Contacts of the helix formed by residues 73 - 96 (chain T) in PDB entry 1IBL
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 73 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A U 5.1 7.2 - - - -
325A A 4.7 11.3 + - - -
67T ALA* 2.4 41.9 + - - +
68T LYS 3.0 16.0 + - - -
69T GLY* 2.8 22.1 + - - -
70T SER* 3.2 21.1 + - - -
72T LEU* 1.3 92.9 - - - +
74T LYS* 1.3 87.3 + - + +
77T ALA* 3.4 13.5 + - - +
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Residues in contact with LYS 74 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A C 3.0 28.4 + - - +
133A U 2.9 30.1 + - - +
262A A 3.5 41.1 + - - +
325A A 3.9 26.4 + - - -
326A G 4.4 5.9 + - - -
67T ALA* 5.0 1.0 - - - +
72T LEU 3.9 4.9 - - - +
73T HIS* 1.3 98.4 + - + +
75T ASN* 1.3 68.0 + - - +
76T ALA 3.5 1.8 + - - +
77T ALA* 4.0 8.5 + - - +
78T ALA* 4.4 1.9 + - - +
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Residues in contact with ASN 75 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A C 3.7 1.2 + - - -
132A C 3.2 30.2 + - - +
262A A 2.9 38.5 + - - +
263A A 4.2 5.8 + - - +
74T LYS* 1.3 82.8 - - - +
76T ALA* 1.3 59.6 + - - +
77T ALA 3.3 0.9 - - - -
78T ALA* 3.3 14.7 + - + +
79T ARG* 2.8 34.1 + - - +
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Residues in contact with ALA 76 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A A 3.6 18.3 - - - +
72T LEU* 3.7 27.1 - - + +
74T LYS* 3.2 2.0 - - - +
75T ASN* 1.3 75.9 - - - +
77T ALA* 1.3 58.2 + - - +
79T ARG* 3.2 37.0 + - - +
80T ARG* 2.7 38.8 + - - +
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Residues in contact with ALA 77 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63T ILE* 3.5 27.6 - - + +
64T ASP* 4.9 5.2 - - - +
67T ALA* 3.5 31.9 - - + -
72T LEU* 3.8 10.2 - - + +
73T HIS 3.4 6.6 + - - +
74T LYS 4.2 3.8 - - - +
76T ALA* 1.3 80.2 - - - +
78T ALA* 1.3 64.7 + - - +
80T ARG* 3.3 3.8 + - - +
81T LYS* 3.1 24.4 + - + +
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Residues in contact with ALA 78 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A A 3.7 37.4 + - - +
186A C 3.6 14.5 - - - +
74T LYS 4.4 1.3 + - - +
75T ASN* 3.4 21.4 - - + +
76T ALA 3.1 0.4 - - - -
77T ALA* 1.3 77.4 - - - +
79T ARG* 1.3 70.2 + - - +
81T LYS* 3.4 3.0 + - - +
82T SER* 2.9 22.6 + - - -
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Residues in contact with ARG 79 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A G 5.7 1.4 + - - -
261A U 2.8 67.7 + - - -
262A A 3.6 6.9 + - - -
263A A 2.8 41.0 + - - +
75T ASN 2.8 24.0 + - - +
76T ALA* 3.2 38.1 + - - +
78T ALA* 1.3 69.5 - - - +
80T ARG* 1.3 62.3 + - + +
82T SER* 2.8 13.9 + - - -
83T ARG* 2.6 59.5 + - - +
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Residues in contact with ARG 80 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A G 5.6 6.4 + - - -
261A U 3.6 26.6 + - - -
262A A 5.8 0.2 + - - -
30T LYS* 4.8 15.8 - - - +
33T ILE* 5.0 16.2 - - + +
34T LYS* 5.1 12.5 - - - +
63T ILE* 3.7 19.3 - - + -
72T LEU* 3.6 41.3 - - - +
76T ALA* 2.7 23.6 + - - +
77T ALA* 3.3 6.3 - - - +
79T ARG* 1.3 80.5 - - + +
81T LYS* 1.3 68.4 + - - +
82T SER 3.1 0.3 + - - -
83T ARG* 3.1 8.1 + - - +
84T LEU* 2.8 25.2 + - - +
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Residues in contact with LYS 81 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A A 2.7 49.5 + - - +
186A C 3.7 17.9 - - - +
60T GLU* 3.9 25.1 - - + +
63T ILE* 3.9 23.8 - - + +
64T ASP* 2.4 45.5 + - - +
77T ALA 3.1 18.0 + - - +
78T ALA 3.8 3.1 - - - +
80T ARG* 1.3 77.6 - - - +
82T SER* 1.3 66.2 + - - +
84T LEU* 3.0 5.1 + - - +
85T MET* 2.8 31.5 + - + +
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Residues in contact with SER 82 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A C 3.1 23.9 + - - -
187A C 2.5 27.7 + - - +
78T ALA 2.9 11.8 + - - -
79T ARG* 2.8 17.1 + - - -
81T LYS* 1.3 78.7 - - - +
83T ARG* 1.3 63.6 + - - +
84T LEU 2.8 1.9 + - - -
85T MET* 3.2 1.7 + - - +
86T ARG* 2.9 24.1 + - - +
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Residues in contact with ARG 83 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A G 3.4 33.9 + - - +
260A G 3.0 68.6 + - - -
261A U 3.3 11.1 + - - -
79T ARG* 2.6 42.4 + - - +
80T ARG* 3.8 5.8 - - - +
82T SER* 1.3 74.9 + - - +
84T LEU* 1.3 56.0 + - - +
86T ARG* 3.0 22.8 - - - +
87T LYS* 3.1 32.5 + - - +
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Residues in contact with LEU 84 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37T SER* 4.3 19.5 - - - +
40T ALA* 4.3 11.7 - - + -
41T ILE* 4.3 14.8 - - + -
56T MET* 3.9 20.0 - - + +
59T ALA* 3.7 29.4 - - + -
60T GLU* 4.8 2.7 - - + +
63T ILE* 4.7 8.3 - - + -
80T ARG 2.8 16.8 + - - +
81T LYS* 3.3 9.2 - - - +
82T SER 2.8 2.8 + - - -
83T ARG* 1.3 67.5 - - - +
85T MET* 1.3 65.8 + - + +
86T ARG 2.7 5.6 + - - -
87T LYS* 3.2 4.4 + - - +
88T VAL* 2.9 44.1 + - + +
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Residues in contact with MET 85 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A C 3.2 37.0 - - - +
187A C 3.4 22.6 + - - +
191A G 3.3 24.2 - - - +
56T MET* 3.4 24.4 - - + +
60T GLU* 4.2 17.0 - - + +
81T LYS* 2.8 24.1 + - + +
82T SER 4.0 0.2 - - - +
84T LEU* 1.3 74.0 - - + +
86T ARG* 1.3 64.6 + - - +
88T VAL 4.1 0.2 - - - -
89T ARG* 3.3 20.6 + - - +
103T GLY* 3.4 13.5 - - - +
104T LEU* 3.2 32.6 - - + +
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Residues in contact with ARG 86 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A C 3.6 20.0 + - - -
188A C 2.8 37.1 + - - -
258A G 6.0 2.0 - - - +
82T SER* 2.9 16.8 + - - +
83T ARG* 3.0 17.9 - - - +
84T LEU 2.7 0.2 - - - -
85T MET* 1.3 79.9 - - - +
87T LYS* 1.3 70.6 + - + +
88T VAL 2.7 2.4 + - - -
89T ARG* 2.9 9.4 + - - +
90T GLN* 3.1 39.5 + - - +
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Residues in contact with LYS 87 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A G 4.2 17.2 + - - +
259A G 3.0 27.7 + - - -
41T ILE* 3.9 35.0 - - + +
83T ARG* 3.1 32.3 + - - +
84T LEU* 4.0 2.9 - - - +
86T ARG* 1.3 80.7 - - + +
88T VAL* 1.3 57.7 + - - +
90T GLN* 4.3 9.9 - - - +
91T LEU* 2.7 43.2 + - + +
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Residues in contact with VAL 88 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40T ALA* 4.3 23.1 - - + +
41T ILE* 4.4 4.9 - - + +
44T ALA* 3.5 16.4 - - + +
52T ALA* 5.0 5.8 - - + +
53T LEU* 4.4 6.7 - - + -
56T MET* 3.2 32.5 - - + -
84T LEU* 2.9 37.4 + - + +
86T ARG 2.7 4.8 + - - -
87T LYS* 1.3 71.6 - - - +
89T ARG* 1.3 56.0 + - - +
91T LEU* 5.4 0.2 - - - -
92T LEU* 2.7 48.2 + - + +
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Residues in contact with ARG 89 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A C 2.8 30.5 + - - +
188A C 3.1 31.8 + - - -
85T MET 3.3 11.4 + - - +
86T ARG* 2.9 6.9 + - - +
88T VAL* 1.3 74.4 - - - +
90T GLN* 1.3 67.8 + - + +
92T LEU* 3.0 17.5 + - + +
93T GLU* 3.1 30.0 + - - +
98T PRO* 5.2 6.8 - - + +
104T LEU* 3.3 33.8 - - + +
105T SER 2.6 33.1 + - - -
106T ALA* 3.9 18.8 - - - +
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Residues in contact with GLN 90 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A G 5.2 8.1 + - - -
86T ARG* 3.1 52.1 + - - +
87T LYS* 3.7 11.1 - - - +
89T ARG* 1.3 79.8 - - + +
91T LEU* 1.3 54.7 + - + +
93T GLU* 2.5 43.9 + - + +
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Residues in contact with LEU 91 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41T ILE* 3.3 41.5 - - + +
44T ALA* 3.2 27.0 - - + +
45T GLN* 4.0 32.2 - - + +
87T LYS* 2.7 29.5 + - + +
90T GLN* 1.3 76.0 - - + +
92T LEU* 1.3 61.0 + - - +
93T GLU 2.9 1.3 + - - -
94T ALA* 3.5 16.8 - - - +
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Residues in contact with LEU 92 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44T ALA* 3.8 21.8 - - + -
47T GLY* 4.4 8.5 - - - -
49T ALA* 3.4 45.8 - - + +
52T ALA* 4.6 0.9 - - + -
53T LEU* 4.2 24.7 - - + -
88T VAL* 2.7 32.4 + - + +
89T ARG* 3.0 12.5 + - + +
91T LEU* 1.3 72.7 - - - +
93T GLU* 1.3 57.6 + - - +
94T ALA* 2.8 10.1 + - - -
96T GLY* 3.0 26.5 + - - -
97T ALA 4.2 3.3 + - - +
98T PRO* 4.9 13.0 - - + -
104T LEU* 4.9 4.3 - - + -
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Residues in contact with GLU 93 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89T ARG* 3.1 30.4 + - - +
90T GLN* 2.5 35.9 + - + +
91T LEU* 3.8 0.6 - - - +
92T LEU* 1.3 70.3 - - - +
94T ALA* 1.3 59.1 + - - +
95T ALA 3.6 2.2 - - - +
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Residues in contact with ALA 94 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44T ALA 5.1 2.9 - - - +
45T GLN 5.1 6.3 - - - +
47T GLY* 5.4 8.3 - - - -
91T LEU 3.5 15.5 - - - +
92T LEU 2.8 5.4 + - - +
93T GLU* 1.3 74.5 - - - +
95T ALA* 1.3 72.9 + - - +
96T GLY* 3.5 0.9 - - - -
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Residues in contact with ALA 95 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47T GLY* 5.4 1.3 - - - +
93T GLU* 3.6 1.4 - - - +
94T ALA* 1.3 84.5 - - - +
96T GLY* 1.3 62.5 + - - +
97T ALA* 3.9 1.1 - - - -
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Residues in contact with GLY 96 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47T GLY* 4.7 9.6 - - - -
49T ALA* 4.6 3.8 - - - -
92T LEU* 3.0 31.6 + - - -
94T ALA 3.5 1.2 - - - -
95T ALA* 1.3 80.3 - - - +
97T ALA* 1.3 76.5 + - - +
99T LEU* 3.2 16.9 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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