Contacts of the helix formed by residues 62 - 74 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C ILE* 4.7 2.5 - - - -
60C GLY 3.6 0.2 - - - -
61C VAL* 1.3 81.9 - - - +
63C LYS* 1.3 69.8 + - - +
64C THR 3.1 2.9 - - - -
65C GLU* 2.9 17.9 + - - -
66C ILE* 2.9 23.4 + - - +
333C LEU* 4.1 2.7 - - - -
452C ATP 3.2 24.7 + - - -
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Residues in contact with LYS 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C MET* 3.7 34.2 - - + +
57C GLY* 3.1 40.4 + - - +
58C PRO 2.3 28.3 + - - -
59C THR* 4.5 0.4 - - - +
61C VAL* 4.1 1.9 - - + +
62C GLY* 1.3 76.6 - - - +
64C THR* 1.3 62.2 + - - +
66C ILE* 3.5 3.7 + - - +
67C ALA* 3.2 19.2 + - - +
255C PHE* 4.2 12.6 - - + -
308C SER* 3.9 21.8 - - - +
309C GLY 4.2 5.6 - - - +
310C ALA 5.4 0.2 - - - +
333C LEU* 3.5 22.7 - - + +
452C ATP 2.8 34.7 + - - +
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Residues in contact with THR 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C GLY 2.9 2.0 + - - -
63C LYS* 1.3 70.6 - - - +
65C GLU* 1.3 60.4 + - + +
67C ALA* 2.9 4.3 + - + +
68C ARG* 2.8 59.9 + - + +
78C PHE* 5.4 1.6 - - + -
80C LYS* 3.4 27.7 + - + +
255C PHE* 3.4 20.4 - - + -
452C ATP 2.8 39.6 + - - +
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Residues in contact with GLU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C HIS* 4.6 6.3 - - - +
17C ILE* 4.0 15.0 - - + -
62C GLY* 2.9 11.9 + - - +
64C THR* 1.3 73.6 - - - +
66C ILE* 1.3 56.5 + - - +
67C ALA 3.0 0.2 + - - -
68C ARG* 3.1 17.2 + - - +
69C ARG* 2.6 79.9 + - - +
452C ATP 3.2 52.9 + - - +
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Residues in contact with ILE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 4.3 12.1 - - + +
17C ILE* 3.7 28.5 - - + -
20C GLN* 4.0 17.0 - - + +
23C ALA* 3.8 24.9 - - + +
24C LYS* 4.5 8.5 - - + +
27C VAL* 3.8 30.7 - - + -
55C MET* 4.7 5.6 - - + -
62C GLY 2.9 20.3 + - - +
63C LYS* 3.6 4.3 - - - +
65C GLU* 1.3 74.3 - - - +
67C ALA* 1.3 58.4 + - - +
69C ARG* 3.7 1.7 - - - +
70C LEU* 3.0 28.8 + - - +
333C LEU* 3.9 14.8 - - + -
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Residues in contact with ALA 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL* 5.4 0.4 - - - -
55C MET* 4.3 7.2 - - + +
63C LYS 3.2 7.2 + - - +
64C THR 2.9 8.7 + - - +
66C ILE* 1.3 79.4 - - - +
68C ARG* 1.3 64.0 + - - +
70C LEU* 3.3 7.7 + - - +
71C ALA* 3.1 17.7 + - - +
78C PHE* 3.5 19.9 - - + -
253C ILE* 4.9 1.7 - - - +
255C PHE* 3.6 31.4 - - + -
306C ILE* 4.4 12.1 - - + -
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Residues in contact with ARG 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C THR* 2.8 40.7 + - - +
65C GLU* 3.8 19.1 + - - +
67C ALA* 1.3 72.6 - - - +
69C ARG* 1.3 59.3 + - + +
71C ALA* 3.3 5.0 - - - +
72C LYS* 2.9 27.2 + - - +
78C PHE* 3.8 34.8 - - + -
80C LYS* 3.9 20.0 - - - +
287D GLU* 4.6 12.3 + - - +
288D GLY 4.6 15.2 + - - -
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Residues in contact with ARG 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 3.9 17.0 - - + -
16C HIS* 3.2 43.2 + - + +
17C ILE* 3.9 15.9 - - + -
65C GLU* 2.6 56.8 + - - +
66C ILE 3.7 3.4 - - - +
68C ARG* 1.3 71.2 - - - +
70C LEU* 1.3 67.3 + - - +
72C LYS* 2.7 25.8 + - - +
73C LEU* 2.7 26.0 + - + +
47D GLU* 3.3 30.5 + - - -
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Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 4.2 15.5 - - + -
13C LEU* 4.1 3.5 - - + +
27C VAL* 3.4 55.6 - - + +
31C LEU* 3.7 29.4 - - + -
66C ILE 3.0 19.1 + - - +
67C ALA* 3.4 5.6 - - - +
69C ARG* 1.3 76.5 - - - +
71C ALA* 1.3 65.8 + - - +
73C LEU* 3.2 10.1 + - + +
74C ALA* 3.0 23.3 + - + +
253C ILE* 4.8 7.4 - - + -
304C LEU* 4.3 21.3 - - + -
306C ILE* 4.3 6.3 - - + -
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Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ALA 3.1 2.2 + - - +
68C ARG 3.3 9.6 - - - +
70C LEU* 1.3 80.1 - - - +
72C LYS* 1.3 58.4 + - - +
74C ALA* 2.9 4.0 + - - -
75C ASN 2.8 25.5 + - - -
76C ALA* 3.0 19.3 + - - +
78C PHE* 3.4 43.7 - - + -
253C ILE* 4.0 15.9 - - + +
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Residues in contact with LYS 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ARG 2.9 14.3 + - - +
69C ARG* 2.7 38.4 + - - +
71C ALA* 1.3 70.8 - - - +
73C LEU* 1.3 57.8 + - - +
75C ASN* 2.9 20.8 + - - +
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Residues in contact with LEU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C GLU* 5.1 4.5 - - - +
4C MET* 3.9 24.6 - - + +
9C ILE* 3.4 37.7 - - + -
12C GLU* 3.4 34.3 - - + +
13C LEU* 3.6 22.2 - - + -
31C LEU* 4.0 13.7 - - + -
69C ARG* 2.7 14.6 + - + +
70C LEU* 3.4 10.5 - - - +
72C LYS* 1.3 73.2 - - - +
74C ALA* 1.3 59.3 + - - +
75C ASN* 3.3 0.8 - - - +
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Residues in contact with ALA 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C GLU* 5.2 12.0 - - - +
31C LEU* 3.6 31.6 - - + -
70C LEU* 3.0 16.0 + - + +
71C ALA* 2.9 5.2 + - - +
73C LEU* 1.3 80.4 - - - +
75C ASN* 1.3 74.6 + - - +
76C ALA* 3.2 13.1 + - + +
251C ASN* 5.5 3.4 + - + +
253C ILE* 5.9 1.3 - - + -
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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