Contacts of the helix formed by residues 64 - 69 (chain U) in PDB entry 1G3I
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 THR 64 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63U LYS* 1.3 80.6 - - - +
65U GLU* 1.3 59.5 + - - +
66U ILE 3.3 0.7 - - - -
67U ALA* 3.1 1.9 + - - +
68U ARG* 2.8 45.1 + - + +
78U PHE* 5.3 1.1 - - + -
80U LYS* 3.4 36.7 + - + +
255U PHE* 2.9 24.3 - - + -
458U ATP 3.1 39.0 + - - +
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Residues in contact with GLU 65 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16U HIS* 4.5 10.0 - - - +
17U ILE* 3.2 20.9 - - + -
62U GLY* 4.6 1.6 - - - -
63U LYS 3.5 0.8 - - - +
64U THR* 1.3 79.9 - - - +
66U ILE* 1.3 56.8 + - - +
68U ARG* 3.1 14.8 + - - -
69U ARG* 2.8 61.6 + - - +
458U ATP 3.2 70.8 + - + +
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Residues in contact with ILE 66 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13U LEU* 4.7 10.2 - - + +
17U ILE* 3.1 39.4 - - + +
20U GLN* 4.0 8.7 - - + -
23U ALA* 3.9 19.1 - - + -
24U LYS* 3.8 24.2 - - + -
27U VAL* 3.3 39.4 - - + +
55U MET* 4.9 6.7 - - + -
62U GLY 4.1 11.4 - - - +
63U LYS 4.2 8.1 + - - +
64U THR 3.3 0.6 - - - -
65U GLU* 1.3 75.4 - - - +
67U ALA* 1.3 57.7 + - - +
69U ARG* 4.3 4.6 - - - +
70U LEU* 3.6 15.1 + - - +
333U LEU* 5.0 1.6 - - + -
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Residues in contact with ALA 67 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55U MET* 4.3 1.6 - - + -
63U LYS 3.7 2.6 + - - +
64U THR 3.1 7.4 + - - +
65U GLU 3.0 0.6 - - - -
66U ILE* 1.3 77.6 - - - +
68U ARG* 1.3 62.4 + - - +
69U ARG 3.5 0.2 - - - -
70U LEU* 3.6 16.7 + - - +
78U PHE* 2.9 29.9 - - + -
253U ILE* 4.5 2.1 - - - +
255U PHE* 3.4 40.6 - - + -
306U ILE* 4.2 15.7 - - + -
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Residues in contact with ARG 68 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288T GLY 4.8 12.2 + - - -
64U THR* 2.8 28.3 + - - +
65U GLU* 3.7 18.4 - - - +
67U ALA* 1.3 75.7 - - - +
69U ARG* 1.3 70.9 + - - +
70U LEU 2.9 9.9 + - - -
71U ALA* 3.1 17.1 + - + +
72U LYS* 3.6 17.1 + - + +
78U PHE* 3.2 44.4 - - + -
80U LYS* 4.5 18.2 - - - +
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Residues in contact with ARG 69 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46T HIS* 6.0 0.2 + - - -
47T GLU* 3.0 29.5 + - - +
9U ILE* 5.7 0.2 - - - +
13U LEU* 3.0 36.1 - - + +
16U HIS* 3.5 45.7 + - + +
17U ILE* 4.6 5.6 - - + -
65U GLU* 2.8 39.5 + - - +
66U ILE* 4.4 2.2 - - - -
68U ARG* 1.3 92.6 - - - +
70U LEU* 1.3 59.2 + - - +
71U ALA 3.6 0.9 - - - -
72U LYS* 5.5 5.4 - - - +
73U LEU* 3.9 40.4 - - + +
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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
------------------------------------------------------------
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