Contacts of the helix formed by residues 140 - 160 (chain B) in PDB entry 5U8T
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 140 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B THR* 4.1 20.9 + - + -
136B ASP* 3.6 23.1 - - - +
137B PRO 3.1 3.8 + - - +
138B ILE 2.7 13.3 + - - +
139B HIS* 1.3 92.3 + - - +
141B LEU* 1.3 70.0 + - + +
142B ARG 3.4 2.4 - - - +
143B GLY* 3.1 5.8 + - - +
144B LYS* 2.9 58.7 + - + +
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TRP* 5.8 0.2 - - + -
93B LEU* 3.5 38.6 - - + -
94B THR* 4.3 8.7 - - - +
95B THR* 4.3 15.0 - - + +
98B LEU* 3.5 26.5 - - + -
127B PHE* 4.3 14.1 - - + -
135B HIS 5.8 0.4 - - - +
136B ASP 4.0 7.2 - - - +
137B PRO* 2.9 31.1 + - + +
140B GLU* 1.3 82.9 - - + +
142B ARG* 1.3 59.9 + - - +
144B LYS* 2.7 26.4 + - + -
145B ILE* 2.7 23.0 + - + +
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Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395 ARG* 3.1 56.1 - - - +
415 ASP* 5.3 1.2 + - - +
425 SER* 3.6 21.2 - - - +
445 PHE* 3.6 7.6 - - + -
127B PHE* 3.4 39.5 - - + +
137B PRO 4.1 2.7 + - - +
138B ILE* 4.1 9.8 - - - +
139B HIS 3.7 11.1 - - - +
140B GLU 3.4 0.8 - - - +
141B LEU* 1.3 76.2 - - - +
143B GLY* 1.3 55.7 + - - +
145B ILE* 3.3 15.8 - - + +
146B GLN* 3.0 30.1 + - - +
314E ASP* 2.4 37.0 + - - -
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Residues in contact with GLY 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365 LEU* 5.1 3.1 - - - -
395 ARG* 4.5 1.0 - - - +
445 PHE* 3.5 21.4 - - - -
475 ARG* 3.8 8.2 + - - -
139B HIS 5.2 1.1 - - - -
140B GLU 3.1 10.3 + - - +
141B LEU 3.0 0.8 - - - -
142B ARG* 1.3 78.1 - - - +
144B LYS* 1.3 59.8 + - - +
146B GLN* 3.2 1.7 + - - +
147B ASP* 2.9 30.3 + - - +
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Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B THR* 5.2 6.3 - - - +
98B LEU* 3.5 30.3 - - + -
99B ASP* 5.0 14.4 + - - +
102B ILE* 4.5 14.6 - - + +
140B GLU* 2.9 54.5 + - + +
141B LEU* 2.7 11.2 + - + +
143B GLY* 1.3 74.4 - - - +
145B ILE* 1.3 51.2 + - - +
147B ASP* 3.6 6.5 + - - +
148B LEU* 2.8 32.6 + - - +
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Residues in contact with ILE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TRP* 5.9 3.6 - - + -
98B LEU* 4.1 24.7 - - + -
119B TRP* 4.5 22.4 - - + -
120B LEU* 5.4 8.0 - - + +
123B ALA* 5.1 17.5 - - + -
127B PHE* 5.2 6.1 - - + -
141B LEU* 2.7 30.5 + - + +
142B ARG* 3.3 20.9 - - + +
144B LYS* 1.3 70.3 - - - +
146B GLN* 1.3 69.8 + - + +
147B ASP 3.2 0.4 - - - -
148B LEU* 3.6 8.7 - - + -
149B ARG* 2.9 31.1 + - + +
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Residues in contact with GLN 146 (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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425 SER 5.0 0.4 + - - -
435 GLN* 4.2 11.3 - - - +
445 PHE* 3.5 33.3 - - + +
475 ARG* 3.5 27.1 - - - +
485 ASP* 4.2 11.6 + - - +
142B ARG 3.0 23.1 + - - +
143B GLY 3.2 5.1 + - - +
145B ILE* 1.3 85.0 - - - +
147B ASP* 1.3 56.7 + - - +
149B ARG* 3.7 14.5 + - - +
150B GLU* 2.9 28.8 + - - +
192C PHE* 5.2 5.3 - - - -
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Residues in contact with ASP 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365 LEU* 5.3 1.4 - - + +
475 ARG* 3.1 25.6 + - - +
1005 ARG* 4.0 28.1 + - - +
1015 ILE* 5.6 0.3 - - - +
102B ILE* 5.8 5.4 - - + +
106B LYS* 5.3 9.4 + - - -
143B GLY 2.9 12.2 + - - +
144B LYS* 3.7 6.3 - - - +
146B GLN* 1.3 76.2 - - - +
148B LEU* 1.3 59.5 + - - +
150B GLU* 3.0 10.8 - - - +
151B ILE* 2.9 43.3 + - - +
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Residues in contact with LEU 148 (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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98B LEU* 4.1 25.8 - - + +
101B LYS* 5.2 6.1 - - + -
102B ILE* 3.6 27.4 - - + -
105B GLU* 5.9 0.7 - - + -
115B LEU* 4.3 7.9 - - + -
119B TRP* 3.7 25.1 - - + -
144B LYS 2.8 19.1 + - - +
145B ILE* 3.7 9.6 - - + +
147B ASP* 1.3 72.8 - - - +
149B ARG* 1.3 60.8 + - - +
151B ILE* 3.3 12.6 - - + +
152B ARG* 2.9 69.0 + - - +
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Residues in contact with ARG 149 (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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515 ARG* 4.8 2.2 - - - +
119B TRP* 4.6 5.6 - - + -
120B LEU* 4.2 26.1 - - + +
145B ILE* 2.9 20.7 + - + +
146B GLN* 3.7 13.7 + - - +
148B LEU* 1.3 78.4 - - - +
150B GLU* 1.3 55.6 + - - +
152B ARG* 3.8 6.8 - - + +
153B GLN* 2.5 76.8 + - + +
176B LEU* 5.3 0.6 - - - +
177B GLU* 5.4 8.0 - - + +
180B GLU* 3.0 33.5 + - - -
184C TYR* 5.1 8.3 - - - -
191C MET* 4.2 19.9 - - - +
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475 ARG* 5.4 8.7 + - - +
515 ARG* 3.1 37.7 + - - +
1005 ARG 5.0 0.7 - - - +
1015 ILE* 3.1 55.6 - - + +
146B GLN* 2.9 18.6 + - - +
147B ASP* 3.0 22.2 - - - +
149B ARG* 1.3 72.2 - - - +
151B ILE* 1.3 59.7 + - + +
152B ARG 3.1 1.6 - - - -
153B GLN* 2.7 26.3 + - - +
154B ILE* 2.9 17.9 + - - +
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Residues in contact with ILE 151 (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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1005 ARG 5.2 6.5 - - - +
1015 ILE 5.8 1.8 - - - +
1035 ILE 6.4 1.1 - - - -
1045 LEU* 5.4 12.3 - - + -
102B ILE* 4.0 21.8 - - + +
105B GLU* 3.6 34.5 - - + -
106B LYS* 4.6 22.7 - - + -
147B ASP* 2.9 32.1 + - - +
148B LEU* 3.3 14.4 - - + +
150B GLU* 1.3 76.1 - - + +
152B ARG* 1.3 60.0 + - - +
154B ILE* 3.1 18.0 - - + +
155B LYS* 3.0 29.2 + - - +
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Residues in contact with ARG 152 (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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101B LYS* 5.5 2.6 + - - +
105B GLU* 3.4 21.9 + - - +
112B PHE* 2.3 66.1 + - + +
113B SER* 3.0 13.1 + - - -
115B LEU* 3.3 35.5 - - - +
119B TRP* 4.3 2.5 - - - -
148B LEU* 2.9 39.0 + - - +
149B ARG* 3.9 4.9 - - - +
151B ILE* 1.3 79.7 - - - +
153B GLN* 1.3 54.9 + - - +
155B LYS* 3.2 1.2 + - - -
156B VAL* 2.9 32.8 + - + +
172B ASN* 4.3 3.0 + - - +
173B LEU* 4.7 2.0 - - + -
177B GLU* 3.0 35.2 - - - +
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Residues in contact with GLN 153 (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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515 ARG* 2.9 58.3 + - - +
149B ARG* 2.5 54.8 + - - +
150B GLU* 2.7 13.4 + - - +
152B ARG* 1.3 76.0 - - - +
154B ILE* 1.3 59.0 + - + +
156B VAL* 3.3 11.3 - - + +
157B LEU* 2.9 32.2 + - + +
139C ALA* 6.2 0.4 - - - +
184C TYR* 5.1 10.9 + - - -
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Residues in contact with ILE 154 (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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515 ARG* 4.9 9.0 - - + -
545 ILE* 6.3 1.1 - - + -
1015 ILE 3.6 14.1 - - - +
1025 SER* 3.4 23.6 - - - +
1035 ILE* 4.5 6.5 - - + -
1045 LEU* 4.1 31.2 - - + +
150B GLU* 2.9 19.9 + - - +
151B ILE* 3.1 28.0 - - + +
153B GLN* 1.3 74.0 - - + +
155B LYS* 1.3 68.8 + - + +
157B LEU* 4.0 8.5 - - + +
158B LYS* 2.9 47.7 + - + +
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Residues in contact with LYS 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLU* 2.7 44.8 + - - +
108B HIS 2.3 27.9 + - - -
109B PRO* 3.3 28.9 - - - +
110B ASP* 3.6 11.4 - - - +
111B ARG 3.0 21.7 + - - +
112B PHE* 3.4 22.6 - - + -
151B ILE* 3.0 17.7 + - - +
152B ARG* 3.2 1.5 + - - +
154B ILE* 1.3 82.2 - - + +
156B VAL* 1.3 56.3 + - - +
158B LYS* 3.1 13.0 - - + +
159B GLY* 2.9 24.9 + - - -
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Residues in contact with VAL 156 (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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112B PHE* 3.5 19.0 - - + -
152B ARG* 2.9 23.0 + - + +
153B GLN* 3.3 12.8 - - + +
155B LYS* 1.3 74.9 - - - +
157B LEU* 1.3 63.7 + - + +
159B GLY* 2.8 20.1 + - - -
160B LEU* 2.9 19.3 + - + +
170B LEU* 6.6 0.4 - - + -
173B LEU* 3.7 24.9 - - + -
177B GLU* 6.0 1.8 - - + -
181B LEU* 3.8 28.5 - - + -
136C ASN* 5.8 1.1 - - - +
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Residues in contact with LEU 157 (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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515 ARG* 5.1 7.6 - - - +
555 LEU* 3.8 25.4 - - + -
153B GLN* 2.9 24.1 + - + +
154B ILE* 4.0 9.2 - - + +
156B VAL* 1.3 77.4 - - + +
158B LYS* 1.3 59.6 + - + +
160B LEU* 3.1 25.8 + - - +
161B LYS* 4.3 8.7 + - - +
133C GLN* 4.7 1.2 - - - +
136C ASN* 3.8 21.5 - - - +
137C HIS* 3.2 40.4 - - + +
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Residues in contact with LYS 158 (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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1045 LEU* 5.5 6.7 + - - +
109B PRO* 3.6 35.0 + - - +
110B ASP* 5.2 2.3 + - - -
154B ILE* 2.9 36.8 + - + +
155B LYS* 3.1 20.1 - - + +
157B LEU* 1.3 76.0 - - + +
159B GLY* 1.3 64.8 + - - +
160B LEU 3.0 5.7 + - - -
161B LYS* 3.3 36.8 + - - +
162B TYR* 4.8 7.0 + - - -
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Residues in contact with GLY 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 6.2 0.7 - - - -
155B LYS 2.9 13.4 + - - -
156B VAL* 2.8 10.0 + - - -
158B LYS* 1.3 77.3 - - - +
160B LEU* 1.3 57.1 + - - +
161B LYS 3.1 6.3 + - - -
162B TYR* 3.2 33.0 + - - +
163B LEU* 4.2 4.7 + - - +
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Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B VAL* 2.9 15.1 + - + +
157B LEU* 3.1 20.4 - - + +
158B LYS 3.0 0.8 - - - -
159B GLY* 1.3 77.7 - - - +
161B LYS* 1.3 50.7 + - - +
162B TYR 3.3 0.7 - - - -
163B LEU* 3.1 37.2 - - + +
181B LEU* 6.2 2.2 - - + -
184B PHE* 3.6 37.2 - - + -
185B ILE* 5.0 8.3 - - + -
132C ALA* 4.5 0.4 - - + +
133C GLN* 2.4 51.5 + - - +
136C ASN* 3.4 28.3 - - - +
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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
------------------------------------------------------------
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