Contacts of the helix formed by residues 85 - 105 (chain C) in PDB entry 2X06
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 LEU 85 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LEU* 4.7 13.2 - - + -
21C VAL* 4.2 31.0 - - + -
25C ASP* 5.1 0.2 - - + -
29C THR* 3.4 25.1 - - + +
52C TYR* 4.2 26.0 - - + -
56C LEU* 5.4 0.4 - - + -
61C ILE* 3.9 24.9 - - + -
62C ASN 4.3 3.8 + - - +
63C PRO* 5.7 0.7 - - + -
65C PRO* 5.1 1.0 - - - +
84C GLY* 1.3 71.4 - - - -
86C GLY* 1.3 67.0 + - - +
87C GLN* 3.8 11.0 - - - +
88C VAL* 2.9 34.7 + - + +
89C VAL* 3.0 13.5 + - - +
115C ASN* 4.5 3.8 - - + -
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Residues in contact with GLY 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C TYR* 6.1 0.2 - - - -
84C GLY 3.5 3.4 + - - -
85C LEU* 1.3 71.8 - - - +
87C GLN* 1.3 56.5 + - - +
89C VAL* 4.7 3.6 - - - -
90C GLY* 2.7 34.6 + - - -
114C ALA* 4.8 1.6 - - - -
115C ASN* 2.9 36.7 + - - +
116C HIS 3.6 5.5 + - - -
117C PHE* 3.5 14.2 - - - +
260C LYS* 5.0 1.1 - - - -
262C ASP* 5.7 0.2 - - - +
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Residues in contact with GLN 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ILE* 3.6 5.2 - - + +
29C THR* 3.7 42.8 - - + +
32C VAL* 3.5 32.0 - - + +
33C PHE* 4.1 7.3 - - - -
52C TYR* 2.9 31.0 + - - -
85C LEU* 3.1 5.9 - - - +
86C GLY* 1.3 80.5 + - - +
88C VAL* 1.3 57.9 + - - +
91C LYS* 3.0 31.0 + - - +
116C HIS 3.7 3.4 + - - +
117C PHE 3.5 17.7 - - - -
118C GLY* 3.6 4.9 - - - +
123C TYR* 3.2 14.1 + - - +
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Residues in contact with VAL 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ASP* 3.6 61.2 - - + +
28C ILE* 4.5 12.2 - - + +
29C THR* 3.9 9.2 - - - +
65C PRO* 5.5 3.4 - - + -
67C ILE* 4.0 19.2 - - + +
85C LEU* 2.9 23.1 + - + +
87C GLN* 1.3 74.7 - - - +
89C VAL* 1.3 66.2 + - - +
91C LYS* 3.9 2.4 - - - +
92C LYS* 3.2 22.6 + - + +
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Residues in contact with VAL 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ILE* 3.6 26.0 - - + -
79C ILE* 3.9 26.8 - - + +
81C GLY* 3.8 22.9 - - - +
84C GLY* 4.5 5.8 - - - -
85C LEU 3.0 14.8 + - - +
86C GLY 4.2 1.3 - - - +
88C VAL* 1.3 74.8 - - + +
90C GLY* 1.3 53.4 + - - +
92C LYS* 3.2 6.4 + - - +
93C ALA* 2.7 34.7 + - - +
111C THR* 4.4 15.0 - - + +
114C ALA* 4.0 22.9 - - + -
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Residues in contact with GLY 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C GLY 2.7 23.5 + - - -
89C VAL* 1.3 74.6 - - - +
91C LYS* 1.3 61.1 + - - +
93C ALA* 3.1 2.9 + - - +
94C MSE 3.0 27.0 + - - +
111C THR* 5.6 0.2 - - - -
117C PHE* 5.0 1.1 - - - -
123C TYR* 3.7 13.6 - - - -
262C ASP* 5.6 0.9 - - - -
264C PHE* 3.8 24.0 - - - -
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Residues in contact with LYS 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A LYS* 6.1 2.9 - - - +
28C ILE* 3.9 42.0 - - + +
87C GLN 3.0 20.9 + - - +
88C VAL 3.9 3.6 - - - +
89C VAL 3.3 0.2 - - - -
90C GLY* 1.3 74.8 - - - +
92C LYS* 1.3 63.9 + - - +
94C MSE 3.5 1.2 + - - +
95C GLU* 3.0 63.9 + - - +
122C TYR* 4.9 11.4 - - + +
123C TYR* 3.6 11.2 - - + -
126C LEU* 3.8 19.4 - - + +
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Residues in contact with LYS 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ILE* 3.7 44.1 + - + -
69C ILE* 4.4 24.2 - - - +
79C ILE* 4.3 15.7 - - + -
88C VAL* 3.2 14.3 + - + +
89C VAL 3.2 3.9 + - - +
91C LYS* 1.3 81.6 - - - +
93C ALA* 1.3 64.2 + - - +
95C GLU* 3.5 6.3 + - - +
96C LEU* 3.1 23.6 + - + +
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Residues in contact with ALA 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C ILE* 3.6 22.2 - - + -
89C VAL 2.7 17.2 + - - +
90C GLY 3.4 5.4 - - - +
92C LYS* 1.3 77.5 - - - +
94C MSE 1.3 58.3 + - - +
96C LEU* 3.2 6.4 + - - +
97C ALA* 3.1 21.3 + - - +
109C VAL* 3.7 14.7 - - + +
111C THR* 3.9 9.0 - - + -
264C PHE* 3.6 28.3 - - + -
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Residues in contact with MSE 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLY 3.0 15.5 + - - +
91C LYS 4.2 1.8 - - - +
93C ALA* 1.3 72.5 - - - +
95C GLU* 1.3 61.0 + - - +
96C LEU 3.1 1.6 - - - -
97C ALA* 3.2 8.5 + - - -
98C ILE* 2.9 55.0 + - + +
123C TYR* 3.4 29.6 - - + +
124C SER* 4.1 2.9 - - - -
126C LEU* 4.1 11.2 - - + -
127C ALA* 4.4 2.7 - - + -
134C GLY* 4.3 2.2 - - - -
135C ILE 4.0 7.0 - - - +
136C THR* 3.3 26.0 - - - +
264C PHE* 4.0 20.8 - - + -
265C ILE 3.6 33.7 - - - +
266C ALA* 4.4 2.0 - - - -
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Residues in contact with GLU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LYS* 3.0 63.9 + - - +
92C LYS* 4.1 5.7 - - - +
94C MSE 1.3 76.7 - - - +
96C LEU* 1.3 57.4 + - - +
98C ILE* 3.7 17.3 - - + +
99C LYS* 3.0 28.4 + - - +
126C LEU* 4.3 10.3 - - + +
130C GLN* 5.9 4.7 - - - +
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ILE* 4.3 21.8 - - + -
72C GLU* 4.0 16.6 - - - +
77C ALA* 3.6 29.2 - - + -
79C ILE* 4.5 13.5 - - + -
92C LYS* 3.1 15.7 + - + +
93C ALA 3.3 9.6 - - - +
94C MSE 3.1 0.2 - - - -
95C GLU* 1.3 76.6 - - - +
97C ALA* 1.3 60.5 + - - +
99C LYS* 3.3 23.3 + - + +
100C LYS* 2.9 40.1 + - - +
109C VAL* 4.1 6.1 - - + -
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Residues in contact with ALA 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C ALA 3.1 12.7 + - - +
94C MSE 3.2 13.9 + - - +
96C LEU* 1.3 75.3 - - - +
98C ILE* 1.3 57.9 + - - +
100C LYS* 3.3 1.6 + - - -
101C ALA* 2.9 26.9 + - - +
107C GLY* 3.5 34.0 - - - +
109C VAL* 3.8 15.1 - - + +
264C PHE 4.0 10.3 - - - +
266C ALA* 3.9 10.8 - - + +
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Residues in contact with ILE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C MSE 2.9 30.7 + - + +
95C GLU* 3.7 15.5 - - + +
97C ALA* 1.3 74.1 - - - +
99C LYS* 1.3 68.0 + - - +
101C ALA* 3.2 3.6 + - - +
102C LYS* 2.9 23.5 + - + +
126C LEU* 3.7 14.1 - - + +
127C ALA* 3.6 34.3 - - + +
130C GLN* 4.1 25.4 - - + +
132C MSE 3.9 15.7 - - + +
266C ALA* 3.9 19.5 - - + -
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Residues in contact with LYS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C GLU 3.0 18.7 + - - +
96C LEU* 3.5 23.8 - - + +
98C ILE* 1.3 76.5 - - - +
100C LYS* 1.3 67.8 + - + +
102C LYS* 3.0 22.8 + - + +
103C ASN* 3.3 22.8 + - - +
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Residues in contact with LYS 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C GLU* 3.3 26.5 + - - -
73C SER 2.9 17.4 + - - -
74C PRO* 3.5 14.2 + - - +
75C ALA 3.7 22.9 - - - +
76C THR* 3.4 22.9 - - - +
77C ALA* 4.0 9.4 - - - +
96C LEU* 2.9 32.3 + - + +
97C ALA* 3.5 6.3 - - - +
99C LYS* 1.3 81.2 - - + +
101C ALA* 1.3 57.0 + - - +
103C ASN* 3.0 11.6 + - - +
104C VAL* 3.0 30.5 + - - +
106C VAL 4.2 2.5 - - - +
107C GLY* 4.0 10.1 - - - -
109C VAL* 4.9 2.0 - - + -
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Residues in contact with ALA 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ALA 2.9 16.5 + - - +
98C ILE 3.2 4.7 + - - +
100C LYS* 1.3 73.2 - - - +
102C LYS* 1.3 65.3 + - - +
105C GLY* 3.0 29.2 + - - +
106C VAL 3.8 11.2 - - - +
107C GLY 3.8 2.8 - - - +
132C MSE 3.8 18.8 - - - -
266C ALA* 3.7 22.7 - - + +
268C ASN* 3.3 12.3 - - + +
271C PHE* 3.6 0.9 - - - -
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Residues in contact with LYS 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLN* 5.7 4.2 - - - +
98C ILE* 2.9 12.4 + - + +
99C LYS* 3.0 15.9 + - + +
101C ALA* 1.3 77.6 - - - +
103C ASN* 1.3 62.7 + - - +
130C GLN* 4.8 9.1 + - - -
132C MSE 3.6 21.8 - - + +
268C ASN* 3.9 1.8 - - - -
270C GLU* 3.2 35.1 + - - +
271C PHE* 3.5 14.4 - - - -
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Residues in contact with ASN 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C PRO 5.6 0.9 - - - +
99C LYS* 3.6 30.9 + - - +
100C LYS* 3.0 9.8 + - - +
102C LYS* 1.3 88.7 - - - +
104C VAL* 1.3 69.1 + - + +
271C PHE* 3.5 11.9 - - - -
73D SER* 5.7 0.3 - - - -
74D PRO* 5.7 0.5 - - - +
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Residues in contact with VAL 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C PRO* 3.6 31.0 - - + +
75C ALA* 4.2 2.5 - - + -
100C LYS 3.0 16.9 + - - +
103C ASN* 1.3 87.8 - - + +
105C GLY* 1.3 59.3 + - - +
106C VAL 3.4 17.7 - - - +
271C PHE* 3.7 10.3 - - - -
73D SER* 2.8 27.1 + - - +
74D PRO* 4.3 22.2 - - + -
75D ALA* 4.1 17.3 - - + +
76D THR* 3.4 8.8 + - - +
104D VAL* 6.2 0.2 - - + -
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Residues in contact with GLY 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ALA* 3.0 20.1 + - - -
104C VAL* 1.3 78.7 - - - +
106C VAL* 1.3 57.5 + - - +
267C ILE* 3.5 4.9 - - - +
268C ASN* 2.7 31.4 + - - +
271C PHE* 3.4 27.4 - - - -
272C PHE* 4.1 1.6 - - - -
76D THR* 3.8 6.3 - - - -
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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
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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