82D TYR* 1.3 55.7 + - - +
85D PHE* 3.1 37.3 + - - +
89D PHE* 3.4 8.7 - - - -
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Residues in contact with TYR 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D ALA* 3.9 15.0 - - + +
78D ASP 5.2 0.7 - - - -
79D GLU 3.4 12.2 + - - +
80D GLU 3.0 1.2 - - - -
81D SER* 1.3 76.3 - - - +
83D GLU* 1.3 65.4 + - - +
86D LYS* 3.1 26.0 + - - +
89D PHE* 3.4 47.3 - + + +
93D ILE* 4.8 2.5 - - + -
277D LEU* 3.6 28.3 - - + -
280D VAL* 4.3 15.3 - - + -
281D LEU 3.3 26.4 + - - -
282D THR 4.1 2.4 + - - -
284D PRO* 3.5 27.6 - - + +
287D LEU* 3.5 27.1 - - + +
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Residues in contact with GLU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D GLU 4.3 1.6 + - - +
80D GLU* 3.0 13.0 + - + +
82D TYR* 1.3 78.9 - - - +
84D VAL* 1.3 66.2 + - + +
86D LYS* 3.1 26.3 - - - +
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Residues in contact with VAL 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU* 5.3 3.6 - - - +
45D LYS* 4.3 19.9 - - + +
46D GLU 4.5 10.8 - - - +
47D THR* 4.3 16.2 - - + -
48D PRO* 5.1 1.8 - - + -
80D GLU* 2.8 29.2 + - + +
83D GLU* 1.3 74.8 - - + +
85D PHE* 1.3 89.9 + - + +
86D LYS* 3.2 4.7 + - - +
87D GLU* 4.9 3.6 + - - +
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Residues in contact with PHE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU* 4.1 19.1 - - + -
45D LYS 3.9 12.8 - - - -
46D GLU* 4.5 0.2 - - - -
47D THR* 3.6 24.7 - - + -
51D PHE 3.7 5.2 - - - -
52D THR* 3.6 9.4 - - - -
53D VAL* 3.2 57.7 - - + -
56D VAL* 4.2 17.9 - - + -
81D SER* 3.1 26.1 + - - +
82D TYR 3.7 3.8 - - - -
84D VAL* 1.3 87.3 - - + +
86D LYS* 1.3 63.6 + - - +
87D GLU 3.3 2.7 - - - -
88D LEU* 3.0 20.5 + - + +
89D PHE* 3.1 23.4 + + + -
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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