Contacts of the helix formed by residues 93 - 116 (chain L) in PDB entry 1Q0K
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 ASP 93 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L GLN* 3.4 2.6 + - - -
91L SER* 3.0 13.4 + - - +
92L THR* 1.3 79.1 + - - +
94L PRO* 1.3 69.1 - - - +
95L ALA* 2.8 39.3 + - - +
96L THR* 2.7 35.4 + - + +
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Residues in contact with PRO 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L LYS* 3.7 15.9 - - + +
25L GLN* 3.5 13.2 - - + +
26L GLU* 4.0 39.7 - - + +
29L ALA* 5.3 7.9 - - + -
92L THR 3.3 9.8 - - - +
93L ASP* 1.3 90.7 - - - +
95L ALA* 1.3 60.6 + - - +
96L THR 3.2 0.2 - - - -
97L GLY* 3.1 3.0 + - - -
98L GLN* 3.0 21.5 + - - +
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Residues in contact with ALA 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93L ASP* 2.8 25.9 + - - +
94L PRO* 1.3 72.9 - - - +
96L THR* 1.3 58.5 + - + +
98L GLN* 3.2 8.3 + - - +
99L LYS* 2.9 28.1 + - - +
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Residues in contact with THR 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L GLN* 2.9 20.3 + - - -
84L ALA 4.4 3.5 - - - +
87L ALA* 4.6 9.6 - - + +
88L ALA* 3.6 21.0 - - - +
91L SER* 3.7 23.2 + - - +
93L ASP* 2.7 26.1 + - + +
95L ALA* 1.3 77.2 - - + +
97L GLY* 1.3 61.8 + - - +
99L LYS* 3.3 16.1 + - - +
100L ALA* 3.3 12.8 + - - +
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Residues in contact with GLY 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L ALA* 5.0 1.7 - - - +
21L VAL* 4.7 5.2 - - - -
22L LYS* 4.4 15.0 - - - +
25L GLN* 3.2 19.5 + - - -
88L ALA* 4.4 8.7 - - - -
94L PRO 3.1 4.9 + - - -
96L THR* 1.3 82.6 + - - +
98L GLN* 1.3 62.0 + - - +
100L ALA* 3.3 7.6 + - - +
101L LEU* 3.1 23.4 + - - +
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Residues in contact with GLN 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L LYS* 2.5 40.0 + - - +
94L PRO 3.0 12.6 + - - +
95L ALA* 3.2 12.3 + - - +
97L GLY* 1.3 75.8 - - - +
99L LYS* 1.3 65.0 + - - +
101L LEU* 3.1 21.2 + - - +
102L ASP* 2.9 49.7 + - - +
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Residues in contact with LYS 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84L ALA* 4.8 8.7 - - + +
95L ALA 2.9 14.1 + - - +
96L THR* 3.6 12.3 - - - +
97L GLY 3.2 0.4 - - - -
98L GLN* 1.3 75.8 - - - +
100L ALA* 1.3 62.5 + - - +
102L ASP* 3.1 12.4 + - + +
103L TYR* 3.1 56.9 + - + -
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Residues in contact with ALA 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L ALA* 5.1 2.5 - - + -
81L ALA* 4.9 1.4 - - - +
84L ALA* 3.9 20.1 - - + +
85L LEU* 3.5 36.1 - - + -
88L ALA* 5.2 1.1 - - + -
96L THR 3.3 8.0 + - - +
97L GLY* 3.3 11.8 + - - +
98L GLN 3.2 0.6 - - - -
99L LYS* 1.3 77.4 - - - +
101L LEU* 1.3 58.0 + - - +
103L TYR* 3.3 5.0 + - - +
104L ILE* 2.9 35.7 + - + +
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Residues in contact with LEU 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L ARG* 3.9 25.3 - - + +
18L ALA* 3.5 28.9 - - + +
19L GLU* 4.1 17.3 - - + +
22L LYS* 4.2 21.3 - - + -
97L GLY 3.1 14.7 + - - +
98L GLN* 3.1 31.9 + - - +
100L ALA* 1.3 78.6 - - - +
102L ASP* 1.3 57.8 + - - +
104L ILE* 3.3 6.1 + - + +
105L ALA* 2.9 29.3 + - - +
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Residues in contact with ASP 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98L GLN* 2.9 43.7 + - - +
99L LYS* 3.1 14.7 + - + +
101L LEU* 1.3 77.6 - - - +
103L TYR* 1.3 62.6 + - + +
105L ALA* 3.2 8.8 + - - +
106L GLN* 3.2 30.9 + - - +
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Residues in contact with TYR 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L LEU* 3.7 24.0 - - + +
80L GLU* 3.7 47.6 + - + +
81L ALA* 3.7 18.6 - - + -
84L ALA* 3.7 17.0 - - + -
99L LYS* 3.1 55.3 + - + -
100L ALA 3.3 6.5 + - - +
102L ASP* 1.3 77.4 - - + +
104L ILE* 1.3 64.4 + - - +
106L GLN* 3.1 18.3 + - - +
107L ILE* 3.0 26.7 + - - +
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Residues in contact with ILE 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L PRO* 4.4 11.8 - - + +
14L ALA* 4.1 18.4 - - + +
15L ARG* 4.2 29.4 - - + +
18L ALA* 3.6 30.3 - - + -
51L ALA* 5.2 0.2 - - + -
55L LEU* 4.2 27.1 - - + -
81L ALA* 5.2 0.9 - - + -
85L LEU* 4.8 9.2 - - + -
100L ALA 2.9 23.3 + - - +
101L LEU* 3.6 6.5 - - - +
103L TYR* 1.3 78.6 - - + +
105L ALA* 1.3 56.0 + - - +
107L ILE* 3.2 8.8 + - + +
108L ASP* 2.8 28.6 + - + +
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Residues in contact with ALA 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101L LEU 2.9 13.3 + - - +
102L ASP* 3.5 12.1 - - - +
103L TYR 3.2 0.2 - - - -
104L ILE* 1.3 76.0 - - - +
106L GLN* 1.3 62.7 + - + +
108L ASP* 3.2 9.1 + - - +
109L LYS* 3.1 21.0 + - - +
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Residues in contact with GLN 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77L LEU* 3.5 31.4 - - + +
102L ASP* 3.2 20.6 - - - +
103L TYR* 3.1 19.5 + - - +
105L ALA* 1.3 74.6 - - + +
107L ILE* 1.3 65.1 + - - +
109L LYS* 3.3 15.0 + - - +
110L ILE* 3.3 18.3 + - + +
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Residues in contact with ILE 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L PRO* 5.3 1.8 - - + -
55L LEU* 4.0 20.0 - - + -
58L LEU* 4.5 18.8 - - + -
63L PHE* 4.4 22.4 - - + -
74L LEU* 5.3 1.1 - - + -
77L LEU* 3.8 23.3 - - + +
78L VAL* 4.0 23.8 - - + -
81L ALA* 3.8 29.4 - - + -
103L TYR 3.0 15.9 + - - +
104L ILE* 3.6 7.6 - - + +
106L GLN* 1.3 75.9 - - - +
108L ASP* 1.3 59.8 + - - +
110L ILE* 3.3 5.1 + - - +
111L PHE* 2.9 27.9 + - + +
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Residues in contact with ASP 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10L ASP* 5.0 0.9 - - - +
11L PRO* 3.4 29.2 - - + +
12L ALA 4.8 1.0 + - - -
15L ARG* 5.4 9.5 + - - -
104L ILE* 2.8 18.2 + - + +
105L ALA* 3.4 11.6 - - - +
107L ILE* 1.3 78.4 - - - +
109L LYS* 1.3 62.3 + - - +
111L PHE* 3.4 5.6 + - - +
112L TRP* 3.0 57.4 + - - -
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Residues in contact with LYS 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105L ALA 3.1 12.4 + - - +
106L GLN* 3.6 10.1 - - - +
107L ILE 3.2 0.6 - - - -
108L ASP* 1.3 78.1 + - - +
110L ILE* 1.3 65.4 + - + +
112L TRP* 3.2 8.1 + - - +
113L GLU* 3.0 45.4 + - + +
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Residues in contact with ILE 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L PHE* 4.2 14.1 - - + -
71L TYR* 3.9 49.1 - - + -
74L LEU* 4.1 15.0 - - + -
77L LEU* 3.7 30.5 - - + -
106L GLN* 3.3 9.0 + - + +
107L ILE* 3.8 6.3 - - - +
109L LYS* 1.3 77.3 - - + +
111L PHE* 1.3 64.2 + - - +
113L GLU* 3.2 11.2 + - - +
114L THR* 3.0 32.3 + - + +
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Residues in contact with PHE 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L TYR* 3.5 35.0 - - + -
11L PRO* 3.4 35.7 - - + -
58L LEU* 4.1 9.0 - - + -
62L TYR* 3.5 40.6 - + - -
63L PHE* 4.2 11.2 - + + -
107L ILE* 2.9 17.9 + - + +
108L ASP 3.5 4.0 - - - +
110L ILE* 1.3 76.0 - - - +
112L TRP* 1.3 90.4 + + - +
114L THR* 2.5 23.5 + - - -
115L LYS* 3.0 37.9 + - + +
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Residues in contact with TRP 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L TYR 5.4 2.0 - - - -
10L ASP* 4.4 20.4 - - - -
108L ASP* 3.0 52.9 + - - +
109L LYS* 3.2 5.8 + - - +
111L PHE* 1.3 94.5 - + - +
113L GLU* 1.3 66.1 + - - +
115L LYS* 2.9 27.4 + - + +
116L LYS* 2.9 50.1 + - + +
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Residues in contact with GLU 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71L TYR* 2.9 35.7 + - - +
109L LYS* 3.0 44.5 + - + +
110L ILE* 3.6 8.8 - - - +
112L TRP* 1.3 77.2 - - - +
114L THR* 1.3 62.8 + - - +
115L LYS 3.3 0.3 + - - -
116L LYS* 3.4 19.6 + - - +
117L ALA* 3.4 18.4 + - - +
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Residues in contact with THR 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62L TYR* 2.7 25.0 + - - -
63L PHE* 4.2 11.0 - - + -
67L HIS* 3.8 35.7 + - + -
71L TYR* 4.0 21.8 - - + -
110L ILE* 3.0 14.5 + - + +
111L PHE* 2.5 23.0 + - - -
113L GLU* 1.3 73.2 - - - +
115L LYS* 1.3 64.1 + - - +
117L ALA* 3.2 20.1 - - - +
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Residues in contact with LYS 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L GLY 4.7 12.1 + - - -
9L TYR* 5.8 5.1 + - - +
62L TYR* 3.2 22.4 - - + +
111L PHE* 3.0 46.9 + - + +
112L TRP* 2.9 31.1 + - + +
114L THR* 1.3 76.0 + - - +
116L LYS* 1.3 57.6 + - + +
117L ALA* 2.9 14.5 + - - +
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Residues in contact with LYS 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L TRP* 2.9 45.1 + - + +
113L GLU* 3.4 22.0 + - - +
115L LYS* 1.3 73.6 - - + +
117L ALA* 1.3 62.6 + - - +
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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