Contacts of the helix formed by residues 112 - 131 (chain B) in PDB entry 2BTU
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 GLU 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ASP* 5.2 8.2 - - - +
108B CYS* 4.7 1.8 - - - -
110B LYS 2.9 7.4 + - - +
111B ALA* 1.3 67.2 - - - +
113B PRO* 1.3 60.7 - - + -
114B SER* 2.7 21.6 + - - +
115B LYS* 2.5 53.2 + - + +
116B ILE* 2.9 12.3 + - - +
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Residues in contact with PRO 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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15B GLY 5.7 4.7 - - - +
19B VAL* 6.1 4.2 - - - -
111B ALA* 3.0 16.5 - - + +
112B GLU* 1.3 83.9 - - + +
114B SER* 1.3 62.2 + - - +
116B ILE* 4.0 7.8 - - + +
117B GLU* 3.4 23.2 + - - +
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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
----------------------------------------------------------
112B GLU* 2.7 20.0 + - - +
113B PRO* 1.3 77.1 - - - +
115B LYS* 1.3 56.3 + - - -
117B GLU* 3.6 10.2 + - - +
118B ASN* 2.5 46.5 + - - -
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Residues in contact with LYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASP* 5.7 0.4 - - - +
77B HIS* 3.8 35.7 - - + +
112B GLU* 2.5 43.8 + - + +
114B SER* 1.3 72.9 + - - +
116B ILE* 1.3 54.6 + - - +
118B ASN* 3.0 9.9 + - - +
119B ILE* 2.7 48.5 + - + +
151B TYR* 4.8 6.3 - - + -
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Residues in contact with ILE 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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106B ILE* 5.9 3.4 - - + -
108B CYS* 6.3 1.1 - - - -
111B ALA* 5.1 10.1 - - + -
112B GLU 2.9 13.1 + - - +
113B PRO* 4.0 9.4 - - + +
115B LYS* 1.3 75.2 - - - +
117B GLU* 1.3 52.4 + - - +
119B ILE* 3.0 13.9 + - - +
120B VAL* 2.8 42.8 + - + +
139B THR* 4.4 17.5 - - + +
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Residues in contact with GLU 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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19B VAL* 5.5 5.4 - - - +
22B MET* 3.0 48.5 - - + +
23B LYS* 5.8 2.5 - - + -
25B HIS* 3.8 22.8 - - + +
113B PRO 3.4 18.5 + - - +
114B SER* 3.7 9.9 - - - +
115B LYS 3.3 0.2 - - - -
116B ILE* 1.3 73.6 - - - +
118B ASN* 1.3 62.2 + - - +
120B VAL* 3.2 13.2 + - + +
121B LYS* 2.8 29.5 + - - +
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Residues in contact with ASN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B HIS* 4.0 22.3 - - + -
78B ASP* 3.7 16.9 - - - +
114B SER* 2.5 41.2 + - - +
115B LYS* 3.2 9.9 - - - +
117B GLU* 1.3 73.9 + - - +
119B ILE* 1.3 64.8 + - - +
121B LYS* 2.8 26.0 + - - +
122B GLY 3.3 3.6 + - - -
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Residues in contact with ILE 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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77B HIS* 3.4 29.4 + - + +
80B ILE* 4.8 3.6 - - + -
81B GLY* 4.6 2.0 - - - -
106B ILE* 3.3 34.5 - - + -
115B LYS* 2.7 32.7 + - + +
116B ILE* 3.5 8.5 - - - +
118B ASN* 1.3 73.4 - - - +
120B VAL* 1.3 62.6 + - + +
122B GLY* 3.4 2.6 + - - -
123B ILE* 3.1 24.4 + - + +
151B TYR* 3.6 23.3 - - + +
153B LEU* 3.7 30.5 - - + -
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LYS* 4.6 24.9 - - + -
25B HIS* 4.3 15.8 - - + +
26B VAL* 5.8 3.6 - - + -
104B ASP* 5.0 13.7 - - - +
116B ILE* 2.8 24.5 + - + +
117B GLU* 3.4 15.5 - - - +
118B ASN 3.1 0.2 - - - -
119B ILE* 1.3 75.5 - - + +
121B LYS* 1.3 61.6 + - - +
122B GLY 3.2 0.2 - - - -
123B ILE* 3.7 11.9 - - + +
124B SER* 3.1 28.8 + - - -
134B LEU* 4.8 8.4 - - + +
139B THR* 5.9 2.5 - - - +
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Residues in contact with LYS 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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25B HIS* 4.0 30.0 - - + +
78B ASP* 4.3 10.1 - - + -
117B GLU 2.8 13.1 + - - +
118B ASN* 3.0 18.6 - - - +
120B VAL* 1.3 77.9 - - - +
122B GLY* 1.3 56.0 + - - +
124B SER* 4.3 2.3 - - - -
125B GLU* 3.5 18.7 + - - +
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Residues in contact with GLY 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ASP 2.9 26.6 + - - -
81B GLY* 4.0 9.0 - - - -
82B ILE* 3.5 17.9 + - - +
118B ASN 3.3 5.5 + - - -
119B ILE 3.4 4.5 + - - -
120B VAL 3.2 0.4 - - - -
121B LYS* 1.3 78.2 - - - +
123B ILE* 1.3 60.2 + - - +
124B SER 3.4 0.4 - - - -
125B GLU* 3.4 5.4 + - - +
126B GLY 3.2 16.1 + - - -
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLY* 3.7 17.0 - - - +
84B ALA* 5.7 1.1 - - + -
85B VAL* 3.5 3.8 - - + +
102B PHE* 3.9 29.4 - - + -
104B ASP* 3.5 32.1 - - + +
119B ILE* 3.1 20.8 + - + +
120B VAL* 3.5 12.5 + - + +
122B GLY* 1.3 74.3 - - - +
124B SER* 1.3 60.1 + - - +
126B GLY 3.4 0.5 + - - -
127B CYS* 3.0 27.6 + - - -
134B LEU* 3.8 22.0 - - + -
153B LEU* 3.9 23.1 - - + -
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Residues in contact with SER 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B HIS* 3.4 26.0 - - - -
26B VAL* 5.4 0.2 - - - -
28B THR* 4.6 3.9 - - - +
29B THR* 3.3 31.1 - - - +
120B VAL 3.1 15.4 + - - -
121B LYS 4.3 4.5 - - - -
123B ILE* 1.3 79.6 - - - +
125B GLU* 1.3 56.9 + - - +
127B CYS* 3.8 0.9 - - - -
128B ARG* 3.1 24.9 + - - +
134B LEU* 4.4 7.6 - - - -
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Residues in contact with GLU 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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78B ASP 5.6 0.4 - - - +
82B ILE* 3.8 13.2 - - + -
121B LYS 3.5 13.8 + - - +
122B GLY* 3.4 11.6 + - - +
123B ILE 3.2 0.6 - - - -
124B SER* 1.3 77.1 - - - +
126B GLY* 1.3 62.7 + - - +
128B ARG* 2.6 40.1 + - - +
129B GLN* 2.8 60.3 + - - +
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Residues in contact with GLY 126 (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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82B ILE* 4.0 11.3 - - - +
85B VAL* 3.6 15.9 - - - -
122B GLY 3.2 9.7 + - - -
123B ILE 3.9 2.0 - - - -
125B GLU* 1.3 78.6 - - - +
127B CYS* 1.3 52.8 + - - +
130B ALA* 2.6 38.3 + - - +
227B ILE* 3.4 21.4 - - - +
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Residues in contact with CYS 127 (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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29B THR* 3.6 17.3 - - + -
85B VAL* 4.2 3.4 - - - -
102B PHE* 3.5 39.5 - - - -
123B ILE* 3.0 23.9 + - - +
126B GLY* 1.3 73.4 - - - +
128B ARG* 1.3 56.5 + - - +
131B GLY* 2.7 27.9 + - - -
132B CYS* 2.9 37.0 + - - +
134B LEU* 4.0 17.3 - - - -
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Residues in contact with ARG 128 (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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28B THR* 3.1 33.1 - - - +
29B THR* 4.5 5.1 - - - +
124B SER 3.1 17.4 + - - +
125B GLU* 2.6 42.3 + - - +
126B GLY 3.3 0.2 - - - -
127B CYS* 1.3 75.7 - - - +
129B GLN* 1.3 64.1 + - - +
131B GLY* 2.9 20.1 + - - -
230B LYS* 3.9 8.5 - - - -
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Residues in contact with GLN 129 (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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82B ILE* 4.1 15.2 - - - +
125B GLU* 2.8 52.3 + - - +
126B GLY 3.7 2.7 - - - +
128B ARG* 1.3 82.3 - - - +
130B ALA* 1.3 58.7 + - - +
227B ILE* 3.8 28.7 + - + +
230B LYS* 2.8 35.6 + - - +
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Residues in contact with ALA 130 (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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85B VAL* 4.1 3.6 - - + -
89B VAL* 3.7 38.1 - - + -
99B PRO* 3.9 3.8 - - - +
126B GLY 2.6 22.0 + - - +
129B GLN* 1.3 73.7 - - - +
131B GLY* 1.3 62.9 + - - +
132B CYS* 4.0 12.3 - - - -
227B ILE* 3.8 11.6 - - + +
229B VAL* 3.2 24.7 - - - +
230B LYS* 4.7 2.0 - - - +
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Residues in contact with GLY 131 (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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31B ARG* 2.8 35.5 + - - -
99B PRO 3.4 4.7 - - - +
127B CYS 2.7 8.6 + - - -
128B ARG* 2.9 15.5 + - - -
129B GLN 3.0 1.5 - - - -
130B ALA* 1.3 80.5 - - - +
132B CYS* 1.3 49.4 + - - -
230B LYS* 4.1 15.0 - - - -
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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