Contacts of the helix formed by residues 70 - 83 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B GLU* 3.1 33.3 + - + -
387B LYS* 4.1 14.7 + - - -
388B THR* 4.2 5.8 + - - -
67H HIS* 2.9 27.1 + - + +
68H GLN* 3.7 28.5 + - + +
69H GLY* 1.3 69.3 - - - -
71H LEU* 1.3 69.7 + - - +
72H LEU* 3.3 3.1 - - + -
73H LYS* 2.9 23.4 + - + +
74H SER* 2.9 19.9 + - - +
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Residues in contact with LEU 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H VAL* 4.0 21.8 - - + -
60H PHE* 3.4 25.7 - - + -
64H LEU* 4.0 7.0 - - + -
69H GLY 2.8 10.1 + - - +
70H HIS* 1.3 72.4 - - - +
72H LEU* 1.3 66.5 + - - +
74H SER* 3.2 2.1 + - - -
75H ALA* 3.0 18.6 + - + -
97H VAL* 3.9 22.7 - - + +
98H ALA* 4.2 6.1 - - - +
99H ASP* 3.6 35.0 + - + +
102H GLU* 4.3 13.5 - - + -
104H LEU* 3.5 29.4 - - + -
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Residues in contact with LEU 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ASN* 5.6 3.8 - - - +
438B ASP* 4.0 4.3 - - - +
439B LEU* 3.3 29.6 - - + -
443B ILE* 3.5 30.3 - - + -
70H HIS* 3.0 2.3 + - + -
71H LEU* 1.3 84.0 - - - +
73H LYS* 1.3 65.4 + - - +
75H ALA* 3.3 3.3 + - - +
76H VAL* 3.1 22.7 + - + +
102H GLU* 3.8 34.5 - - + +
104H LEU* 3.6 25.4 - - + -
114H GLN* 4.7 4.7 - - - +
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Residues in contact with LYS 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B ASP* 4.1 30.4 + - + +
315C ARG* 5.1 9.9 - - - +
67H HIS* 3.5 29.1 + - + -
70H HIS* 2.9 26.9 + - + +
72H LEU* 1.3 76.5 - - - +
74H SER* 1.3 67.7 + - - +
76H VAL* 2.7 18.4 + - + +
77H GLU* 2.7 46.8 + - + +
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Residues in contact with SER 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H PHE* 4.2 4.3 - - - -
63H LYS* 3.4 16.9 + - - +
64H LEU* 3.3 46.9 - - - +
67H HIS* 3.8 11.7 - - - +
70H HIS 2.9 12.5 + - - -
71H LEU 3.4 8.7 - - - -
73H LYS* 1.3 79.4 - - - +
75H ALA* 1.3 65.1 + - - +
77H GLU* 3.2 4.4 + - - +
78H LEU* 2.9 23.2 + - - +
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Residues in contact with ALA 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H PHE* 3.7 14.9 - - + -
71H LEU* 3.0 12.0 + - + +
72H LEU 3.4 9.4 - - - +
74H SER* 1.3 75.6 - - - +
76H VAL* 1.3 57.9 + - - +
78H LEU* 3.0 6.5 + - - +
79H ALA* 2.9 26.9 + - - +
104H LEU* 3.8 21.5 - - + -
106H ILE* 3.8 23.2 - - + +
112H VAL* 3.8 11.0 - - + +
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Residues in contact with VAL 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B ASP* 4.8 6.5 - - + +
439B LEU 5.1 1.3 - - - +
442B PHE* 3.4 44.6 - - + +
443B ILE* 4.2 16.4 - - + -
72H LEU* 3.2 33.2 - - + +
73H LYS* 2.7 13.4 + - - +
75H ALA* 1.3 69.4 - - - +
77H GLU* 1.3 56.0 + - + +
79H ALA* 3.1 4.8 + - + +
80H LYS* 2.6 38.6 + - + +
83H ARG* 5.6 0.9 - - - +
112H VAL* 4.2 11.4 - - + -
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Residues in contact with GLU 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C ARG* 5.5 5.7 + - - -
63H LYS* 3.9 20.7 + - + -
66H MET* 6.1 0.2 - - - +
67H HIS* 4.0 21.2 + - + +
73H LYS* 2.7 46.7 + - + +
74H SER* 3.5 9.2 - - - +
76H VAL* 1.3 74.0 - - + +
78H LEU* 1.3 61.5 + - - +
80H LYS* 3.2 12.5 - - - +
81H ASP* 3.2 26.5 + - - +
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Residues in contact with LEU 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H LEU* 4.1 16.8 - - + -
59H LEU* 4.3 17.9 - - + +
60H PHE* 3.7 43.7 - - + +
63H LYS* 4.0 14.8 - - + +
74H SER 2.9 12.5 + - - +
75H ALA* 3.0 10.1 + - - +
77H GLU* 1.3 74.4 - - - +
79H ALA* 1.3 67.2 + - - +
81H ASP* 2.9 24.9 + - + +
82H TRP* 3.1 35.3 - - + -
88H LEU* 6.5 0.2 - - + -
106H ILE* 4.5 10.5 - - + -
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Residues in contact with ALA 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H ALA 2.9 11.4 + - - +
76H VAL* 3.5 6.1 - - - +
78H LEU* 1.3 77.0 - - - +
80H LYS* 1.3 63.0 + - - +
82H TRP* 3.1 12.7 + - - +
83H ARG* 3.0 49.8 + - - +
106H ILE* 5.5 2.5 - - + -
110H GLY* 3.8 19.1 - - - +
111H ASP 4.0 2.5 - - - +
112H VAL* 4.1 13.5 - - + -
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Residues in contact with LYS 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B PHE* 6.4 1.6 - - + -
76H VAL* 2.6 20.9 + - + +
77H GLU* 3.2 23.1 - - - +
79H ALA* 1.3 73.7 - - - +
81H ASP* 1.3 63.2 + - - +
83H ARG* 2.9 30.3 + - - +
84H THR* 3.9 4.5 + - - +
58I GLU* 5.6 3.4 - - - +
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Residues in contact with ASP 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H LEU* 6.2 0.4 - - + +
63H LYS* 2.9 30.9 + - - -
77H GLU* 3.2 9.5 + - - +
78H LEU* 2.9 19.5 + - + +
80H LYS* 1.3 78.8 - - - +
82H TRP* 1.3 58.1 + - + +
84H THR* 3.6 11.1 + - - -
86H ARG* 4.0 2.4 - - - +
88H LEU* 3.6 31.6 - - + +
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Residues in contact with TRP 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H LEU* 4.2 12.1 - - + -
59H LEU* 4.2 10.1 - - + -
78H LEU* 3.1 50.4 + - + -
79H ALA* 3.1 6.6 + - - +
81H ASP* 1.3 78.3 - - + +
83H ARG* 1.3 53.3 + - - +
84H THR* 2.8 25.6 + - - +
86H ARG 4.6 4.3 - - - +
87H ALA* 5.8 0.9 - - - -
88H LEU* 3.3 40.1 + - + +
90H LYS* 3.4 15.0 - - + +
91H LEU* 3.3 37.0 - - + -
106H ILE* 5.4 0.7 - - + -
107H THR 4.5 5.8 - - - -
108H GLY* 2.7 30.5 + - - -
109H ILE 3.9 10.8 - - - +
110H GLY* 3.7 24.0 - - - +
89I ARG* 4.3 14.4 + - - -
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Residues in contact with ARG 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B PHE* 3.2 24.0 + - - +
76H VAL* 5.2 1.0 + - - +
79H ALA* 3.0 40.9 + - - +
80H LYS* 2.9 12.4 + - - +
82H TRP* 1.3 71.7 - - - +
84H THR* 1.3 64.2 + - - +
110H GLY 3.4 17.6 + - - +
111H ASP* 3.7 11.1 - - - +
112H VAL* 4.1 2.6 - - - +
51I ALA* 4.4 2.1 + - - +
54I PHE* 3.0 39.1 - - - +
55I THR* 3.2 44.5 - - + +
58I GLU* 2.7 49.8 + - - +
59I LEU* 4.7 5.2 - - - +
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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
------------------------------------------------------------
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