Contacts of the helix formed by residues 89 - 111 (chain Q) in PDB entry 1KD1
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 ASN 89 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792A G 5.7 2.8 + - - -
85Q GLY 3.6 11.3 + - - +
86Q ALA 4.8 2.0 + - - +
88Q GLN* 1.3 72.0 - - - +
90Q SER* 1.3 63.3 + - - +
91Q LYS* 2.9 13.9 + - - +
92Q GLU* 2.7 61.5 + - + +
93Q ASP* 3.1 11.8 + - - +
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Residues in contact with SER 90 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815A U 4.5 9.1 + - - -
8106A MG 4.2 14.2 - - - -
85Q GLY* 4.7 4.3 + - - -
88Q GLN* 3.1 9.3 + - - -
89Q ASN* 1.3 72.2 + - - +
91Q LYS* 1.3 64.6 + - - +
93Q ASP* 3.5 9.3 + - - +
94Q TRP* 3.2 21.5 + - - +
97Q ARG* 4.9 2.6 + - - +
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Residues in contact with LYS 91 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815A U 5.7 0.4 - - - -
816A G 2.4 52.7 + - - +
817A G 3.1 28.8 + - - +
1539A U 4.1 26.0 - - - +
1540A G 5.5 0.7 - - - +
1597A A 3.3 22.4 + - - -
89Q ASN* 2.9 14.7 + - - +
90Q SER* 1.3 78.1 + - - +
92Q GLU* 1.3 64.4 + - - +
94Q TRP* 3.1 7.9 + - + +
95Q GLU* 3.0 48.5 + - + +
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Residues in contact with GLU 92 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1540A G 5.7 2.7 - - - +
1640A C 4.9 8.4 + - - -
1797A A 5.5 4.5 - - - +
89Q ASN* 2.7 35.1 + - + +
91Q LYS* 1.3 77.9 - - - +
93Q ASP* 1.3 55.9 + - - +
95Q GLU* 3.4 20.5 + - - +
96Q SER* 3.0 25.3 + - - -
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Residues in contact with ASP 93 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1793A C 4.5 10.0 + - - +
1794A G 5.7 0.5 - - - +
1799A G 5.1 1.4 + - - -
88Q GLN* 3.4 38.3 + - + +
89Q ASN 3.1 10.7 + - - +
90Q SER* 3.7 13.2 - - - +
92Q GLU* 1.3 76.4 - - - +
94Q TRP* 1.3 59.3 + - - +
96Q SER* 3.3 9.2 + - - -
97Q ARG* 2.8 59.4 + - - +
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Residues in contact with TRP 94 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814A G 3.9 17.5 - - - -
815A U 3.6 46.4 + - - +
816A G 4.2 2.7 - - - -
1597A A 3.1 36.6 + - - -
1598A A 3.4 15.2 - - - -
90Q SER 3.2 9.7 + - - +
91Q LYS* 3.1 12.2 + - - +
93Q ASP* 1.3 75.8 - - - +
95Q GLU* 1.3 65.8 + - - +
96Q SER 3.1 0.2 - - - -
97Q ARG* 3.9 25.3 - - - +
98Q ILE* 2.8 60.1 + - + +
126Q ALA 3.9 5.4 - - - -
127Q GLY 3.9 20.0 - - - -
129Q GLY* 4.2 12.6 - - - -
131Q PHE 6.1 0.4 - - - -
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Residues in contact with GLU 95 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1540A G 3.4 29.1 + - - +
1597A A 3.0 51.5 - - - +
91Q LYS* 3.0 28.3 + - + +
92Q GLU* 3.5 25.3 - - - +
94Q TRP* 1.3 76.7 - - - +
96Q SER* 1.3 69.8 + - - +
98Q ILE* 4.4 0.4 - - - -
99Q ARG* 3.2 44.2 + - - +
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Residues in contact with SER 96 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1794A G 3.1 37.4 + - - +
1795A G 5.0 2.3 + - - -
1796A A 4.0 11.9 + - - -
92Q GLU 3.0 15.3 + - - -
93Q ASP* 3.3 16.2 - - - -
95Q GLU* 1.3 80.6 - - - +
97Q ARG* 1.3 64.3 + - - +
99Q ARG* 3.8 3.9 - - - +
100Q ALA* 3.1 20.8 + - - +
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Residues in contact with ARG 97 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815A U 4.7 6.3 + - - -
1793A C 3.7 24.4 + - - +
1794A G 4.3 15.2 + - - +
90Q SER* 4.9 2.6 + - - +
93Q ASP* 2.8 44.4 + - - +
94Q TRP* 3.8 36.0 - - + +
96Q SER* 1.3 75.0 - - - +
98Q ILE* 1.3 65.2 + - - +
99Q ARG 3.1 0.9 + - - -
100Q ALA* 3.1 5.5 + - - +
101Q GLN* 3.0 34.1 + - - +
131Q PHE 5.3 4.2 + - - -
132Q ASP* 3.5 24.7 + - - +
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Residues in contact with ILE 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1597A A 3.8 33.2 - - - +
94Q TRP* 2.8 57.6 + - + +
95Q GLU 3.9 0.7 - - - +
97Q ARG* 1.3 74.1 - - - +
99Q ARG* 1.3 62.7 + - + +
101Q GLN* 3.7 9.1 + - + +
102Q ARG* 2.8 66.0 + - + +
126Q ALA* 4.5 10.3 - - + +
127Q GLY 4.4 12.6 - - - +
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Residues in contact with ARG 99 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1540A G 3.0 37.0 + - - -
1541A G 3.1 22.8 + - - -
1597A A 2.6 54.2 + - - +
95Q GLU* 3.2 32.7 + - - +
96Q SER* 3.8 4.0 - - - +
97Q ARG 3.1 0.8 - - - -
98Q ILE* 1.3 77.8 - - - +
100Q ALA* 1.3 69.2 + - - +
102Q ARG* 3.0 5.9 + - - +
103Q THR* 2.7 30.2 + - - +
106Q ARG* 5.1 0.5 + - - -
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Residues in contact with ALA 100 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1794A G 3.8 7.9 - - - +
1795A G 3.3 38.3 + - - +
96Q SER 3.1 9.1 + - - +
97Q ARG 3.1 9.6 + - - +
99Q ARG* 1.3 82.5 - - - +
101Q GLN* 1.3 58.9 + - - +
103Q THR* 2.9 7.0 + - - -
104Q LYS* 2.8 27.4 + - - +
134Q VAL* 3.7 16.3 - - + +
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Residues in contact with GLN 101 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1794A G 5.3 0.2 - - - +
97Q ARG* 3.0 25.5 + - - +
98Q ILE* 4.0 8.7 - - - +
100Q ALA* 1.3 78.5 - - - +
102Q ARG* 1.3 61.0 + - - +
104Q LYS* 3.5 8.0 - - - +
105Q LEU* 3.2 30.6 + - - +
126Q ALA* 3.6 30.2 - - + +
129Q GLY* 6.0 0.2 - - - -
131Q PHE* 2.8 40.7 + - - +
132Q ASP 3.8 2.2 + - - -
133Q SER* 3.5 33.1 - - - +
134Q VAL* 4.2 6.5 - - - +
137Q LEU* 3.9 10.2 - - + +
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Residues in contact with ARG 102 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1596A U 3.3 45.8 + - - -
1597A A 3.2 23.3 + - - -
1598A A 2.9 42.6 + - - -
98Q ILE* 2.8 45.6 + - + +
99Q ARG* 3.0 5.6 + - - +
101Q GLN* 1.3 74.3 - - - +
103Q THR* 1.3 66.7 + - - +
105Q LEU* 3.6 6.8 + - + +
106Q ARG* 3.0 38.8 + - - +
119Q TYR* 5.0 2.8 + - - -
123Q TYR* 3.5 33.4 + - + -
126Q ALA* 5.5 4.0 - - + -
127Q GLY* 4.2 10.7 - - - +
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Residues in contact with THR 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99Q ARG* 2.7 18.0 + - - +
100Q ALA* 3.4 9.8 - - - -
102Q ARG* 1.3 77.3 - - - +
104Q LYS* 1.3 66.2 + - - +
106Q ARG* 3.1 29.6 + - + +
107Q GLU* 3.0 44.2 + - + +
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Residues in contact with LYS 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Q ALA 2.8 11.0 + - - +
101Q GLN* 3.5 14.1 - - - +
102Q ARG 3.2 0.2 - - - -
103Q THR* 1.3 76.2 - - - +
105Q LEU* 1.3 64.6 + - - +
107Q GLU* 3.0 32.2 + - - +
108Q LEU* 3.1 38.9 + - + +
134Q VAL* 4.0 20.9 - - + -
137Q LEU* 4.2 13.0 - - + -
138Q GLU* 3.4 40.6 + - + -
141Q ILE* 5.8 0.2 - - + -
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Residues in contact with LEU 105 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q GLN 3.2 17.6 + - - +
102Q ARG* 3.9 3.6 - - - +
104Q LYS* 1.3 78.7 - - - +
106Q ARG* 1.3 61.7 + - - +
108Q LEU* 3.5 7.7 + - + +
109Q ARG* 3.1 18.0 + - - +
114Q LEU* 4.4 4.7 - - + +
119Q TYR* 3.4 27.1 - - + +
122Q LEU* 3.7 25.8 - - + +
123Q TYR* 3.4 44.9 - - + +
126Q ALA* 4.7 7.2 - - + -
137Q LEU* 3.3 33.9 - - + -
141Q ILE* 4.4 7.6 - - + -
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Residues in contact with ARG 106 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1595A G 5.1 6.8 + - - -
1596A U 3.5 25.4 + - - -
99Q ARG 5.1 0.2 + - - -
102Q ARG* 3.0 36.5 + - - +
103Q THR* 3.1 45.0 + - - +
105Q LEU* 1.3 77.2 - - - +
107Q GLU* 1.3 59.3 + - + +
109Q ARG* 3.5 16.2 + - - +
110Q ASP* 2.7 41.3 + - - +
119Q TYR* 3.9 15.1 + - + +
123Q TYR* 5.7 0.8 - - - -
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Residues in contact with GLU 107 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103Q THR* 3.1 34.0 - - + +
104Q LYS* 3.0 22.1 + - + +
106Q ARG* 1.3 73.7 - - + +
108Q LEU* 1.3 63.4 + - + +
109Q ARG 3.0 2.3 + - - -
110Q ASP* 3.1 7.7 + - - +
111Q GLU* 2.8 37.7 + - - +
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Residues in contact with LEU 108 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Q LYS* 3.1 38.9 + - + +
105Q LEU* 3.8 5.4 - - - +
107Q GLU* 1.3 82.0 - - + +
109Q ARG* 1.3 59.0 + - - +
111Q GLU* 3.6 26.9 - - - +
112Q GLY 3.2 1.4 + - - -
113Q THR* 2.9 40.0 + - + +
114Q LEU* 3.1 28.9 + - + -
138Q GLU* 5.9 0.7 - - + -
141Q ILE* 3.6 33.2 - - + -
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Residues in contact with ARG 109 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1594A C 2.7 37.7 + - - -
1595A G 3.3 24.2 + - - -
1607A A 5.5 4.4 + - - -
105Q LEU 3.1 17.1 + - - +
106Q ARG* 3.7 16.2 + - - +
107Q GLU 3.0 1.0 + - - -
108Q LEU* 1.3 76.1 - - - +
110Q ASP* 1.3 81.6 + - - +
112Q GLY* 3.0 14.0 + - - -
114Q LEU* 3.8 22.5 - - - +
116Q SER* 4.5 12.1 - - - +
119Q TYR* 3.0 45.5 + - + -
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Residues in contact with ASP 110 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106Q ARG* 2.7 29.1 - - - +
107Q GLU* 3.1 6.0 + - - +
109Q ARG* 1.3 89.1 + - - +
111Q GLU* 1.3 63.8 + - - +
112Q GLY* 3.0 7.5 + - - -
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Residues in contact with GLU 111 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107Q GLU* 2.8 19.9 + - - +
108Q LEU* 3.6 24.8 - - - +
110Q ASP* 1.3 76.4 - - - +
112Q GLY* 1.3 57.5 + - - +
113Q THR* 2.5 25.1 + - - +
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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