Contacts of the helix formed by residues 70 - 84 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D GLU* 3.0 33.4 + - + -
387D LYS* 4.5 9.1 - - + -
388D THR* 4.2 8.0 + - - -
67J HIS* 2.9 26.3 + - + +
68J GLN* 3.7 27.5 + - + +
69J GLY* 1.3 75.0 - - - +
71J LEU* 1.3 68.3 + - - +
72J LEU* 3.3 2.5 - - + +
73J LYS* 3.0 24.0 + - + +
74J SER* 2.9 20.3 + - - -
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Residues in contact with LEU 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J VAL* 4.0 21.3 - - + -
60J PHE* 3.5 23.9 - - + -
64J LEU* 3.9 6.7 - - + -
69J GLY 2.9 10.3 + - - +
70J HIS* 1.3 71.7 - - - +
72J LEU* 1.3 65.4 + - - +
74J SER* 3.2 2.4 + - - -
75J ALA* 2.9 19.3 + - + +
97J VAL* 3.9 23.8 - - + +
98J ALA* 4.3 6.1 - - - +
99J ASP* 3.7 32.4 + - + +
102J GLU* 4.3 15.7 - - + -
104J LEU* 3.6 29.4 - - + -
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Residues in contact with LEU 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D ASN* 6.1 0.9 - - - +
438D ASP* 4.6 3.1 - - + -
439D LEU* 3.4 35.4 - - + +
443D ILE* 3.6 27.4 - - + -
70J HIS* 3.0 3.9 + - + -
71J LEU* 1.3 81.6 - - - +
73J LYS* 1.3 64.8 + - - +
75J ALA* 3.2 2.8 + - - +
76J VAL* 3.0 27.5 + - + +
102J GLU* 3.9 25.7 - - + +
104J LEU* 3.6 32.3 - - + -
114J GLN* 4.7 2.7 - - - +
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Residues in contact with LYS 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D ASN* 6.0 0.4 - - - +
438D ASP* 3.8 37.6 + - - +
315E ARG* 5.9 2.6 - - - +
67J HIS* 3.4 33.1 + - + -
70J HIS* 3.0 26.2 + - + +
72J LEU* 1.3 74.6 - - - +
74J SER* 1.3 71.6 + - - +
76J VAL* 3.0 7.5 + - + +
77J GLU* 2.7 50.8 + - + +
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Residues in contact with SER 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60J PHE* 4.1 8.3 - - - -
63J LYS* 3.4 15.7 + - - +
64J LEU* 3.1 48.4 + - - +
67J HIS* 4.0 9.1 - - - +
70J HIS 2.9 11.2 + - - -
71J LEU 3.3 9.0 - - - -
73J LYS* 1.3 79.9 - - - +
75J ALA* 1.3 66.3 + - - +
77J GLU* 3.1 4.4 + - - +
78J LEU* 2.9 22.0 + - - +
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Residues in contact with ALA 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60J PHE* 3.7 13.1 - - + -
71J LEU* 2.9 10.9 + - + +
72J LEU 3.3 9.2 - - - +
74J SER* 1.3 74.4 - - - +
76J VAL* 1.3 65.8 + - - +
78J LEU* 2.9 6.8 + - - +
79J ALA* 2.9 19.6 + - - +
104J LEU* 3.5 27.1 - - + -
106J ILE* 4.0 16.9 - - + +
112J VAL* 3.7 14.8 - - + +
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Residues in contact with VAL 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438D ASP* 4.4 13.0 - - + +
442D PHE* 3.4 41.1 - - + +
443D ILE* 4.3 16.6 - - + -
72J LEU* 3.3 31.9 - - + +
73J LYS* 3.0 7.3 + - - +
75J ALA* 1.3 75.2 - - - +
77J GLU* 1.3 54.8 + - + +
79J ALA* 2.9 6.5 + - + +
80J LYS* 2.7 38.1 + - + +
83J ARG* 5.5 1.3 - - - +
112J VAL* 3.9 9.6 - - + +
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Residues in contact with GLU 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J LYS* 3.8 26.1 + - + -
67J HIS* 3.8 22.2 + - + +
73J LYS* 2.7 48.8 + - + +
74J SER* 3.4 6.3 - - - +
76J VAL* 1.3 74.3 - - + +
78J LEU* 1.3 61.7 + - - +
80J LYS* 3.4 12.8 + - - +
81J ASP* 3.4 20.3 + - - +
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Residues in contact with LEU 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J LEU* 4.1 16.8 - - + -
59J LEU* 4.3 22.0 - - + -
60J PHE* 3.5 45.8 - - + +
63J LYS* 3.9 17.9 - - + +
74J SER 2.9 11.4 + - - +
75J ALA* 3.2 10.3 - - - +
77J GLU* 1.3 74.9 - - - +
79J ALA* 1.3 69.1 + - - +
81J ASP* 2.8 22.1 + - + +
82J TRP* 3.5 27.7 - - + -
88J LEU* 5.3 0.7 - - + -
106J ILE* 4.6 8.3 - - + -
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Residues in contact with ALA 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75J ALA 2.9 11.0 + - - +
76J VAL* 3.3 12.6 - - + +
78J LEU* 1.3 76.5 - - - +
80J LYS* 1.3 63.7 + - - +
82J TRP* 2.8 34.0 + - - +
83J ARG* 3.6 20.0 + - - +
106J ILE* 5.5 2.6 - - + +
110J GLY 3.8 24.4 - - - +
111J ASP* 4.1 5.8 - - - +
112J VAL* 4.3 8.7 - - + -
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Residues in contact with LYS 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76J VAL* 2.7 20.3 + - + +
77J GLU* 3.4 19.7 - - - +
78J LEU 3.1 0.2 - - - -
79J ALA* 1.3 72.7 - - - +
81J ASP* 1.3 61.0 + - - +
82J TRP 2.9 5.6 + - - -
83J ARG* 3.3 20.0 + - - +
84J THR* 3.2 22.1 + - + +
58K GLU* 5.7 4.0 - - - +
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Residues in contact with ASP 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I ASP* 5.7 0.3 - - - +
63J LYS* 2.8 31.0 + - - -
77J GLU* 3.4 8.8 + - - +
78J LEU* 2.8 18.8 + - + +
79J ALA 3.8 0.2 - - - -
80J LYS* 1.3 78.4 - - - +
82J TRP* 1.3 58.0 + - - +
84J THR* 4.2 15.5 + - - +
87J ALA 3.6 18.2 - - - +
88J LEU* 3.7 22.7 - - + +
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Residues in contact with TRP 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J LEU* 4.0 21.1 - - + -
59J LEU* 4.9 2.2 - - + -
78J LEU* 3.5 44.9 - - + -
79J ALA* 2.8 9.8 + - - +
81J ASP* 1.3 77.8 - - - +
83J ARG* 1.3 65.0 + - + +
84J THR* 3.3 8.6 + - - +
87J ALA* 4.7 5.5 - - - -
88J LEU* 2.8 43.4 + - + +
89J ARG 3.7 8.7 + - - -
91J LEU* 3.6 21.5 - - + +
106J ILE* 4.8 2.2 - - + -
107J THR 3.8 16.6 - - - -
108J GLY* 2.8 27.3 + - - -
109J ILE* 3.5 20.5 - - - +
110J GLY* 3.1 23.3 - - - +
55K THR* 5.4 0.9 - - - +
89K ARG* 4.0 14.6 + - - -
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Residues in contact with ARG 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442D PHE* 3.4 29.9 + - - +
76J VAL* 5.5 1.6 - - - +
79J ALA* 4.1 20.1 + - - +
80J LYS* 3.3 12.5 + - - +
82J TRP* 1.3 77.5 - - + +
84J THR* 1.3 65.1 + - - +
85J ASP* 3.6 6.1 + - - +
109J ILE 6.1 0.2 - - - +
110J GLY 3.5 23.6 + - - +
111J ASP* 3.9 17.2 - - - +
112J VAL 4.5 1.0 - - - +
51K ALA* 4.7 3.1 + - + +
54K PHE* 3.6 24.1 - - - +
55K THR* 3.3 48.0 + - + +
58K GLU* 2.5 49.2 + - - +
59K LEU* 4.5 8.0 - - - +
89K ARG* 5.1 2.4 + - - +
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Residues in contact with THR 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E LYS 5.4 8.3 - - - +
80J LYS* 3.2 19.3 - - + +
81J ASP* 4.2 17.6 + - - +
82J TRP 3.8 1.4 - - - +
83J ARG* 1.3 83.1 - - - +
85J ASP* 1.3 60.5 + - - +
86J ARG* 3.0 34.4 + - - +
87J ALA* 3.7 7.4 + - - -
89K ARG* 3.4 13.9 + - - -
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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