Contacts of the helix formed by residues 106 - 126 (chain A) in PDB entry 2XGZ
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 GLY 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.7 7.6 - - - -
48A MET* 3.9 13.7 - - - +
102A LYS* 2.9 17.9 + - - -
104A LYS 3.7 0.6 - - - -
105A LEU* 1.3 80.3 - - - +
107A ALA* 1.3 62.1 + - - -
108A ASN* 3.1 11.7 - - - -
109A ALA 3.0 15.7 + - - -
110A ILE* 3.1 14.9 + - - +
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 5.5 0.4 - - - -
45A ALA* 3.7 29.6 - - + +
46A LEU 2.7 22.9 + - - +
47A GLU* 5.1 0.7 - - - -
102A LYS* 3.5 17.0 + - + -
106A GLY* 1.3 72.1 - - - -
108A ASN* 1.3 54.0 + - - +
109A ALA 3.2 0.2 - - - -
110A ILE* 4.5 1.1 - - - +
111A LEU* 2.9 34.5 + - - +
347A ASN* 4.4 10.1 - - + +
350A GLY* 4.2 12.8 - - - +
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Residues in contact with ASN 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A THR* 5.5 2.1 + - - +
19A VAL* 3.3 31.0 - - + +
34A VAL* 3.8 34.2 - - + +
46A LEU 4.0 0.4 + - - -
47A GLU* 3.9 16.9 - - + +
48A MET* 3.0 53.9 + - - +
61A VAL* 3.9 14.8 - - - +
64A ALA* 3.8 11.2 - - - +
106A GLY* 3.8 2.8 - - - -
107A ALA* 1.3 73.7 - - - +
109A ALA* 1.3 60.0 + - - +
112A GLY 4.8 0.2 + - - -
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 4.6 0.3 - - - +
64A ALA* 3.5 24.0 - - - +
67A ASN* 4.1 3.1 - - + -
68A VAL* 3.4 24.8 - - + +
72A ILE* 3.9 12.1 - - + +
105A LEU 3.2 26.7 - - - +
106A GLY 3.0 2.5 + - - +
108A ASN* 1.3 80.4 + - - +
110A ILE* 1.3 66.5 + - - +
111A LEU 3.6 0.2 - - - -
112A GLY* 4.0 5.1 + - - -
113A VAL* 3.7 11.8 + - - +
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Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE* 4.3 8.1 - - + -
93A LEU* 3.9 27.3 - - + +
94A ILE* 5.4 0.9 - - - +
97A ASP* 3.7 31.9 - - + +
102A LYS* 3.7 25.6 - - + -
105A LEU* 4.2 17.0 - - + -
106A GLY 3.1 14.6 + - - +
107A ALA* 4.1 3.6 - - - +
109A ALA* 1.3 75.8 - - - +
111A LEU* 1.3 64.4 + - - +
113A VAL* 3.2 7.2 + - - +
114A SER* 3.1 17.8 + - - -
350A GLY 3.4 16.8 - - - +
351A THR* 3.7 19.1 - - + -
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 4.3 16.6 - - + -
35A PRO* 4.3 4.5 - - + -
107A ALA 2.9 23.6 + - - +
110A ILE* 1.3 73.6 - - - +
112A GLY* 1.3 58.4 + - - +
114A SER* 3.2 3.3 + - - -
115A LEU* 2.9 59.0 + - + +
346A VAL* 3.9 23.3 - - + +
347A ASN* 3.5 36.6 - - + +
350A GLY* 3.3 27.3 + - - +
351A THR* 4.1 8.5 - - - +
352A LEU 4.4 0.2 - - - +
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Residues in contact with GLY 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 3.7 24.4 - - - +
32A SER* 3.6 14.0 - - - -
34A VAL* 3.7 19.9 - - - +
108A ASN 5.4 0.2 - - - -
109A ALA 4.0 3.2 + - - -
110A ILE 3.4 1.0 - - - -
111A LEU* 1.3 78.9 - - - +
113A VAL* 1.3 59.8 + - - +
115A LEU* 4.8 1.1 - - - -
116A ALA* 3.1 26.7 + - - +
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 4.2 5.8 - - + -
21A VAL* 4.0 18.1 - - + +
23A LEU* 4.1 9.4 - - + +
68A VAL* 4.1 12.1 - - + -
72A ILE* 3.9 21.1 - - + -
76A PHE* 3.8 36.3 - - + -
89A VAL* 5.1 0.2 - - + -
93A LEU* 3.9 14.4 - - + -
109A ALA 3.7 15.5 - - - +
110A ILE 3.2 6.6 + - - +
112A GLY* 1.3 73.5 - - - +
114A SER* 1.3 66.9 + - - +
116A ALA* 3.4 1.6 + - - +
117A ALA* 2.9 26.2 + - - +
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLN* 3.0 24.5 + - - +
89A VAL* 4.5 2.0 - - - -
90A ASP* 2.6 28.3 + - - -
93A LEU* 3.8 6.6 - - - +
110A ILE 3.1 12.2 + - - -
111A LEU* 3.3 14.8 - - - -
113A VAL* 1.3 78.4 - - - +
115A LEU* 1.3 61.9 + - - +
117A ALA* 3.6 1.2 - - - +
118A SER* 3.5 10.6 + - - -
350A GLY 4.5 0.2 - - - -
351A THR* 4.2 4.5 - - - -
352A LEU* 3.0 26.2 + - - +
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A SER* 3.3 22.2 - - - +
33A ILE 4.7 11.4 - - - +
34A VAL* 5.8 0.2 - - + -
35A PRO* 5.7 1.3 - - + -
111A LEU* 2.9 55.7 + - + +
112A GLY* 5.2 0.4 - - - -
114A SER* 1.3 70.7 - - - +
116A ALA* 1.3 65.8 + - - +
118A SER* 2.7 24.9 + - - -
119A ARG* 3.2 9.2 + - - +
346A VAL* 4.6 11.7 - - + -
352A LEU* 4.2 16.2 - - + -
380A ASP* 5.5 1.1 - - - +
382A PHE* 3.7 47.1 - - + -
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 4.3 9.2 - - + -
23A LEU* 3.9 15.5 - - + -
30A PHE* 3.6 25.7 - - - +
32A SER* 2.9 18.2 + - - +
112A GLY 3.1 17.1 + - - +
113A VAL 3.9 2.5 - - - +
115A LEU* 1.3 74.4 - - - +
117A ALA* 1.3 57.2 + - - +
119A ARG* 3.1 8.5 + - - +
120A ALA* 2.9 28.6 + - - +
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.9 14.3 - - + +
76A PHE* 4.8 1.1 - - + -
83A VAL* 3.7 15.8 - - + +
86A GLN* 4.3 3.4 - - - +
89A VAL* 3.8 33.4 - - + -
113A VAL 2.9 18.5 + - - +
114A SER 3.6 6.5 - - - +
115A LEU 3.2 0.2 - - - -
116A ALA* 1.3 75.9 - - - +
118A SER* 1.3 56.2 + - - +
120A ALA* 3.3 3.8 + - - +
121A ALA* 2.9 28.6 + - - +
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLN* 3.4 19.4 + - - -
114A SER 3.5 2.7 + - - -
115A LEU 2.7 19.8 + - - -
117A ALA* 1.3 79.5 - - - +
119A ARG* 1.3 56.6 + - - +
121A ALA* 3.4 6.0 + - - -
122A ALA 3.0 22.5 + - - -
129A LEU* 3.7 6.0 - - - +
132A HIS* 3.4 20.5 - - - -
133A LEU* 4.2 2.9 - - - -
352A LEU* 3.5 17.2 - - - +
382A PHE* 3.2 23.4 - - - -
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Residues in contact with ARG 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PHE* 3.8 26.0 - - + -
31A ARG* 2.7 51.6 + - - +
32A SER* 4.0 7.6 - - - +
115A LEU 3.6 11.9 - - - +
116A ALA 3.1 7.7 + - - +
118A SER* 1.3 76.0 + - - +
120A ALA* 1.3 64.6 + - - +
122A ALA* 3.5 5.1 + - - +
123A ALA* 3.2 16.8 + - - +
129A LEU* 4.1 30.6 - - + +
380A ASP* 5.5 3.0 + - - -
381A THR* 5.9 1.0 + - - -
382A PHE* 4.6 6.1 - - + -
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.9 10.8 - - + -
25A THR* 3.8 22.1 + - + +
27A LYS* 4.9 2.1 - - - +
30A PHE* 3.6 30.3 - - + -
83A VAL* 4.2 8.1 - - + +
116A ALA 2.9 11.4 + - - +
117A ALA 3.5 8.1 - - - +
119A ARG* 1.3 75.7 - - - +
121A ALA* 1.3 58.2 + - - +
123A ALA* 3.3 3.8 + - - +
124A GLU* 3.0 27.0 + - - +
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A VAL* 3.4 34.5 - - - +
84A LYS* 3.7 12.3 - - + -
117A ALA 2.9 9.9 + - - +
118A SER* 3.6 1.6 - - - +
119A ARG 3.2 0.2 - - - -
120A ALA* 1.3 74.4 - - - +
122A ALA* 1.3 66.8 + - - +
124A GLU* 3.1 6.3 + - - +
125A LYS* 2.9 28.3 + - - +
132A HIS* 3.5 22.4 - - + +
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A SER 3.0 17.6 + - - +
119A ARG* 3.8 4.9 - - - +
120A ALA 3.5 0.2 - - - -
121A ALA* 1.3 75.3 - - - +
123A ALA* 1.3 57.7 + - - +
125A LYS* 3.3 1.6 + - - -
126A ASN 2.9 22.2 + - - -
127A VAL* 2.9 32.5 + - - +
129A LEU* 3.8 19.5 - - + +
132A HIS* 3.8 25.0 - - + -
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LYS* 3.4 24.5 - - + +
30A PHE* 3.4 40.8 - - + -
119A ARG 3.2 6.0 + - - +
120A ALA 3.6 3.1 - - - +
121A ALA 3.2 1.0 - - - -
122A ALA* 1.3 76.7 - - - +
124A GLU* 1.3 63.7 + - - +
126A ASN* 3.0 15.1 + - - +
127A VAL 5.0 0.4 - - - -
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Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ALA* 5.3 7.2 - - - +
26A GLU* 4.3 16.9 - - - +
27A LYS* 4.0 19.6 + - + +
82A ASP* 4.4 2.1 - - - +
83A VAL* 3.9 20.2 - - + +
84A LYS* 2.7 40.1 + - + +
120A ALA 3.0 14.1 + - - +
121A ALA* 3.1 9.2 + - - +
123A ALA* 1.3 75.0 - - - +
125A LYS* 1.3 60.5 + - - +
126A ASN* 3.4 2.6 + - - +
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Residues in contact with LYS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS* 3.7 29.1 - - + +
121A ALA 2.9 17.0 + - - +
122A ALA 3.8 3.8 - - - +
124A GLU* 1.3 75.0 - - - +
126A ASN* 1.3 69.9 + - - +
127A VAL* 3.3 25.8 - - + +
132A HIS* 2.9 35.9 + - + +
135A ASP* 2.7 35.3 + - - +
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Residues in contact with ASN 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LYS* 6.0 2.7 - - - +
122A ALA 2.9 3.6 + - - -
123A ALA* 3.0 14.9 + - - +
124A GLU 3.2 2.6 - - - +
125A LYS* 1.3 81.5 - - - +
127A VAL* 1.3 61.8 + - - +
128A PRO* 4.8 0.9 - - - +
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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
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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