Contacts of the helix formed by residues 70 - 81 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64N LEU* 4.3 1.6 - - - +
67N HIS* 2.9 20.7 + - + +
68N GLN* 3.6 35.8 + - - -
69N GLY* 1.3 73.9 - - - +
71N LEU* 1.3 68.8 + - - +
72N LEU 3.7 0.9 - - - -
73N LYS* 3.0 16.0 + - + +
74N SER* 2.8 20.6 + - - -
386T GLU* 3.0 35.8 + - + +
387T LYS* 4.0 3.6 - - - -
388T THR* 4.0 14.7 - - - -
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Residues in contact with LEU 71 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42N VAL* 4.0 15.5 - - + -
60N PHE* 3.5 31.2 - - + -
64N LEU* 4.2 2.7 - - + -
69N GLY 3.0 9.6 + - - +
70N HIS* 1.3 67.3 - - - +
72N LEU* 1.3 57.1 + - - +
73N LYS 2.5 14.2 + - - -
74N SER* 2.6 20.6 + - - -
75N ALA* 3.0 10.0 + - + +
97N VAL* 4.0 18.8 - - + +
98N ALA* 3.8 10.3 - - - +
99N ASP* 3.4 53.3 + - - +
102N GLU* 3.8 16.2 - - + +
103N SER 4.5 0.2 - - - +
104N LEU* 5.3 4.5 - - + +
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Residues in contact with LEU 72 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70N HIS 3.7 0.6 - - - -
71N LEU* 1.3 79.0 - - - +
73N LYS* 1.3 56.2 + - - +
75N ALA* 4.0 2.8 - - - +
76N VAL* 2.8 26.0 + - - +
102N GLU* 4.1 31.4 - - + +
104N LEU* 3.8 26.7 - - + -
114N GLN* 4.5 15.3 - - - +
438T ASP* 3.6 18.1 - - + +
439T LEU* 4.3 22.2 - - + -
443T ILE* 4.3 14.4 - - + -
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Residues in contact with LYS 73 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67N HIS* 5.4 7.9 - - + -
70N HIS* 3.0 19.6 + - + +
71N LEU 2.5 5.9 + - - -
72N LEU* 1.3 73.2 - - - +
74N SER* 1.3 55.8 + - - +
75N ALA 2.8 3.8 - - - -
76N VAL* 2.6 29.5 + - - +
77N GLU* 2.9 12.0 + - - -
438T ASP* 3.4 19.0 + - - +
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Residues in contact with SER 74 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60N PHE* 4.0 5.8 - - - -
63N LYS* 3.0 39.4 - - - +
64N LEU* 3.1 27.1 - - - +
67N HIS* 4.6 7.5 - - - +
70N HIS* 2.8 14.7 + - - +
71N LEU* 2.6 19.8 + - - -
73N LYS* 1.3 72.6 - - - +
75N ALA* 1.3 62.4 + - - +
77N GLU* 3.4 7.6 + - - +
78N LEU* 3.1 19.1 + - - +
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Residues in contact with ALA 75 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60N PHE* 3.6 20.2 - - + -
71N LEU 3.0 14.3 + - - +
72N LEU 4.0 6.7 - - - +
73N LYS 2.7 4.2 + - - -
74N SER* 1.3 73.9 + - - +
76N VAL* 1.3 55.1 + - - +
78N LEU* 2.7 26.9 + - - +
79N ALA* 2.9 10.7 + - - +
97N VAL* 5.5 0.7 - - + -
104N LEU* 4.1 9.2 - - + -
106N ILE* 4.0 15.3 - - + +
112N VAL* 4.1 22.7 - - + +
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Residues in contact with VAL 76 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72N LEU 2.8 24.9 - - - +
73N LYS* 2.6 10.5 + - - +
75N ALA* 1.3 72.6 - - + +
77N GLU* 1.3 57.3 + - - +
79N ALA* 3.1 4.1 + - + +
80N LYS* 2.9 29.5 + - - +
112N VAL* 4.2 8.3 - - + -
438T ASP* 3.2 21.8 - - - +
442T PHE* 3.2 57.4 - - + +
443T ILE* 4.3 15.3 - - + -
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Residues in contact with GLU 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63N LYS* 3.7 25.5 + - + +
67N HIS* 4.7 15.9 - - + +
73N LYS 2.9 10.6 + - - +
74N SER* 3.7 13.2 - - - +
76N VAL* 1.3 77.4 - - - +
78N LEU* 1.3 62.7 + - - +
80N LYS* 3.7 12.1 + - - +
81N ASP* 3.7 10.0 + - - +
265S LYS* 4.7 5.3 + - - +
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Residues in contact with LEU 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56N LEU* 4.5 7.6 - - + +
59N LEU* 3.8 34.3 - - + +
60N PHE* 3.6 45.5 - - + +
63N LYS* 4.1 11.0 - - + +
74N SER 3.1 11.2 + - - +
75N ALA* 2.7 14.4 + - - +
77N GLU* 1.3 76.4 - - - +
79N ALA* 1.3 64.5 + - - +
81N ASP* 3.0 33.6 + - + +
82N TRP* 3.7 21.4 - - + -
106N ILE* 4.8 11.7 - - + -
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Residues in contact with ALA 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75N ALA 2.9 5.1 + - - -
76N VAL* 3.4 9.2 - - + +
78N LEU* 1.3 76.9 - - - +
80N LYS* 1.3 53.1 + - - +
82N TRP* 2.7 46.1 + - - +
83N ARG* 3.6 34.2 + - - +
106N ILE* 5.5 2.6 - - + +
110N GLY* 4.4 1.9 - - - -
111N ASP 4.2 8.1 - - - +
112N VAL* 3.8 21.3 - - + -
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Residues in contact with LYS 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76N VAL 2.9 15.4 + - - +
77N GLU* 3.8 10.5 - - - +
78N LEU 3.3 0.2 - - - -
79N ALA* 1.3 75.2 - - - +
81N ASP* 1.3 61.7 + - - +
82N TRP 3.1 0.9 - - - -
83N ARG* 3.0 26.9 + - - +
84N THR* 3.3 14.9 - - - +
265S LYS* 4.7 13.4 - - + +
442T PHE* 5.4 12.1 - - + -
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Residues in contact with ASP 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59N LEU* 5.8 1.0 - - - +
63N LYS* 3.3 28.0 + - - -
77N GLU 3.7 10.1 + - - +
78N LEU* 3.0 19.5 + - + +
79N ALA 2.7 3.6 + - - -
80N LYS* 1.3 74.4 - - - +
82N TRP* 1.3 59.2 + - + +
84N THR* 4.1 16.0 + - - +
86N ARG 4.2 2.9 - - - +
88N LEU* 4.1 35.9 + - + +
85O ASP* 5.7 0.5 - - - +
265S LYS* 3.9 17.7 + - - -
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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