Contacts of the helix formed by residues 124 - 144 (chain A) in PDB entry 3VUM
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 1.3 76.8 - - - +
125A HIS* 1.3 64.4 + - - +
126A GLU* 3.6 23.8 - - - +
127A ARG* 3.0 44.2 + - - +
128A MET* 3.1 20.7 + - - +
281A PRO* 3.9 12.8 - - + -
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Residues in contact with HIS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASP* 1.3 72.6 - - - +
126A GLU* 1.3 74.7 + - - +
128A MET* 4.8 2.6 - - - -
129A SER* 3.0 27.2 + - - -
280A PHE* 3.8 26.1 - + - +
281A PRO* 3.6 28.1 + - + +
282A ALA 3.4 24.6 + - - -
283A ASP* 4.2 2.6 + - - -
284A SER* 4.3 2.7 - - - -
289A LEU* 3.7 32.8 - - + -
290A LYS* 3.8 5.6 - - - -
291A ALA* 3.6 23.5 + - - -
320A TYR* 2.8 32.6 + + - -
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Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASP* 3.3 21.0 - - - +
125A HIS* 1.3 79.4 + - - +
127A ARG* 1.3 57.1 + - - +
130A TYR* 2.8 34.8 + - - +
284A SER* 3.3 28.1 + - - -
286A HIS* 4.0 22.5 - - - -
289A LEU* 4.0 8.8 - - + +
324A TRP* 3.6 27.7 - - + -
554F PRO* 4.3 5.0 - - - +
555F LYS 5.0 3.8 - - - +
557F PRO* 3.9 12.6 - - + -
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Residues in contact with ARG 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 4.3 18.2 - - + +
124A ASP* 3.0 34.4 + - - +
126A GLU* 1.3 76.3 - - - +
128A MET* 1.3 56.4 + - - +
130A TYR* 3.7 1.9 - - - +
131A LEU* 2.8 39.2 + - + +
163A ALA* 5.5 2.9 - - + -
557F PRO* 3.8 25.9 - - + +
558F THR 4.9 0.2 - - - +
559F THR* 2.0 57.5 + - - +
560F LEU* 3.8 23.6 - - + +
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Residues in contact with MET 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A MET 5.9 0.2 - - - +
123A LEU* 3.7 38.6 - - + +
124A ASP 3.1 15.7 + - - +
125A HIS* 4.1 1.1 - - - +
127A ARG* 1.3 75.3 - - - +
129A SER* 1.3 60.3 - - - +
131A LEU* 3.3 1.7 + - - +
132A LEU* 2.9 40.6 + - + +
215A MET* 6.0 1.6 - - - -
218A MET* 3.4 47.5 - - + +
219A ILE* 3.9 28.0 - - + +
279A LEU 5.7 1.6 - - - +
280A PHE* 5.6 1.6 - - - -
281A PRO* 4.7 15.0 - - + -
320A TYR* 3.9 18.6 - - - +
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Residues in contact with SER 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A HIS 3.0 17.0 + - - -
126A GLU 3.8 1.3 - - - -
128A MET* 1.3 78.5 - - - +
130A TYR* 1.3 53.1 + - - +
132A LEU* 3.2 5.5 + - - +
133A TYR* 2.7 34.7 + - - +
289A LEU* 3.9 7.2 - - - +
320A TYR* 2.8 44.7 + - - -
321A ILE* 3.8 4.0 - - - +
324A TRP* 2.8 25.7 + - - -
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Residues in contact with TYR 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LYS* 5.5 4.3 + - - -
126A GLU 2.8 19.0 + - - +
127A ARG* 3.7 3.1 - - + +
129A SER* 1.3 77.2 + - - +
131A LEU* 1.3 59.2 + - + +
133A TYR* 4.1 14.1 - + - -
134A GLN* 2.9 72.5 + - + +
162A ASP 5.5 0.4 - - - -
163A ALA* 3.7 13.2 - - + -
164A THR* 5.1 7.0 - - + +
324A TRP* 3.4 21.7 - + + +
556F ARG* 3.6 42.5 + - + +
557F PRO* 3.5 44.6 + - + -
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LEU* 4.6 6.5 - - + -
118A VAL* 3.8 32.8 - - + -
123A LEU* 4.4 9.9 - - + -
127A ARG* 2.8 27.9 + - + +
128A MET 3.8 3.1 - - - +
130A TYR* 1.3 76.1 - - + +
132A LEU* 1.3 56.5 + - - +
134A GLN* 3.3 10.3 + - - +
135A MET* 2.9 25.0 + - - +
159A VAL* 4.2 11.4 - - + -
163A ALA* 3.8 26.2 - - + +
165A LEU* 3.6 26.6 - - + +
218A MET* 4.4 9.0 - - + -
560F LEU* 4.6 14.6 - - + -
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A MET* 2.9 30.1 + - + +
129A SER 3.4 3.6 - - - +
131A LEU* 1.3 73.1 - - - +
133A TYR* 1.3 66.9 + - - +
135A MET* 3.2 19.2 + - - +
136A LEU* 2.9 33.0 + - + +
211A VAL* 4.4 13.2 - - + +
215A MET* 3.7 51.1 - - + +
218A MET* 3.7 25.8 - - + -
297A LEU* 5.7 0.7 - - + -
301A MET* 5.5 1.6 - - + -
320A TYR* 4.2 10.3 - - + -
321A ILE* 4.0 10.3 - - + -
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Residues in contact with TYR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASN* 5.7 1.1 - - - -
129A SER 2.7 20.9 + - - +
130A TYR* 3.5 16.4 - + - +
132A LEU* 1.3 71.1 - - - +
134A GLN* 1.3 58.5 + - + +
136A LEU* 2.9 5.4 + - - +
137A VAL* 2.8 62.0 + - + +
316A LEU* 3.6 18.2 - - + -
321A ILE* 3.9 24.1 - - + +
324A TRP* 3.5 29.4 - - + -
325A TYR* 3.9 19.3 - + - -
326A ASP 3.1 16.6 + - - -
329A GLU* 2.6 35.2 + - - +
330A ALA* 4.6 0.5 - - - +
556F ARG* 3.6 11.4 - - - -
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Residues in contact with GLN 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LYS* 6.1 0.7 - - - -
84A ASN* 3.2 35.4 + - - +
130A TYR* 2.9 55.1 + - + +
131A LEU* 3.4 15.6 - - - +
133A TYR* 1.3 81.4 - - + +
135A MET* 1.4 63.8 + - - +
137A VAL* 4.6 0.7 - - - +
138A GLY* 3.0 18.7 + - - -
163A ALA 3.0 22.4 + - - -
164A THR* 3.5 7.4 - - - +
165A LEU* 3.0 34.1 + - + +
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Residues in contact with MET 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LEU* 4.2 9.2 - - - -
131A LEU* 2.9 22.1 + - - +
132A LEU* 3.2 24.0 + - + +
134A GLN* 1.4 72.6 - - - +
136A LEU* 1.3 59.2 + - - +
138A GLY* 3.1 1.4 + - - -
139A ILE* 2.8 36.2 + - + +
152A LEU* 5.6 2.0 - - + -
157A ILE* 4.1 13.2 - - + -
165A LEU* 3.7 28.7 - - + +
167A ILE* 3.9 7.8 - - + +
211A VAL* 3.9 36.1 - - + -
214A ILE* 4.0 36.3 - - + -
218A MET* 5.3 1.1 - - - +
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU* 2.9 18.5 + - + +
133A TYR 3.5 5.6 - - - +
135A MET* 1.3 78.5 - - - +
137A VAL* 1.3 57.8 + - - +
139A ILE* 3.2 6.6 + - + +
140A LYS* 2.8 31.6 + - - +
208A ILE* 3.6 31.2 - - + -
211A VAL* 4.4 24.2 - - + -
297A LEU* 5.4 1.3 - - + -
301A MET* 5.0 3.8 - - + -
312A VAL* 4.4 10.6 - - + +
315A ALA* 4.0 26.7 - - + -
316A LEU* 3.8 14.5 - - + +
321A ILE* 4.0 28.9 - - + -
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A HIS* 3.4 29.2 - - + +
84A ASN* 3.5 9.9 - - - +
133A TYR* 2.8 53.8 + - + +
134A GLN* 4.0 3.8 - - - +
136A LEU* 1.3 76.5 - - - +
138A GLY* 1.3 62.4 + - - +
140A LYS* 3.2 8.0 + - - +
141A HIS* 3.0 21.7 + - - +
316A LEU* 3.9 8.7 - - + -
329A GLU* 3.9 14.5 - - + +
330A ALA* 4.0 17.2 - - + -
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Residues in contact with GLY 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A HIS* 4.7 1.8 - - - -
84A ASN* 4.0 18.1 - - - +
85A ILE* 4.2 6.7 - - - +
134A GLN 3.0 13.6 + - - -
135A MET 3.5 3.1 - - - -
137A VAL* 1.3 78.8 - - - +
139A ILE* 1.3 63.1 + - - +
141A HIS* 3.1 16.5 + - - +
142A LEU* 3.2 15.8 + - - +
167A ILE* 4.1 13.0 - - - -
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Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A MET* 2.8 25.9 + - + +
136A LEU* 3.6 7.6 - - + +
138A GLY* 1.3 72.5 - - - +
140A LYS* 1.3 57.6 + - - +
142A LEU* 3.2 11.7 + - + +
143A HIS* 2.9 64.3 + - + +
149A HIS* 5.9 0.9 - - + -
152A LEU* 3.2 34.5 - - + -
167A ILE* 3.9 8.7 - - + +
207A ASP* 4.1 9.0 - - + +
211A VAL* 3.6 25.1 - - + -
312A VAL* 3.7 13.9 - - + -
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Residues in contact with LYS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LEU 2.8 19.3 + - - +
137A VAL 3.7 5.2 - - - +
138A GLY 3.1 0.4 - - - -
139A ILE* 1.3 70.9 - - - +
141A HIS* 1.3 68.3 + - - +
143A HIS* 3.3 4.3 + - + +
144A SER* 2.9 32.4 + - - -
312A VAL* 3.7 21.1 - - + -
313A ASP* 3.3 31.7 + - - +
316A LEU* 4.3 12.5 - - + +
325A TYR* 4.8 3.0 + - - -
330A ALA* 2.8 35.5 + - - +
331A GLU* 4.4 11.0 - - - +
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Residues in contact with HIS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A VAL* 4.0 20.6 - - + +
81A ASN 3.5 20.8 + - - -
82A HIS* 3.5 38.4 + - + +
85A ILE* 4.4 3.1 - - + -
137A VAL 3.0 12.1 + - - +
138A GLY* 3.1 9.6 + - - +
140A LYS* 1.3 78.1 - - - +
142A LEU* 1.3 61.3 + - - +
144A SER* 2.6 26.9 + - - -
329A GLU 5.8 0.2 - - - +
332A ALA* 4.2 14.9 + - + +
333A PRO 3.5 16.9 + - - -
335A PRO* 3.3 38.1 - - + +
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A VAL* 4.2 26.7 - - + -
85A ILE* 3.7 33.0 - - + -
138A GLY 3.2 9.6 + - - +
139A ILE* 3.5 13.0 - - + +
141A HIS* 1.3 76.2 - - + +
143A HIS* 1.3 68.8 + - + +
145A ALA* 3.0 13.3 + - - +
147A ILE* 3.1 48.4 + - + +
149A HIS* 4.6 25.8 - - + +
167A ILE* 4.9 6.3 - - + -
170A PHE* 4.8 13.9 - - + -
335A PRO* 5.2 0.7 - - - -
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Residues in contact with HIS 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ILE* 2.9 46.1 + - + +
140A LYS* 3.9 7.2 - - + +
142A LEU* 1.3 77.9 - - + +
144A SER* 1.3 56.4 + - - +
145A ALA 2.9 0.2 - - - -
146A GLY* 2.6 25.2 + - - +
147A ILE 3.0 29.4 - - - +
148A ILE* 4.2 4.6 - - + -
204A GLU* 3.1 63.2 + - + +
207A ASP* 2.5 26.8 + - + -
312A VAL* 3.8 19.9 - - + +
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Residues in contact with SER 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LYS* 2.9 22.6 + - - +
141A HIS* 2.6 24.2 + - - -
142A LEU 3.1 0.4 - - - -
143A HIS* 1.3 75.2 - - - +
145A ALA* 1.3 58.2 + - - +
146A GLY 3.3 1.2 + - - -
332A ALA 4.8 4.4 + - - -
334A PRO* 3.5 38.5 - - - +
335A PRO* 3.9 0.2 - - - +
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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