Contacts of the helix formed by residues 70 - 81 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386E GLU* 3.1 31.3 + - + -
387E LYS* 4.5 9.1 + - - -
388E THR* 4.1 8.0 + - - -
67K HIS* 2.9 30.4 + - + +
68K GLN* 3.6 29.7 + - + +
69K GLY* 1.3 68.2 + - - +
71K LEU* 1.3 69.7 + - - +
72K LEU* 2.9 3.9 + - + -
73K LYS* 3.0 22.8 + - + +
74K SER* 2.9 20.8 + - - -
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Residues in contact with LEU 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K VAL* 3.9 21.5 - - + -
60K PHE* 3.5 24.7 - - + -
64K LEU* 4.1 6.3 - - - -
69K GLY 2.9 10.6 + - - +
70K HIS* 1.3 70.2 - - - +
72K LEU* 1.3 69.3 + - - +
74K SER* 3.5 1.9 + - - -
75K ALA* 3.0 16.5 + - - +
97K VAL* 3.9 23.8 - - + +
98K ALA* 4.3 5.6 - - - +
99K ASP* 3.6 35.0 + - - +
102K GLU* 4.1 14.8 - - + -
104K LEU* 3.7 27.4 - - + -
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Residues in contact with LEU 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438E ASP* 4.8 2.9 - - + -
439E LEU* 3.9 16.4 - - + +
443E ILE* 3.4 31.2 - - + -
70K HIS* 2.9 4.3 + - + -
71K LEU* 1.3 82.4 - - - +
73K LYS* 1.3 65.4 + - - +
75K ALA* 3.2 3.3 + - - +
76K VAL* 3.1 24.7 + - + -
102K GLU* 4.0 26.4 - - + +
104K LEU* 3.6 33.4 - - + -
114K GLN* 4.6 5.6 - - - +
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Residues in contact with LYS 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437E GLU* 5.7 4.7 + - - -
438E ASP* 4.9 17.4 - - + +
315F ARG* 5.8 4.2 - - - +
67K HIS* 3.6 29.9 + - + -
70K HIS* 3.0 26.1 + - + +
72K LEU* 1.3 74.4 - - - +
74K SER* 1.3 70.7 + - - +
76K VAL* 2.8 9.5 + - + +
77K GLU* 2.7 51.8 + - + +
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Residues in contact with SER 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60K PHE* 4.2 6.5 - - - -
63K LYS* 3.2 29.5 + - - +
64K LEU* 3.3 32.1 - - - +
67K HIS* 3.9 10.5 - - - +
70K HIS 2.9 17.3 + - - -
71K LEU 3.7 3.6 - - - -
73K LYS* 1.3 78.3 - - - +
75K ALA* 1.3 64.7 - - - +
77K GLU* 3.1 4.9 + - - +
78K LEU* 2.8 23.6 + - - +
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Residues in contact with ALA 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60K PHE* 3.7 21.4 - - + -
71K LEU* 3.0 12.1 + - + +
72K LEU 3.3 9.9 - - - +
74K SER* 1.3 76.4 - - - +
76K VAL* 1.3 63.7 + - - +
78K LEU* 3.0 6.5 + - - +
79K ALA* 2.8 20.6 + - - +
104K LEU* 3.6 24.5 - - + -
106K ILE* 4.1 9.6 - - + +
112K VAL* 3.8 14.7 - - + +
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Residues in contact with VAL 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438E ASP* 4.9 3.6 - - + -
439E LEU 4.4 5.8 - - - +
442E PHE* 3.4 42.8 - - + +
443E ILE* 4.3 17.0 - - + -
72K LEU* 3.4 31.6 - - + +
73K LYS* 2.8 13.8 + - + +
75K ALA* 1.3 71.8 - - - +
77K GLU* 1.3 52.9 + - + +
79K ALA* 2.7 14.0 + - + +
80K LYS* 2.7 35.0 + - + +
83K ARG* 5.3 0.9 - - - +
112K VAL* 4.0 6.0 - - + +
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Residues in contact with GLU 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63K LYS* 3.6 26.9 + - + -
66K MET* 5.9 1.0 - - - +
67K HIS* 4.0 19.3 + - + +
73K LYS* 2.7 47.7 + - + +
74K SER* 3.4 10.3 - - - +
76K VAL* 1.3 74.6 - - + +
78K LEU* 1.3 57.0 + - - +
80K LYS* 3.1 27.4 - - - +
81K ASP* 3.6 6.9 + - - +
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Residues in contact with LEU 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56K LEU* 3.9 20.9 - - + -
59K LEU* 4.3 21.3 - - + -
60K PHE* 3.7 39.5 - - + +
63K LYS* 4.0 16.1 - - + +
74K SER 2.8 12.1 + - - +
75K ALA* 3.1 11.2 - - - +
77K GLU* 1.3 72.6 - - - +
79K ALA* 1.3 68.8 + - - +
81K ASP* 3.0 22.0 + - + +
82K TRP* 3.6 27.1 - - + -
88K LEU* 4.5 4.9 - - + -
106K ILE* 4.6 8.7 - - + -
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Residues in contact with ALA 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75K ALA 2.8 12.3 + - - +
76K VAL* 2.7 20.4 + - - +
78K LEU* 1.3 71.9 - - - +
80K LYS* 1.3 60.2 - - - +
82K TRP* 2.8 25.8 + - - +
83K ARG* 3.0 40.2 + - - +
106K ILE* 5.7 2.4 - - + +
110K GLY* 4.2 12.5 - - - +
111K ASP 4.8 0.2 - - - +
112K VAL* 4.1 11.9 - - + -
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Residues in contact with LYS 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76K VAL* 2.7 16.0 + - + +
77K GLU* 3.1 24.7 - - - +
79K ALA* 1.3 71.5 - - - +
81K ASP* 1.3 57.7 + - - +
82K TRP 2.6 13.9 + - - -
83K ARG* 2.6 22.9 + - - +
84K THR* 3.3 17.4 + - + +
58L GLU* 5.8 1.8 - - - -
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Residues in contact with ASP 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59K LEU* 5.9 0.3 - - - +
63K LYS* 3.2 26.5 + - - -
77K GLU* 3.8 7.1 - - - +
78K LEU* 3.0 17.8 + - + +
80K LYS* 1.3 81.0 - - - +
82K TRP* 1.3 57.4 + - - +
84K THR* 3.9 18.7 + - - +
87K ALA 4.4 1.2 - - - -
88K LEU* 3.3 40.2 + - + +
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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