Contacts of the helix formed by residues 106 - 125 (chain B) in PDB entry 1TE6
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B LEU 3.7 4.7 - - - -
48B LEU* 3.8 11.9 - - - -
97B ASP* 4.2 0.2 + - - -
102B LYS* 3.0 17.6 + - - -
103B SER* 4.8 1.8 - - - -
104B LYS 3.4 1.8 - - - -
105B PHE* 1.3 81.1 - - - +
107B ALA* 1.3 66.4 + - - -
108B ASN* 3.1 13.0 - - - -
109B ALA 3.0 11.1 + - - -
110B ILE* 3.1 14.4 + - - +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ALA* 3.6 30.1 - - + +
46B LEU 2.7 25.4 + - - +
47B GLU* 4.2 2.2 - - + +
102B LYS* 3.3 18.8 + - + -
106B GLY* 1.3 71.7 - - - -
108B ASN* 1.3 57.6 + - - +
110B ILE 4.6 0.2 - - - +
111B LEU* 2.9 34.8 + - - +
344B ASN* 4.1 13.7 - - - +
347B GLY* 4.0 2.9 - - - +
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Residues in contact with ASN 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B THR* 5.3 2.6 + - - +
19B VAL* 3.7 19.7 - - + +
34B VAL* 3.3 33.5 - - + +
35B PRO 5.6 0.2 - - - +
47B GLU* 3.8 18.9 + - + +
48B LEU 3.0 43.3 + - - +
49B ARG* 5.6 0.2 - - - -
61B VAL* 3.8 10.7 - - - +
64B ALA* 3.6 15.5 - - - +
106B GLY* 3.4 6.6 - - - -
107B ALA* 1.3 74.7 - - - +
109B ALA* 1.3 63.2 + - - -
112B GLY* 3.2 17.7 + - - -
344B ASN* 6.3 0.2 - - - -
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 4.7 0.2 - - - -
64B ALA* 3.7 25.6 - - + +
67B HIS* 4.9 0.2 - - + -
68B ILE* 3.6 26.9 - - + +
72B ILE* 4.4 7.6 - - + -
105B PHE* 3.4 27.4 - - + +
106B GLY 3.0 2.8 + - - +
108B ASN* 1.3 80.6 + - - +
110B ILE* 1.3 68.7 + - - +
112B GLY 3.4 1.2 + - - -
113B VAL* 3.4 18.5 + - - +
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ILE* 3.7 22.0 - - + -
90B ASP 5.4 0.4 - - - +
93B MET* 3.5 52.0 - - + +
94B LEU* 4.7 5.8 - - + -
97B ASP* 5.2 3.4 - - + +
102B LYS* 4.3 24.0 - - + -
105B PHE* 3.9 22.4 - - + -
106B GLY 3.1 14.8 + - - +
107B ALA 4.1 1.3 - - - +
109B ALA* 1.3 76.5 - - - +
111B LEU* 1.3 63.8 + - - +
113B VAL* 3.2 3.3 + - - +
114B SER* 2.9 19.6 + - - -
347B GLY 3.5 15.0 - - - +
348B SER* 4.7 6.1 - - - -
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B VAL* 3.9 14.8 - - + -
35B PRO* 4.4 2.9 - - + -
107B ALA 2.9 22.2 + - - +
108B ASN 4.3 2.0 - - - +
110B ILE* 1.3 73.4 - - - +
112B GLY* 1.3 54.0 + - - +
114B SER* 4.0 2.2 - - - -
115B LEU* 2.7 70.4 + - + +
343B VAL* 4.2 16.2 - - + +
344B ASN* 3.4 38.4 - - + +
347B GLY* 3.2 24.6 + - - +
348B SER* 4.1 14.1 - - - +
349B VAL 4.5 1.3 - - - +
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Residues in contact with GLY 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 4.7 1.3 - - - -
21B VAL* 3.6 21.1 - - - +
32B ALA* 4.3 7.3 - - - +
34B VAL* 3.5 19.7 - - - +
108B ASN 3.2 12.5 + - - -
109B ALA 3.9 1.8 - - - -
110B ILE 3.2 0.8 - - - -
111B LEU* 1.3 79.4 - - - +
113B VAL* 1.3 59.2 + - - +
115B LEU* 3.6 6.1 + - - +
116B ALA* 3.2 21.3 + - - +
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ILE* 4.4 11.0 - - + -
21B VAL* 4.2 13.0 - - + -
23B LEU* 5.0 2.5 - - + -
68B ILE* 3.7 31.0 - - + -
72B ILE* 4.1 11.0 - - + -
76B LEU* 3.5 31.4 - - + -
93B MET* 3.7 13.7 - - - -
109B ALA 3.4 13.2 + - - +
110B ILE 3.2 1.8 + - - +
112B GLY* 1.3 72.9 - - - +
114B SER* 1.3 56.2 + - - +
116B ALA* 3.1 2.6 + - - +
117B VAL* 2.8 44.0 + - + +
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLN* 3.2 17.7 + - - +
90B ASP* 2.5 30.8 + - - -
93B MET* 3.8 5.1 - - - +
110B ILE 2.9 17.3 + - - -
111B LEU* 3.4 10.3 - - - -
113B VAL* 1.3 78.0 - - - +
115B LEU* 1.3 61.9 + - - +
117B VAL* 3.4 2.6 + - - +
118B CYS* 3.1 18.9 + - - +
348B SER* 4.2 3.4 - - - -
349B VAL* 2.9 28.1 + - - +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ALA* 3.5 18.4 - - + -
33B ALA 3.6 26.0 - - - +
34B VAL* 4.7 1.6 - - + -
35B PRO* 5.4 1.8 - - + -
111B LEU* 2.7 51.5 + - + +
112B GLY* 3.8 1.8 - - - +
114B SER* 1.3 69.1 - - - +
116B ALA* 1.3 64.9 + - - +
118B CYS* 3.3 5.0 + - - +
119B LYS* 3.1 26.5 + - - +
343B VAL* 5.3 6.5 - - + -
349B VAL* 3.9 10.8 - - + -
377B ASP* 4.9 6.3 - - - +
379B PHE* 3.5 43.9 - - + -
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B VAL* 4.2 17.7 - - + +
23B LEU* 3.6 25.4 - - + -
30B PHE* 4.0 13.0 - - - +
32B ALA* 4.0 8.0 - - + +
112B GLY 3.2 11.2 + - - +
113B VAL* 3.1 7.7 + - - +
115B LEU* 1.3 76.2 - - - +
117B VAL* 1.3 67.4 + - - +
119B LYS* 3.2 7.2 + - - +
120B ALA* 2.9 24.4 + - - +
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ILE* 4.7 6.5 - - + -
23B LEU* 4.3 17.3 - - + -
76B LEU* 5.0 1.1 - - + -
83B VAL* 3.4 22.8 - - + +
86B GLN* 3.8 18.2 - - - +
89B LEU* 3.6 36.1 - - + -
90B ASP* 5.8 0.4 - - - +
93B MET* 5.5 1.6 - - + -
113B VAL* 2.8 35.4 + - + +
114B SER* 3.6 7.2 - - - +
116B ALA* 1.3 78.0 - - - +
118B CYS* 1.3 50.9 + - - +
120B ALA* 3.3 3.6 + - - +
121B GLY 2.7 30.5 + - - -
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Residues in contact with CYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLN* 3.0 22.8 + - - +
114B SER 3.1 9.3 + - - +
115B LEU 3.6 8.7 - - - +
116B ALA 3.2 0.2 - - - -
117B VAL* 1.3 76.6 - - - +
119B LYS* 1.3 65.5 + - - +
121B GLY 3.3 0.2 + - - -
122B ALA* 3.0 19.8 + - - +
129B LEU* 3.9 2.1 - - - +
132B HIS* 3.3 24.9 - - - -
133B ILE* 3.1 37.2 - - - -
136B LEU* 4.0 4.9 - - - -
349B VAL* 4.2 4.0 - - + -
379B PHE* 3.9 16.2 - - + -
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Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PHE* 3.9 19.6 - - + -
31B ARG 2.8 31.7 + - - +
32B ALA* 3.4 11.5 - - + +
115B LEU 3.1 11.9 + - - +
116B ALA* 3.2 7.4 + - - +
118B CYS* 1.3 76.5 - - - +
120B ALA* 1.3 63.3 + - - +
122B ALA* 3.4 5.6 + - - +
123B ALA* 3.4 15.2 + - - +
129B LEU* 4.1 26.2 - - + -
377B ASP* 2.9 27.5 + - - +
378B THR* 5.1 2.0 + - - +
379B PHE* 3.9 25.0 - - + +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LEU* 3.8 19.3 - - + -
25B THR* 4.1 2.4 + - + -
27B LYS* 5.3 0.5 - - - +
30B PHE* 3.4 35.7 - - + -
83B VAL* 3.7 18.0 - - + +
116B ALA 2.9 16.9 + - - +
117B VAL 3.7 3.8 - - - +
119B LYS* 1.3 76.7 - - - +
121B GLY* 1.3 63.4 + - - +
123B ALA* 3.1 5.2 + - - +
124B GLU* 3.1 18.0 + - - +
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Residues in contact with GLY 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B VAL* 3.5 31.8 - - - +
84B VAL* 3.7 2.7 - - - +
117B VAL 2.7 15.8 + - - -
118B CYS 3.7 2.0 - - - -
119B LYS 3.2 0.2 - - - -
120B ALA* 1.3 74.0 - - - +
122B ALA* 1.3 61.2 + - - +
124B GLU* 3.2 5.0 + - - +
125B ARG* 3.1 25.3 + - - +
132B HIS* 3.8 11.4 - - - -
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B CYS 3.0 11.8 + - - +
119B LYS 3.6 8.7 - - - +
120B ALA 3.3 0.2 - - - -
121B GLY* 1.3 75.3 - - - +
123B ALA* 1.3 61.2 + - - +
125B ARG* 3.2 4.2 + - - +
126B GLU 3.0 4.2 + - - -
127B LEU 2.9 39.2 + - - +
129B LEU* 3.9 18.2 - - + +
132B HIS* 3.4 33.1 - - + -
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Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LYS* 3.6 21.8 - - + +
30B PHE* 3.4 35.2 - - + -
119B LYS 3.4 3.5 + - - +
120B ALA 3.1 10.0 + - - +
122B ALA* 1.3 77.7 - - - +
124B GLU* 1.3 58.5 + - - +
126B GLU* 2.8 25.4 + - - +
127B LEU 4.7 2.0 - - - +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B SER 5.7 2.3 + - - -
25B THR* 5.4 5.0 - - - -
26B ALA* 5.9 2.3 - - - +
27B LYS* 4.0 26.7 - - + +
82B SER* 4.3 8.7 + - - +
83B VAL* 4.3 10.6 - - + +
84B VAL* 3.5 22.2 - - + -
120B ALA 3.1 11.8 + - - +
121B GLY 3.2 10.1 + - - +
123B ALA* 1.3 76.9 - - - +
125B ARG* 1.3 60.3 + - - +
126B GLU* 3.3 9.9 + - - +
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Residues in contact with ARG 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B VAL* 3.8 39.7 + - + +
85B GLU* 5.0 3.8 + - - -
121B GLY 3.1 16.2 + - - +
122B ALA* 3.6 9.4 - - - +
123B ALA 3.1 0.2 - - - -
124B GLU* 1.3 74.7 - - - +
126B GLU* 1.3 70.6 + - - +
127B LEU* 3.4 24.7 + - + +
132B HIS* 3.9 19.8 + - - +
135B GLN* 4.8 10.1 + - - +
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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
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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