Contacts of the helix formed by residues 64 - 69 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63S LYS* 1.3 78.1 - - - +
65S GLU* 1.3 58.4 + - - +
66S ILE 3.3 0.2 - - - -
67S ALA* 3.1 2.0 + - - +
68S ARG* 2.8 45.7 + - + +
78S PHE* 4.7 1.5 - - + -
80S LYS* 3.5 34.0 - - + +
255S PHE* 2.8 24.2 - - + -
456S ATP 2.7 43.8 + - - +
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Residues in contact with GLU 65 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16S HIS* 4.4 10.2 - - - +
17S ILE* 3.2 22.6 - - + +
62S GLY* 4.6 7.6 - - - -
63S LYS 3.5 1.2 - - - +
64S THR* 1.3 79.5 - - - +
66S ILE* 1.3 56.3 + - - +
68S ARG* 3.1 14.9 + - - -
69S ARG* 2.8 62.1 + - - +
456S ATP 3.4 50.5 + - + +
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Residues in contact with ILE 66 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S LEU* 4.7 9.3 - - + +
17S ILE* 3.1 35.6 - - + +
20S GLN* 4.0 8.1 - - + -
23S ALA* 3.9 19.1 - - + -
24S LYS* 3.8 27.4 - - + -
27S VAL* 3.3 39.1 - - + +
55S MET* 4.9 6.3 - - + -
62S GLY 4.1 12.1 + - - +
63S LYS 4.1 7.9 + - - +
64S THR 3.3 0.6 - - - -
65S GLU* 1.3 75.2 - - - +
67S ALA* 1.3 58.4 + - - +
69S ARG* 4.2 4.8 - - - +
70S LEU* 3.6 15.8 + - - +
333S LEU* 5.0 1.3 - - + -
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Residues in contact with ALA 67 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55S MET* 4.3 1.3 - - + -
63S LYS 3.7 3.1 + - - +
64S THR 3.1 6.8 + - - +
65S GLU 3.0 0.6 - - - -
66S ILE* 1.3 77.4 - - - +
68S ARG* 1.3 62.7 + - - +
69S ARG 3.5 0.7 - - - -
70S LEU* 3.5 17.1 + - - +
78S PHE* 3.0 28.4 - - + -
253S ILE* 4.5 1.7 - - - +
255S PHE* 3.5 40.2 - - + -
306S ILE* 4.2 15.5 - - + -
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Residues in contact with ARG 68 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64S THR* 2.8 28.5 + - - +
65S GLU* 3.8 18.4 - - - +
67S ALA* 1.3 76.6 - - - +
69S ARG* 1.3 69.6 + - - +
70S LEU 2.9 10.7 + - - -
71S ALA* 3.1 16.6 + - - +
72S LYS* 3.6 16.7 + - + +
78S PHE* 3.2 44.1 - - + -
80S LYS* 4.5 18.8 - - - +
288X GLY 4.5 14.0 + - - -
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Residues in contact with ARG 69 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9S ILE* 5.8 0.2 - - - +
13S LEU* 3.0 35.2 - - + +
16S HIS* 3.5 44.4 + - + +
17S ILE* 4.6 6.3 - - + -
65S GLU* 2.8 39.4 + - - +
66S ILE* 4.4 2.5 - - - -
68S ARG* 1.3 91.7 + - - +
70S LEU* 1.3 59.4 + - - +
71S ALA 3.6 1.3 - - - -
72S LYS* 5.5 6.1 - - - +
73S LEU* 3.9 41.2 - - + +
46X HIS* 5.8 1.0 + - - -
47X GLU* 2.6 32.9 + - - +
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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