Contacts of the helix formed by residues 124 - 145 (chain B) in PDB entry 3E7O
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 ASP 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B GLU 4.0 1.6 + - - -
123B LEU* 1.3 76.0 - - - +
125B HIS* 1.3 64.2 + - - +
126B GLU* 3.7 13.7 + - - +
127B ARG* 3.1 48.0 + - - +
128B MET* 3.0 22.0 + - - +
281B PRO* 3.9 13.7 - - + -
287B ASP* 6.1 0.7 - - - +
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Residues in contact with HIS 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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124B ASP* 1.3 71.5 - - - +
126B GLU* 1.3 62.5 + - - +
128B MET* 3.9 3.7 - - + +
129B SER* 2.8 32.3 + - - -
280B PHE* 3.7 23.1 - + - -
281B PRO* 3.8 19.3 + - + +
287B ASP* 3.5 33.2 + - - +
290B LYS* 3.5 39.7 - - + +
291B THR* 3.1 36.0 + - - -
320B TYR* 2.8 28.4 + + + +
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Residues in contact with GLU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASP* 3.7 13.2 + - - +
125B HIS* 1.3 79.5 - - - +
127B ARG* 1.3 64.4 + - + +
129B SER* 3.1 6.8 + - - -
130B TYR* 3.1 29.9 + - + +
290B LYS* 5.4 3.6 - - - +
324B TRP* 3.4 30.6 - - + -
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Residues in contact with ARG 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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123B LEU* 3.9 29.4 - - + -
124B ASP* 3.1 40.2 + - - +
126B GLU* 1.3 82.4 + - + +
128B MET* 1.3 64.8 + - - +
130B TYR* 3.3 3.6 + - + +
131B LEU* 3.0 29.9 + - - +
161B SER 5.7 3.2 + - - -
163B CYS* 3.7 28.5 - - + +
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Residues in contact with MET 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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123B LEU* 3.8 32.3 - - + +
124B ASP 3.0 14.0 + - - +
125B HIS* 3.9 7.4 - - + +
127B ARG* 1.3 75.7 - - - +
129B SER* 1.3 58.7 + - - +
131B LEU* 3.4 9.3 + - - +
132B LEU* 3.0 38.2 + - + +
218B LEU* 4.4 18.7 - - + +
219B VAL* 3.9 37.7 - - + -
280B PHE* 4.7 2.0 - - + -
281B PRO* 3.7 30.5 - - + -
320B TYR* 3.8 21.3 - - + +
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Residues in contact with SER 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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125B HIS 2.8 24.1 + - - -
126B GLU* 3.1 6.2 + - - -
128B MET* 1.3 77.6 - - - +
130B TYR* 1.3 56.9 + - - +
132B LEU* 3.4 4.6 + - - +
133B TYR* 2.9 29.1 + - - +
320B TYR* 3.3 47.2 + - - -
321B ILE* 4.1 3.4 - - - +
323B VAL* 4.5 2.9 - - - +
324B TRP* 2.9 23.6 + - - -
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Residues in contact with TYR 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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126B GLU* 3.1 20.9 + - + +
127B ARG* 3.7 4.7 - - + +
129B SER* 1.3 75.1 + - - +
131B LEU* 1.3 64.8 + - - +
133B TYR* 3.4 8.5 + + - +
134B GLN* 3.1 66.4 + - + +
162B ASP 4.4 3.8 - - - -
163B CYS* 3.4 33.0 - - + -
164B THR* 5.0 3.5 + - - +
324B TRP* 3.5 45.5 - + + +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 4.6 3.6 - - + -
118B VAL* 4.4 16.2 - - + -
123B LEU* 3.7 29.6 - - + -
127B ARG 3.0 19.6 + - - +
128B MET* 3.6 6.3 - - - +
130B TYR* 1.3 75.1 - - - +
132B LEU* 1.3 58.7 + - + +
134B GLN* 3.3 5.4 + - - +
135B MET* 3.0 31.1 + - + +
159B VAL* 3.8 26.2 - - + -
163B CYS* 3.8 32.3 - - - +
165B LEU* 3.6 21.8 - - + +
218B LEU* 4.6 10.5 - - + -
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Residues in contact with LEU 132 (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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128B MET* 3.0 24.4 + - + +
129B SER 3.8 0.4 - - - +
130B TYR 3.3 0.2 - - - -
131B LEU* 1.3 73.9 - - - +
133B TYR* 1.3 64.8 + - - +
135B MET* 3.4 24.6 + - + +
136B LEU* 3.1 32.6 + - + +
211B VAL* 4.1 18.8 - - + +
215B MET* 3.7 59.5 - - + -
218B LEU* 4.8 6.1 - - + -
297B LEU* 5.9 0.9 - - + -
301B MET* 5.9 0.4 - - + -
320B TYR* 4.1 15.3 - - + -
321B ILE* 3.8 17.0 - - + -
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Residues in contact with TYR 133 (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 LYS* 5.7 9.3 + - - -
84B ASN* 6.0 0.2 - - - -
129B SER 2.9 18.7 + - - +
130B TYR* 3.5 11.0 - + - +
132B LEU* 1.3 76.7 - - - +
134B GLN* 1.3 68.4 + - + +
136B LEU* 3.4 3.9 + - - +
137B CYS* 2.9 55.9 + - - -
316B LEU* 3.8 12.3 - - + -
321B ILE* 3.7 36.4 - - + +
324B TRP* 3.5 33.8 + + + -
325B TYR* 3.6 39.0 - + + -
326B ASP 4.4 1.9 + - - -
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Residues in contact with GLN 134 (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 LYS* 6.3 1.3 - - + -
84B ASN* 3.5 33.9 + - - +
130B TYR* 3.1 50.7 + - + +
131B LEU* 3.6 9.3 - - - +
133B TYR* 1.3 81.8 - - + +
135B MET* 1.3 66.0 + - - +
137B CYS* 3.2 4.0 + - - +
138B GLY 2.9 19.9 + - - -
163B CYS 2.8 23.0 + - - -
164B THR* 3.3 10.4 - - - +
165B LEU* 2.8 35.0 + - + +
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Residues in contact with MET 135 (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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115B LEU* 4.0 20.2 - - + -
131B LEU* 3.0 21.1 + - + +
132B LEU* 3.5 36.6 - - + +
134B GLN* 1.3 75.9 - - - +
136B LEU* 1.3 58.8 + - + +
138B GLY* 3.3 1.4 + - - -
139B ILE* 2.9 42.0 + - + +
157B ILE* 4.2 23.6 - - + -
165B LEU* 3.8 24.3 - - + +
167B ILE* 4.0 5.6 - - + +
211B VAL* 4.6 17.7 - - + -
214B ILE* 4.0 17.3 - - + -
218B LEU* 4.3 8.5 - - + -
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Residues in contact with LEU 136 (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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132B LEU* 3.1 19.5 + - + +
133B TYR 3.7 0.4 - - - +
135B MET* 1.3 76.7 - - - +
137B CYS* 1.3 60.4 + - - +
139B ILE* 4.3 5.8 - - + -
140B LYS* 2.8 30.5 + - - +
208B ILE* 3.7 29.6 - - + -
211B VAL* 4.3 22.7 - - + -
301B MET* 4.3 7.0 - - + -
312B VAL* 3.7 13.8 - - + +
315B ALA* 3.9 24.9 - - + -
316B LEU* 3.7 18.6 - - + -
321B ILE* 4.0 29.6 - - + -
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Residues in contact with CYS 137 (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 HIS* 3.9 12.0 + - + +
83B LYS* 5.8 3.4 - - - -
84B ASN* 3.5 19.5 - - - +
133B TYR* 2.9 57.4 + - - +
134B GLN 3.2 4.5 + - - +
136B LEU* 1.3 73.7 - - - +
138B GLY* 1.3 66.6 + - - +
140B LYS* 3.4 7.3 + - - +
141B HIS* 3.1 22.7 + - - +
316B LEU* 4.1 9.2 - - - -
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Residues in contact with GLY 138 (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 HIS* 4.3 3.8 - - - -
84B ASN* 3.9 15.7 - - - +
85B ILE* 3.8 8.7 - - - +
134B GLN 2.9 13.5 + - - -
135B MET 3.7 3.1 - - - -
137B CYS* 1.3 74.3 - - - +
139B ILE* 1.3 61.3 + - - +
141B HIS* 3.2 5.6 + - - +
142B LEU* 3.1 24.6 + - - +
167B ILE* 3.8 18.2 - - - -
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Residues in contact with ILE 139 (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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135B MET* 2.9 27.8 + - + +
136B LEU* 3.8 8.1 - - + +
138B GLY* 1.3 72.0 - - - +
140B LYS* 1.3 60.1 + - - +
142B LEU* 3.2 11.9 + - + +
143B HIS* 2.8 58.2 + - + +
149B HIS* 6.0 0.4 - - + -
152B LEU* 3.5 26.5 - - + -
167B ILE* 4.1 10.1 - - + -
207B ASP* 4.2 10.3 - - + +
211B VAL* 3.4 33.7 - - + -
312B VAL* 3.9 12.3 - - + -
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Residues in contact with LYS 140 (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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136B LEU 2.8 22.2 + - - +
137B CYS* 3.4 7.2 + - - +
139B ILE* 1.3 74.2 - - - +
141B HIS* 1.3 56.6 + - - +
143B HIS* 3.2 7.6 + - + +
144B SER* 2.9 31.4 + - - -
312B VAL* 3.9 13.4 - - + +
313B ASP* 2.7 32.4 + - - +
316B LEU* 3.6 21.6 - - + +
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Residues in contact with HIS 141 (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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80B VAL* 4.0 18.7 - - + +
81B ASN 4.5 5.7 + - - -
82B HIS* 3.5 49.4 - + + +
85B ILE* 4.8 2.5 - - + -
137B CYS 3.1 10.0 + - - +
138B GLY 3.2 8.3 + - - +
140B LYS* 1.3 75.6 - - - +
142B LEU* 1.3 63.9 + - + +
144B SER* 2.7 24.4 + - - -
145B ALA* 3.3 9.9 + - - +
332B ALA* 4.4 11.4 + - + +
333B PRO 3.5 28.4 + - - -
334B PRO* 4.2 2.7 - - + -
335B PRO* 4.0 23.5 - - + +
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Residues in contact with LEU 142 (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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80B VAL* 5.3 4.7 - - + -
85B ILE* 4.0 20.2 - - + -
138B GLY 3.1 16.9 + - - +
139B ILE* 3.5 12.1 - - + +
141B HIS* 1.3 77.7 - - + +
143B HIS* 1.3 60.8 + - + +
145B ALA* 3.2 10.2 + - + -
147B ILE* 2.9 52.2 + - + +
149B HIS* 4.1 32.1 - - + -
167B ILE* 4.6 10.3 - - + -
169B ASP 4.6 5.8 - - - +
170B PHE* 3.5 34.1 - - + -
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Residues in contact with HIS 143 (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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139B ILE* 2.8 39.1 + - + +
140B LYS* 3.6 6.3 - - + +
142B LEU* 1.3 72.5 - - + +
144B SER* 1.3 58.0 + - - +
146B GLY* 3.0 18.9 + - - -
147B ILE 3.2 19.7 - - - +
148B ILE* 4.1 11.1 - - + -
204B GLU* 3.1 62.4 + - + +
207B ASP* 3.0 24.1 + - + -
312B VAL* 3.6 22.2 - - + +
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Residues in contact with SER 144 (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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140B LYS* 2.9 15.6 + - - -
141B HIS* 2.7 33.0 + - - -
143B HIS* 1.3 77.1 - - - +
145B ALA* 1.3 56.6 + - - +
146B GLY 3.3 1.2 + - - -
334B PRO* 4.9 17.0 - - - +
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Residues in contact with ALA 145 (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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80B VAL* 5.9 0.2 - - + -
141B HIS* 3.3 6.5 + - + +
142B LEU* 3.2 9.0 + - - +
143B HIS 3.1 0.4 - - - -
144B SER* 1.3 79.2 + - - +
146B GLY* 1.3 60.2 + - - +
147B ILE* 3.3 22.6 + - + +
334B PRO* 5.7 0.7 - - - -
335B PRO* 3.7 33.4 - - + -
337B ILE* 3.5 24.6 - - + +
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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