Contacts of the helix formed by residues 125 - 146 (chain G) in PDB entry 4U7B
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 125 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLU* 5.1 3.8 + - - -
123G GLU 5.1 0.7 - - - +
124G LEU* 1.3 75.3 - - - +
126G GLU* 1.3 68.1 + - + +
127G ARG* 3.3 31.1 - - - +
128G GLN* 2.7 28.5 + - - +
129G MET* 2.9 26.2 + - - +
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Residues in contact with GLU 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ASN* 4.6 8.0 + - - -
126A GLU* 4.9 12.9 + - + +
127A ARG* 3.4 46.3 + - + +
125G ASN* 1.3 75.7 - - + +
127G ARG* 1.3 61.2 + - - +
129G MET* 3.9 19.3 - - + +
130G GLU* 3.1 18.2 + - - +
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Residues in contact with ARG 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLU* 3.2 58.3 + - - +
129A MET* 3.4 16.8 - - - +
130A GLU* 2.2 58.5 + - - +
133A LYS* 4.5 7.9 - - - +
340A ASP* 3.0 38.4 + - - +
342A LYS* 5.6 0.2 - - - +
125G ASN* 2.9 15.3 + - - +
126G GLU* 1.3 75.5 - - - +
128G GLN* 1.3 67.3 + - + +
129G MET 3.1 0.5 + - - -
130G GLU* 3.8 0.3 - - - -
131G ARG* 2.9 24.0 + - - +
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Residues in contact with GLN 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 5.3 0.2 - - - -
122G HIS* 3.7 10.7 - - - -
123G GLU 4.5 2.0 + - - -
124G LEU* 3.8 18.5 - - + +
125G ASN* 2.7 54.0 + - - +
127G ARG* 1.3 77.5 - - + +
129G MET* 1.3 62.5 + - - +
131G ARG* 3.5 11.6 - - - +
132G ARG* 3.2 29.4 + - - +
275G ALA* 5.1 10.4 - - + +
276G TYR* 3.1 38.6 - - + -
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Residues in contact with MET 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ARG* 3.3 30.5 - - - +
124G LEU* 3.8 22.4 - - + -
125G ASN* 2.9 21.9 + - - +
126G GLU* 4.0 18.4 - - + +
128G GLN* 1.3 74.1 - - - +
130G GLU* 1.3 61.6 + - - +
132G ARG* 2.9 7.9 + - - +
133G LYS 2.8 24.1 + - - -
340G ASP 3.9 2.0 - - - +
341G GLY* 3.1 32.9 - - - +
342G LYS* 3.8 33.9 - - + +
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Residues in contact with GLU 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ARG* 2.4 68.0 + - + +
130A GLU* 4.8 2.7 - - + -
131A ARG* 3.6 34.3 - - + +
126G GLU 3.1 16.4 + - - +
127G ARG 3.9 2.0 - - - +
129G MET* 1.3 78.3 - - - +
131G ARG* 1.3 52.9 + - - +
133G LYS* 3.9 23.4 + - - +
134G ASN* 2.8 42.4 + - - +
137G GLU* 4.6 1.6 - - - +
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Residues in contact with ARG 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 3.6 30.8 + - + +
133A LYS* 5.5 1.8 - - - +
134A ASN* 2.9 29.9 + - - +
137A GLU* 2.5 36.4 + - - -
127G ARG 2.9 16.8 + - - +
128G GLN* 3.5 11.0 - - - +
130G GLU* 1.3 78.2 - - - +
132G ARG* 1.3 54.1 - - - +
134G ASN* 3.8 2.2 - - - +
135G THR* 2.7 39.3 + - - -
250G ASN* 5.0 3.9 - - - +
273G HIS 4.1 9.1 + - - +
274G ALA* 3.9 19.4 - - + +
275G ALA* 4.0 25.5 - - - +
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Residues in contact with ARG 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G LEU* 3.7 13.6 - - - +
128G GLN 3.4 13.7 - - - +
129G MET 2.9 5.8 + - - +
131G ARG* 1.3 75.0 - - - +
133G LYS* 1.3 67.2 - - - +
134G ASN 3.2 0.2 + - - -
135G THR* 3.2 1.9 + - - -
136G CYS* 3.0 29.0 + - - -
274G ALA* 3.5 13.7 - - + -
275G ALA 4.4 7.0 - - - +
276G TYR 3.5 0.9 + - - -
277G SER* 3.1 36.3 + - - +
279G ASP* 2.9 41.8 + - - -
280G LEU* 3.5 12.1 - - + +
336G CYS* 3.8 10.7 - - - +
341G GLY* 3.1 23.3 + - - +
342G LYS 3.3 20.0 + - - -
343G TYR* 3.4 20.2 - - - -
344G PHE* 4.3 5.1 - - - -
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Residues in contact with LYS 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ARG* 4.3 5.2 - - - +
129G MET 2.8 15.8 + - - +
130G GLU* 3.7 27.9 + - - +
132G ARG* 1.3 72.7 - - - +
134G ASN* 1.3 57.9 + - - +
136G CYS* 3.7 2.1 + - - +
137G GLU* 2.9 51.6 + - - +
336G CYS* 4.2 5.6 - - - -
337G VAL* 4.2 24.8 - - - +
340G ASP* 3.3 33.5 + - - +
341G GLY* 3.6 18.7 - - - +
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Residues in contact with ASN 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ARG* 3.1 43.8 - - + +
134A ASN* 4.1 11.6 + - + +
135A THR* 3.1 22.4 + - - -
130G GLU* 2.8 29.9 + - + +
131G ARG* 3.9 3.8 - - - +
133G LYS* 1.3 73.3 - - - +
135G THR* 1.3 64.9 + - - +
137G GLU* 3.3 9.5 + - - +
138G ILE* 3.0 38.4 + - - +
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Residues in contact with THR 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ASN* 3.4 18.2 + - - +
138A ILE* 5.1 1.1 - - + -
131G ARG* 2.7 26.9 + - - +
132G ARG* 3.7 5.6 - - - -
134G ASN* 1.3 76.5 - - - +
136G CYS* 1.3 63.7 - - - +
138G ILE* 3.2 7.9 + - - +
139G LEU* 2.9 37.1 + - + +
272G PRO* 3.7 40.8 - - + +
273G HIS* 4.3 2.2 - - - +
274G ALA* 4.2 14.9 + - - +
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Residues in contact with CYS 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G ARG* 3.0 11.0 + - - +
133G LYS 3.9 2.0 - - - +
135G THR* 1.3 77.7 - - - +
137G GLU* 1.3 65.4 + - - +
138G ILE 2.9 0.5 + - - -
139G LEU* 2.9 10.8 + - - +
140G LEU* 2.8 29.8 + - - +
280G LEU* 4.2 10.5 - - - -
333G TRP* 3.7 35.0 - - + +
336G CYS* 2.1 49.8 - - - -
337G VAL* 4.4 2.5 - - + +
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Residues in contact with GLU 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ARG* 4.1 22.0 + - - -
130G GLU* 4.6 1.7 - - - +
133G LYS* 2.9 51.2 + - - +
134G ASN* 3.3 13.4 + - - +
136G CYS* 1.3 74.7 - - - +
138G ILE* 1.3 61.3 + - + +
140G LEU* 3.7 11.3 - - + +
141G SER* 3.3 21.7 + - - -
337G VAL* 4.0 16.3 - - + +
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Residues in contact with ILE 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A THR* 4.7 5.8 - - + +
138A ILE* 4.1 32.3 - - + -
272A PRO* 3.9 40.6 - - + -
134G ASN* 3.0 38.3 + - - +
135G THR* 3.6 6.3 - - - +
137G GLU* 1.3 76.1 - - - +
139G LEU* 1.3 72.2 + - + +
141G SER* 3.1 9.7 + - - -
142G ARG* 3.1 24.3 + - + +
272G PRO* 6.0 3.6 - - + -
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Residues in contact with LEU 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G THR* 2.9 38.8 + - + +
136G CYS* 3.5 7.4 - - - +
138G ILE* 1.3 79.2 - - + +
140G LEU* 1.3 63.6 + - - +
142G ARG* 3.2 10.9 + - - +
143G TYR* 2.9 23.4 + - - +
148G PHE* 4.1 12.0 - - + -
271G LEU* 3.7 37.7 - - + -
272G PRO* 4.2 18.6 - - + +
333G TRP* 3.8 40.3 - - + +
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Residues in contact with LEU 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G CYS 2.8 19.0 + - - +
137G GLU* 3.7 7.2 - - + +
139G LEU* 1.3 70.1 - - - +
141G SER* 1.3 65.3 + - - +
143G TYR* 2.9 9.8 + - + +
144G LYS* 2.9 42.4 + - - +
330G PRO* 3.5 19.3 - - + +
333G TRP* 3.3 37.2 - - + -
334G GLU* 3.9 23.6 - - + +
337G VAL* 3.6 31.0 - - + -
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Residues in contact with SER 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A VAL* 4.3 18.3 - - - +
137G GLU 3.3 11.7 + - - -
138G ILE* 3.1 12.0 + - - -
140G LEU* 1.3 80.5 - - - +
142G ARG* 1.3 61.1 + - - +
144G LYS* 3.6 9.7 - - - +
145G ARG* 3.4 19.9 + - - +
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Residues in contact with ARG 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A GLU* 4.7 15.3 - - - -
138G ILE* 3.1 15.0 + - + +
139G LEU* 3.5 11.7 - - - +
141G SER* 1.3 74.9 - - - +
143G TYR* 1.3 65.6 + - - +
145G ARG* 2.9 22.9 + - + +
146G LYS* 3.1 13.7 + - - +
148G PHE* 3.8 26.1 - - + +
151G ARG* 4.0 18.6 - - - +
245G ILE* 3.8 14.6 - - - +
269G GLU* 2.7 30.5 + - - -
271G LEU* 3.9 15.8 - - - +
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Residues in contact with TYR 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G LEU 2.9 16.1 + - - +
140G LEU* 3.5 10.1 - - + +
142G ARG* 1.3 72.8 - - - +
144G LYS* 1.3 80.6 + - + +
146G LYS 3.2 23.0 - - - -
147G SER* 3.5 21.3 + - - -
148G PHE* 3.7 11.1 - + + -
149G LEU* 3.2 37.0 - - + -
327G HIS* 5.8 2.4 + + - -
330G PRO* 3.8 31.3 - - + +
333G TRP* 4.2 10.1 - + + -
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Residues in contact with LYS 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ARG* 5.0 15.8 - - - +
264A GLU* 3.5 15.5 - - - +
140G LEU* 2.9 34.0 + - - +
141G SER* 3.6 13.9 - - - +
143G TYR* 1.3 92.7 - - + +
145G ARG* 1.3 64.4 + - - +
146G LYS* 4.3 0.9 - - - -
334G GLU* 4.0 21.1 + - - -
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Residues in contact with ARG 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A HIS* 4.6 11.7 + - - -
264A GLU* 3.8 23.2 - - + +
267A ASN* 2.2 43.9 + - - +
268A TRP 3.5 30.7 - - - -
269A GLU* 3.6 35.2 + - - +
270A VAL* 4.7 6.7 - - - +
141G SER 3.4 9.5 + - - +
142G ARG* 2.9 16.6 + - + +
144G LYS* 1.3 80.9 - - - +
146G LYS* 1.3 67.6 + - + +
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Residues in contact with LYS 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ASN* 6.2 1.6 - - - +
142G ARG* 3.1 11.8 + - - +
143G TYR* 3.2 12.9 + - - +
144G LYS 4.3 0.7 - - - -
145G ARG* 1.3 87.5 - - + +
147G SER* 1.3 78.2 + - - +
148G PHE* 3.5 8.7 + - + +
150G HIS* 4.7 11.1 - - - -
243G ARG* 5.2 14.6 - - - +
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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