Contacts of the helix formed by residues 70 - 81 (chain O) 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 HIS 70 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64O LEU* 4.3 1.8 - - - +
67O HIS* 2.9 19.5 + - + +
68O GLN* 3.6 38.3 + - - -
69O GLY* 1.3 74.8 - - - +
71O LEU* 1.3 68.0 + - - +
72O LEU 3.7 1.6 - - - -
73O LYS* 3.0 15.8 + - + +
74O SER* 2.8 20.8 + - - -
386U GLU* 3.1 36.9 + - + +
387U LYS* 4.2 7.6 - - - -
388U THR* 4.3 7.5 - - - -
435U GLU* 4.1 15.0 + - - +
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Residues in contact with LEU 71 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O VAL* 4.0 16.2 - - + -
60O PHE* 3.5 31.4 - - + -
64O LEU* 4.2 2.9 - - + -
69O GLY 2.9 9.8 + - - +
70O HIS* 1.3 67.3 - - - +
72O LEU* 1.3 57.5 + - - +
73O LYS 2.6 14.2 + - - -
74O SER* 2.6 21.2 + - - -
75O ALA* 3.0 9.8 + - + +
97O VAL* 3.9 20.0 - - + +
98O ALA* 3.8 10.3 - - - +
99O ASP* 3.5 50.9 + - + +
102O GLU* 3.8 16.4 - - + +
103O SER* 4.4 0.7 - - - +
104O LEU* 5.2 4.3 - - + +
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Residues in contact with LEU 72 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70O HIS 3.7 0.4 - - - -
71O LEU* 1.3 78.8 - - - +
73O LYS* 1.3 55.8 + - - +
75O ALA* 4.0 2.3 - - - +
76O VAL* 2.8 26.6 + - + +
102O GLU* 4.1 31.6 - - + +
104O LEU* 3.8 27.4 - - + -
114O GLN* 4.5 17.3 - - - +
438U ASP* 4.3 12.2 - - + +
439U LEU* 4.7 18.2 - - + +
443U ILE* 4.6 17.5 - - + -
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Residues in contact with LYS 73 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67O HIS* 5.4 7.9 - - + -
70O HIS* 3.0 18.5 + - + +
71O LEU 2.6 5.7 + - - -
72O LEU* 1.3 73.1 - - - +
74O SER* 1.3 56.0 + - - +
75O ALA 2.9 4.0 - - - -
76O VAL* 2.6 28.5 + - - +
77O GLU* 2.9 12.1 + - - +
435U GLU* 5.5 7.4 - - - +
438U ASP* 3.8 18.8 - - - +
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Residues in contact with SER 74 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60O PHE* 4.0 5.6 - - - -
63O LYS* 2.9 39.2 - - - +
64O LEU* 3.1 27.0 - - - +
67O HIS* 4.6 7.7 - - - +
70O HIS* 2.8 15.4 + - - +
71O LEU* 2.6 20.4 + - - -
73O LYS* 1.3 71.5 - - - +
75O ALA* 1.3 59.4 + - - +
77O GLU* 3.5 7.9 + - - +
78O LEU* 3.1 21.7 + - - +
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Residues in contact with ALA 75 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O PHE* 3.6 15.4 - - + -
71O LEU 3.0 13.6 + - - +
72O LEU 4.0 7.0 - - - +
73O LYS 2.7 4.4 + - - -
74O SER* 1.3 73.6 + - - +
76O VAL* 1.3 54.2 + - - +
78O LEU* 2.7 26.0 + - - +
79O ALA* 2.9 12.1 + - - +
97O VAL* 5.5 0.7 - - + -
104O LEU* 4.1 8.7 - - + -
106O ILE* 4.0 17.4 - - + +
112O VAL* 4.0 27.3 - - + +
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Residues in contact with VAL 76 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72O LEU 2.8 25.1 - - - +
73O LYS 2.6 10.1 + - - +
75O ALA* 1.3 73.1 - - + +
77O GLU* 1.3 61.4 + - - +
79O ALA* 3.2 2.8 + - + +
80O LYS* 3.0 25.0 + - + +
83O ARG* 6.0 0.2 - - - -
112O VAL* 4.1 8.3 - - - +
438U ASP* 3.2 20.6 - - - +
442U PHE* 3.0 49.8 - - + +
443U ILE* 3.6 20.2 - - + -
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Residues in contact with GLU 77 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63O LYS* 3.7 24.7 + - + +
67O HIS* 4.6 16.8 - - + +
73O LYS 2.9 10.3 + - - +
74O SER* 3.7 12.8 - - - +
76O VAL* 1.3 78.0 - - - +
78O LEU* 1.3 62.2 + - - +
80O LYS* 3.7 12.3 + - - +
81O ASP* 3.7 9.9 + - - +
265T LYS* 5.0 4.9 + - - +
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Residues in contact with LEU 78 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56O LEU* 4.6 8.1 - - + +
59O LEU* 3.8 35.7 - - + +
60O PHE* 3.6 45.1 - - + +
63O LYS* 4.1 10.9 - - + +
74O SER 3.1 12.0 + - - +
75O ALA* 2.7 14.4 + - - +
77O GLU* 1.3 75.8 - - - +
79O ALA* 1.3 64.7 + - - +
81O ASP* 3.0 31.5 + - + +
82O TRP* 3.7 22.1 - - + -
106O ILE* 4.8 11.9 - - + -
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Residues in contact with ALA 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75O ALA 2.9 4.9 + - - -
76O VAL* 3.2 9.2 + - + +
78O LEU* 1.3 76.9 - - - +
80O LYS* 1.3 53.5 + - - +
81O ASP 2.7 0.2 + - - -
82O TRP* 2.6 46.7 + - - +
83O ARG* 3.6 33.7 + - - +
106O ILE* 5.5 2.4 - - + +
110O GLY* 4.5 2.6 - - - -
111O ASP 4.2 8.1 - - - +
112O VAL* 3.8 21.5 - - + -
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Residues in contact with LYS 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76O VAL* 3.0 17.6 + - + +
77O GLU* 3.8 10.5 - - - +
78O LEU 3.3 0.2 - - - -
79O ALA* 1.3 75.2 - - - +
81O ASP* 1.3 61.9 + - - +
82O TRP 3.0 0.4 - - - -
83O ARG* 3.0 26.9 + - - +
84O THR* 3.3 15.4 - - - +
265T LYS* 4.9 12.1 - - + +
442U PHE* 6.4 0.7 - - + -
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Residues in contact with ASP 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59O LEU* 5.8 1.2 - - - +
63O LYS* 3.3 27.3 + - - -
77O GLU 3.7 10.3 + - - +
78O LEU* 3.0 18.7 + - + +
79O ALA 2.7 5.1 + - - -
80O LYS* 1.3 75.1 - - - +
82O TRP* 1.3 58.2 + - + -
83O ARG 3.5 0.2 - - - -
84O THR* 4.1 16.0 + - - +
86O ARG 4.2 2.8 - - - +
87O ALA 4.4 0.2 - - - -
88O LEU* 4.0 35.4 + - + +
85P ASP* 5.7 0.3 - - - +
265T LYS* 4.2 15.8 + - - -
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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