Contacts of the helix formed by residues 94 - 117 (chain C) in PDB entry 2I2X
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 94 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLN* 2.9 33.0 + - - +
91C MET 3.1 12.1 - - - +
92C SER 3.2 0.2 - - - -
93C ASN* 1.3 82.7 - - - +
95C PRO* 1.4 68.1 - - - +
96C SER* 3.1 3.8 - - - +
97C TRP* 2.8 52.0 + - + +
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Residues in contact with PRO 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C MET 4.0 5.7 - - - +
92C SER 3.6 5.4 - - - +
93C ASN 3.3 13.2 - - - +
94C ASN* 1.4 82.2 - - - +
96C SER* 1.3 63.0 + - - +
97C TRP 3.1 1.4 + - - -
98C GLY* 3.5 2.9 + - - -
99C ALA* 3.2 19.1 + - - +
145C VAL* 4.0 14.8 - - + +
148C GLU* 3.5 40.4 - - + +
149C ALA* 4.2 5.6 - - - +
152C GLN* 3.9 26.0 - - + +
153C CYS* 4.9 2.4 - - - -
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Residues in contact with SER 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LYS* 5.1 2.4 + - - -
94C ASN* 3.0 2.2 + - - +
95C PRO* 1.3 79.0 - - - +
97C TRP* 1.3 70.4 + - - +
99C ALA* 3.4 9.2 - - - +
100C GLU* 3.0 44.6 + - - +
152C GLN* 4.6 9.4 - - - +
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Residues in contact with TRP 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLY 4.8 3.4 - - - -
53C ALA 5.0 3.4 - - - -
54C SER* 4.1 9.0 - - - -
55C LYS* 3.6 64.1 - - + +
58C LEU* 4.0 18.6 - - + -
90C GLN* 3.8 31.2 - - + -
91C MET* 4.0 10.1 - - + -
94C ASN* 2.8 42.3 + - + +
96C SER* 1.3 83.0 - - - +
98C GLY* 1.3 65.1 + - - +
99C ALA 3.1 0.9 - - - -
100C GLU* 3.1 3.6 + - - +
101C VAL* 3.0 28.8 + - + +
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Residues in contact with GLY 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C HIS* 3.8 19.3 - - - -
91C MET* 3.3 32.0 + - - +
95C PRO 3.5 0.8 + - - -
97C TRP* 1.3 78.8 - - - +
99C ALA* 1.3 56.7 + - - +
101C VAL* 3.4 0.7 + - - +
102C ALA* 2.8 29.6 + - - +
124C HIS* 3.5 6.4 + - - -
153C CYS* 3.6 7.6 - - - -
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Residues in contact with ALA 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PRO 3.2 14.6 + - - +
96C SER* 3.4 15.9 - - - +
97C TRP 3.1 0.6 - - - -
98C GLY* 1.3 75.7 - - - +
100C GLU* 1.3 58.4 + - + +
102C ALA* 3.4 2.0 + - - +
103C HIS* 2.9 22.9 + - - +
152C GLN* 3.9 29.2 - - + +
153C CYS* 3.8 13.0 - - - +
156C ASN* 3.4 22.6 - - - +
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Residues in contact with GLU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LYS* 2.6 40.5 + - + -
59C ILE* 4.0 22.7 - - + +
96C SER* 3.0 29.6 + - - +
97C TRP* 3.1 4.9 + - - +
99C ALA* 1.3 76.2 - - + +
101C VAL* 1.3 61.1 + - - +
103C HIS* 3.4 7.1 + - + +
104C ALA* 3.0 28.9 + - - +
156C ASN* 6.1 2.2 - - - +
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Residues in contact with VAL 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LYS* 6.3 0.7 - - + -
58C LEU* 4.6 4.9 - - + -
59C ILE* 4.2 22.0 - - + +
62C TYR* 3.5 40.6 - - + -
85C THR* 4.4 0.4 - - + -
91C MET* 4.0 22.9 - - + -
97C TRP 3.0 18.1 + - - +
98C GLY 3.6 6.5 - - - +
100C GLU* 1.3 72.6 - - - +
102C ALA* 1.3 65.9 + - - +
103C HIS 3.2 0.2 + - - -
104C ALA* 3.2 6.0 + - - +
105C GLN* 2.9 47.8 + - - +
124C HIS* 4.1 2.0 - - - +
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C GLY 2.8 18.0 + - - +
99C ALA* 3.5 7.4 - - - +
101C VAL* 1.3 76.4 - - - +
103C HIS* 1.3 57.7 + - - +
106C LYS* 2.9 32.2 + - - +
122C LEU* 3.8 5.6 - - - +
124C HIS* 3.7 26.4 + - + +
153C CYS* 4.1 9.2 - - - +
156C ASN 3.4 10.5 - - - +
158C ALA 4.1 15.3 - - - +
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Residues in contact with HIS 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ALA 2.9 15.6 + - - +
100C GLU* 3.8 8.7 - - + +
101C VAL 3.2 0.4 - - - -
102C ALA* 1.3 77.1 - - - +
104C ALA* 1.3 62.6 + - - +
106C LYS* 3.5 3.2 + - + +
107C THR* 2.9 45.6 + - - -
156C ASN* 3.1 40.1 + - + +
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Residues in contact with ALA 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ILE* 3.7 26.5 - - + +
62C TYR* 6.4 0.2 - - + -
63C GLU* 3.8 20.1 - - + +
100C GLU 3.0 17.3 + - - +
101C VAL* 3.7 4.0 - - - +
103C HIS* 1.3 76.4 + - - +
105C GLN* 1.3 66.0 + - + +
107C THR* 3.4 13.4 + - - -
108C ILE* 3.5 19.3 + - - +
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Residues in contact with GLN 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C TYR* 3.1 21.8 + - - -
62C TYR* 4.2 15.2 - - + +
63C GLU* 5.9 0.2 - - - -
66C THR* 3.0 29.3 + - - +
83C LEU* 4.3 1.0 - - - +
85C THR* 2.6 25.1 + - - +
101C VAL* 2.9 31.4 + - + +
102C ALA 3.9 2.7 - - - +
104C ALA* 1.3 73.2 - - + +
106C LYS* 1.3 66.6 + - - +
107C THR 3.0 1.2 + - - -
108C ILE* 3.1 14.2 + - - +
109C MET* 3.1 31.2 + - + +
122C LEU* 3.7 8.4 - - + +
124C HIS* 3.2 24.4 - - - -
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Residues in contact with LYS 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLY* 5.0 0.9 - - - -
30C LEU* 4.2 28.3 - - + -
102C ALA 2.9 18.9 + - - +
103C HIS* 4.0 4.5 - - + +
104C ALA 3.4 0.2 - - - -
105C GLN* 1.3 77.0 - - - +
107C THR* 1.3 56.8 + - - +
109C MET* 3.4 21.3 + - + +
110C GLU* 2.8 45.9 + - - +
121C ALA* 5.3 1.8 - - - +
122C LEU* 4.3 2.7 - - + +
157C GLY* 2.6 42.7 + - - +
159C ASP* 2.8 33.3 + - - -
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Residues in contact with THR 107 (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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103C HIS* 2.9 39.4 + - - -
104C ALA* 3.7 8.2 - - - -
105C GLN 3.1 1.2 - - - -
106C LYS* 1.3 76.4 - - - +
108C ILE* 1.3 65.8 + - + +
110C GLU* 3.5 15.4 + - - +
111C LYS* 3.2 21.0 + - + +
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Residues in contact with ILE 108 (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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63C GLU* 3.7 39.0 - - + +
66C THR* 4.1 14.1 - - + +
67C THR* 3.4 35.7 - - - +
70C MET* 4.7 0.4 - - + -
104C ALA 3.5 12.5 + - - +
105C GLN 3.1 7.5 + - - +
107C THR* 1.3 76.0 - - + +
109C MET* 1.3 60.1 + - - +
111C LYS* 3.4 11.0 + - + +
112C TYR* 3.1 48.5 + - + -
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Residues in contact with MET 109 (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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30C LEU* 3.7 3.1 - - + +
66C THR* 3.7 18.4 - - + -
70C MET* 4.2 18.8 - - - -
83C LEU* 4.2 18.2 - - + -
105C GLN* 3.1 31.1 + - + +
106C LYS* 3.6 18.8 - - + +
108C ILE* 1.3 75.3 - - - +
110C GLU* 1.3 59.8 + - - +
112C TYR* 3.5 2.4 + - - +
113C HIS* 2.8 29.3 + - - +
120C CYS* 4.2 18.9 - - - -
121C ALA 4.6 8.1 - - - +
122C LEU* 3.5 46.2 - - + -
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Residues in contact with GLU 110 (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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30C LEU* 3.8 28.1 - - + +
106C LYS* 2.8 40.9 + - + +
107C THR* 3.8 14.5 + - - +
109C MET* 1.3 71.7 - - - +
111C LYS* 1.3 58.2 + - - +
113C HIS* 3.7 0.9 - - - +
114C ASP* 2.9 43.1 + - - +
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Residues in contact with LYS 111 (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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107C THR* 3.2 11.8 + - + +
108C ILE* 3.4 16.6 - - + +
109C MET 3.2 0.2 - - - -
110C GLU* 1.3 77.5 - - - +
112C TYR* 1.3 82.9 + - + +
114C ASP* 3.3 8.9 + - - +
115C GLU* 3.0 57.2 + - + +
116C TYR* 5.6 0.6 + - - -
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Residues in contact with TYR 112 (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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67C THR* 3.9 16.9 + - + +
70C MET* 3.5 39.9 - - + -
71C GLU* 2.9 51.3 + - - +
74C VAL* 4.1 3.8 - - + -
108C ILE* 3.1 44.9 + - + +
109C MET 4.0 3.1 - - - +
111C LYS* 1.3 92.6 + - + +
113C HIS* 1.3 66.2 + - - +
115C GLU* 4.6 0.7 - - - -
116C TYR* 3.0 58.6 + + - +
118C ILE* 3.6 6.3 - - + +
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Residues in contact with HIS 113 (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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30C LEU* 3.7 51.1 + - + +
31C ASP* 3.8 16.5 + - + +
109C MET 2.8 18.6 + - - +
110C GLU 3.7 2.9 - - - +
111C LYS 3.3 0.2 - - - -
112C TYR* 1.3 76.5 - - - +
114C ASP* 1.3 69.2 + - - +
117C GLY* 2.9 37.3 + - - +
118C ILE* 3.0 34.9 - - - +
120C CYS* 4.7 0.9 - - - -
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Residues in contact with ASP 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C GLU* 2.9 28.7 + - - +
111C LYS* 3.3 7.4 + - - +
113C HIS* 1.3 88.3 + - - +
115C GLU* 1.3 61.7 + - + +
117C GLY 4.8 0.3 + - - -
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Residues in contact with GLU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 4.0 28.1 - - - +
111C LYS* 3.0 48.1 + - + +
114C ASP* 1.3 79.3 - - + +
116C TYR* 1.3 96.3 + - + +
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Residues in contact with TYR 116 (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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234A LEU* 3.8 28.1 - - + +
14B THR* 5.4 1.2 - - - +
16B TYR* 3.3 49.0 - + + -
20B LEU* 3.6 31.3 - - + +
71C GLU* 4.8 3.1 + - - -
74C VAL* 3.7 19.9 - - + +
111C LYS* 5.6 0.4 + - - -
112C TYR* 3.0 44.6 + + - +
115C GLU* 1.3 108.0 + - + +
117C GLY* 1.3 60.8 + - - +
118C ILE 4.2 1.6 - - - +
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Residues in contact with GLY 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 4.7 1.6 - - - -
31C ASP* 5.6 0.5 - - - +
79C PRO 5.0 0.2 - - - +
112C TYR 3.8 0.2 + - - -
113C HIS* 2.9 28.9 + - - -
114C ASP 4.7 0.2 - - - -
115C GLU 3.8 0.6 - - - -
116C TYR* 1.3 76.8 - - - +
118C ILE* 1.3 64.0 + - - +
119C LYS* 3.5 11.4 + - - +
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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) + - + + + + + -
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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