Contacts of the helix formed by residues 62 - 74 (chain F) 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 GLY 62 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17F ILE* 4.8 2.0 - - - -
61F VAL* 1.3 81.2 - - - +
63F LYS* 1.3 66.6 + - - +
64F THR 2.8 4.3 + - - -
65F GLU* 2.9 17.4 + - - -
66F ILE* 2.9 29.2 + - - +
455F ATP 3.0 24.9 + - - -
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Residues in contact with LYS 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F MET* 3.6 41.3 - - + +
56F ILE 4.5 0.2 - - - -
57F GLY* 3.1 40.6 + - - +
58F PRO 2.4 29.7 + - - -
61F VAL* 4.4 2.2 - - + +
62F GLY* 1.3 71.7 - - - +
64F THR* 1.3 57.2 + - - +
66F ILE* 3.9 0.8 - - - +
67F ALA* 3.4 15.2 + - - +
255F PHE* 3.9 10.2 - - + -
308F SER* 3.8 20.9 - - - +
309F GLY* 4.0 8.8 - - - -
310F ALA* 5.0 1.2 - - - +
333F LEU* 3.5 20.3 - - + +
455F ATP 2.9 33.9 + - - +
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Residues in contact with THR 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F GLY 2.8 3.2 + - - -
63F LYS* 1.3 72.3 - - - +
65F GLU* 1.3 53.2 + - - +
67F ALA* 2.8 3.5 + - - +
68F ARG* 2.5 67.9 + - + +
78F PHE* 5.3 2.0 - - + -
80F LYS* 3.5 19.9 + - + +
255F PHE* 2.9 31.4 - - + -
455F ATP 2.9 37.2 + - - +
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Residues in contact with GLU 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F HIS* 4.5 6.8 - - - +
17F ILE* 3.9 15.0 - - + -
62F GLY* 2.9 13.2 + - - +
64F THR* 1.3 69.5 - - - +
66F ILE* 1.3 71.5 + - - +
68F ARG* 2.8 17.7 + - - -
69F ARG* 2.6 68.7 + - - +
455F ATP 3.3 50.5 + - + +
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Residues in contact with ILE 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F LEU* 4.3 7.9 - - + +
17F ILE* 3.5 28.2 - - + +
20F GLN* 3.9 30.1 - - + +
23F ALA* 4.1 8.7 - - + -
24F LYS* 4.6 13.7 - - + +
27F VAL* 3.8 26.0 - - + -
55F MET* 4.5 11.4 - - + -
62F GLY* 3.3 24.9 - - - +
63F LYS* 3.9 3.6 - - - +
65F GLU* 1.3 75.6 - - - +
67F ALA* 1.3 58.5 + - - +
69F ARG* 3.7 1.6 - - - +
70F LEU* 2.8 30.8 + - - +
333F LEU* 3.9 9.9 - - + -
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Residues in contact with ALA 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F VAL* 5.6 0.4 - - - -
55F MET* 4.5 2.9 - - + -
63F LYS 3.4 12.7 + - - +
64F THR 2.8 10.4 + - - +
65F GLU 2.8 2.4 + - - -
66F ILE* 1.3 74.6 - - - +
68F ARG* 1.3 65.8 + - - +
70F LEU* 3.2 7.3 + - - +
71F ALA* 3.0 23.0 + - - +
78F PHE* 3.9 15.2 - - + -
253F ILE* 5.3 1.2 - - - +
255F PHE* 3.8 24.5 - - + -
306F ILE* 4.1 17.5 - - + -
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Residues in contact with ARG 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A GLU* 4.5 13.9 + - - +
288A GLY 4.5 16.2 + - - -
289A SER* 6.1 0.2 - - - +
64F THR* 2.5 41.3 + - - +
65F GLU* 3.6 17.0 + - - +
67F ALA* 1.3 73.6 - - - +
69F ARG* 1.3 59.1 + - + +
71F ALA* 3.2 5.0 - - - +
72F LYS* 2.9 26.2 + - - +
78F PHE* 3.6 34.3 - - + -
80F LYS* 3.9 18.2 - - - +
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Residues in contact with ARG 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLU* 3.5 29.3 + - - -
13F LEU* 4.0 14.4 - - + -
16F HIS* 3.5 46.3 + - + +
17F ILE* 4.1 11.4 - - + -
65F GLU* 2.6 54.6 + - - +
66F ILE* 3.7 2.9 - - - +
68F ARG* 1.3 69.2 - - + +
70F LEU* 1.3 69.6 + - - +
71F ALA 3.1 1.3 - - - -
72F LYS* 2.7 24.7 + - - +
73F LEU* 2.6 28.7 + - + +
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Residues in contact with LEU 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ILE* 4.4 14.1 - - + -
13F LEU* 4.0 4.2 - - + +
27F VAL* 3.3 59.5 - - + +
31F LEU* 3.9 24.5 - - + -
66F ILE 2.8 22.0 + - - +
67F ALA* 3.5 4.7 - - - +
69F ARG* 1.3 75.4 - - - +
71F ALA* 1.3 64.0 + - - +
73F LEU* 3.0 19.1 + - + +
74F ALA* 3.0 14.0 + - + +
253F ILE* 4.7 8.5 - - + -
304F LEU* 4.4 14.6 - - + -
306F ILE* 4.3 13.7 - - + -
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Residues in contact with ALA 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F ALA 3.0 10.2 + - - +
68F ARG 3.2 10.5 - - - +
70F LEU* 1.3 80.1 - - - +
72F LYS* 1.3 62.9 + - - +
74F ALA* 3.1 3.8 + - - -
75F ASN 2.9 17.8 + - - -
76F ALA* 3.0 18.6 + - - +
78F PHE* 3.4 37.2 - - + -
253F ILE* 4.1 17.5 - - + +
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Residues in contact with LYS 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F ARG* 2.9 13.8 + - + +
69F ARG* 2.7 36.5 + - - +
71F ALA* 1.3 73.1 - - - +
73F LEU* 1.3 58.6 + - - +
75F ASN* 2.9 20.9 + - - +
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Residues in contact with LEU 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F GLU* 5.2 2.6 - - - +
4F MET* 4.0 24.1 - - + +
9F ILE* 3.4 36.3 - - + -
12F GLU* 3.6 30.3 - - + -
13F LEU* 3.5 26.9 - - + -
31F LEU* 3.9 14.1 - - + -
69F ARG* 2.6 15.8 + - + +
70F LEU* 3.2 12.8 - - - +
72F LYS* 1.3 73.1 - - - +
74F ALA* 1.3 59.8 + - - +
75F ASN* 3.3 0.6 - - - +
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Residues in contact with ALA 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F GLU* 5.2 13.5 - - - +
31F LEU* 3.3 40.8 - - + -
70F LEU* 3.0 10.3 + - + +
71F ALA* 3.8 3.8 - - - +
72F LYS 3.0 0.8 - - - -
73F LEU* 1.3 78.0 - - - +
75F ASN* 1.3 73.8 + - - +
76F ALA* 3.2 11.2 + - + +
251F ASN* 5.4 3.4 + - + +
253F ILE* 6.1 0.7 - - + -
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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