Contacts of the helix formed by residues 133 - 149 (chain E) in PDB entry 4DVQ
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 133 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108E PRO 5.3 0.4 - - - +
109E CYS* 3.4 19.3 - - + -
110E ARG* 3.2 34.5 + - - +
112E ILE* 4.8 15.6 - - - +
131E LEU 4.0 6.7 + - - -
132E LEU* 1.3 78.2 + - - +
134E GLY* 1.3 68.0 + - - +
135E PRO* 3.9 0.7 - - - +
136E GLU* 4.1 7.4 + - - +
137E TRP* 3.7 7.6 + - - -
448E ARG* 3.0 22.3 + - - +
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Residues in contact with GLY 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E HIS* 3.5 27.6 + - - +
108E PRO 5.0 3.0 + - - -
109E CYS* 6.2 0.4 - - - +
133E ASN* 1.3 76.9 - - - +
135E PRO* 1.3 70.3 - - - +
137E TRP* 3.0 23.9 + - - +
138E ARG 3.3 4.5 + - - -
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Residues in contact with PRO 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E HIS* 3.8 25.8 - - + +
134E GLY* 1.3 82.3 - - - +
136E GLU* 1.3 66.1 + - - +
138E ARG* 3.9 2.1 - - + +
139E PHE* 2.9 26.9 + - - +
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Residues in contact with GLU 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E LYS* 2.8 36.0 + - - +
127E CYS 5.7 0.2 + - - -
132E LEU* 3.4 31.2 - - + +
133E ASN 4.3 5.4 - - - +
134E GLY 3.3 1.0 - - - -
135E PRO* 1.3 78.7 - - - +
137E TRP* 1.3 60.0 + - - +
139E PHE* 3.6 5.0 - - + +
140E ASN* 2.6 42.9 + - - +
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Residues in contact with TRP 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LEU 3.7 21.5 - - - -
107E HIS* 4.5 7.4 - - - -
108E PRO* 4.0 14.6 - - + -
129E VAL* 3.4 20.9 - - + +
132E LEU* 3.7 27.7 - - + +
133E ASN 3.7 5.3 + - - -
134E GLY 3.0 15.3 + - - +
136E GLU* 1.3 76.9 - - - +
138E ARG* 1.3 89.7 + - + +
140E ASN* 3.3 2.4 + - - +
141E ARG* 2.8 43.5 + - + +
447E MET* 3.5 46.0 - - + -
448E ARG* 3.2 43.0 - - + +
601E HEM 3.0 18.9 + - - -
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Residues in contact with ARG 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E LEU* 2.8 57.7 + - - +
107E HIS* 4.2 21.1 - - + +
134E GLY 3.3 2.8 + - - -
135E PRO* 3.3 5.8 + - + +
137E TRP* 1.3 99.6 - - + +
139E PHE* 1.3 55.2 + - - +
141E ARG* 3.7 2.0 - - + +
142E LEU* 2.8 63.2 + - + +
447E MET* 3.5 37.0 - - + +
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Residues in contact with PHE 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E PRO 2.9 19.0 + - - +
136E GLU* 3.6 6.7 - - + +
138E ARG* 1.3 78.2 - - - +
140E ASN* 1.3 71.6 + - - +
142E LEU* 4.0 3.6 - - - +
143E ARG* 3.1 77.9 + - - +
298E GLU 4.7 7.6 - - - -
299E LEU* 4.0 15.9 - - + -
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Residues in contact with ASN 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E CYS 4.6 1.2 - - - +
129E VAL* 3.9 13.7 - - + -
132E LEU* 3.7 20.1 - - + +
136E GLU* 2.6 39.8 + - - +
137E TRP 3.6 3.4 - - - +
139E PHE* 1.3 81.4 - - - +
141E ARG* 1.3 65.7 + - - +
143E ARG* 2.9 14.7 + - - +
144E LEU* 3.1 21.8 + - + +
299E LEU* 4.1 16.7 - - - +
303E ALA* 4.3 8.9 - - - +
307E ASN* 2.9 26.1 + - - +
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Residues in contact with ARG 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E VAL* 3.8 11.2 - - + +
137E TRP* 2.8 40.0 + - + +
138E ARG* 3.7 5.2 - - + +
140E ASN* 1.3 73.1 - - - +
142E LEU* 1.3 58.5 + - - +
144E LEU* 3.0 4.6 + - - +
145E ASN* 2.8 63.3 + - - +
149E LEU* 3.4 21.2 - - - +
447E MET* 3.2 25.0 + - + +
448E ARG 3.6 1.0 - - - -
449E GLN* 2.6 34.1 + - - +
451E LEU* 3.8 17.6 - - - +
601E HEM 2.7 45.2 + - - +
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Residues in contact with LEU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E ARG* 2.8 50.0 + - + +
139E PHE* 4.0 6.5 - - - +
141E ARG* 1.3 73.3 - - - +
143E ARG* 1.3 72.4 + - - +
145E ASN* 4.7 9.5 - - - +
146E PRO* 3.5 18.9 - - - +
447E MET* 4.5 19.3 - - + -
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Residues in contact with ARG 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E PHE* 3.1 69.7 + - - +
140E ASN 2.9 10.6 + - - +
142E LEU* 1.3 90.5 - - - +
144E LEU* 1.3 57.6 + - - +
146E PRO* 4.1 6.6 - - - +
147E ASP* 4.8 2.6 - - - +
293E LEU* 3.7 18.5 - - - +
298E GLU* 3.7 48.4 + - + +
299E LEU* 3.7 21.7 - - + +
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Residues in contact with LEU 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E VAL* 3.8 25.1 - - + -
140E ASN 3.1 17.8 + - - +
141E ARG 3.0 4.3 + - - +
143E ARG* 1.3 77.7 - - - +
145E ASN* 1.3 66.4 + - - +
146E PRO* 3.2 3.5 - - - -
147E ASP* 3.3 2.1 + - - -
148E VAL* 3.0 31.9 + - + +
293E LEU* 3.6 32.5 - - + -
299E LEU* 3.9 16.4 - - + -
307E ASN* 3.3 39.3 - - + +
311E LEU* 5.3 2.0 - - + -
451E LEU* 3.9 19.7 - - + -
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Residues in contact with ASN 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E ARG* 2.8 63.3 + - - +
142E LEU* 4.7 12.3 - - - +
144E LEU* 1.3 77.0 - - - +
146E PRO* 1.3 69.2 - - + +
149E LEU* 3.1 15.6 + - + +
150E SER* 3.0 24.6 + - - -
447E MET* 5.0 11.3 + - - +
451E LEU* 3.6 7.8 - - - +
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Residues in contact with PRO 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LEU 3.5 18.6 - - - +
143E ARG* 4.1 4.9 - - - +
144E LEU 3.3 6.7 - - - +
145E ASN* 1.3 96.5 - - + +
147E ASP* 1.3 61.4 + - - +
150E SER* 2.8 28.6 + - - -
152E LYS* 5.3 1.6 - - - +
153E ALA* 3.6 7.6 + - - +
296E LYS* 4.3 17.0 - - - +
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Residues in contact with ASP 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E ARG 4.8 2.8 - - - +
144E LEU 3.3 2.0 + - - +
145E ASN 3.2 0.2 - - - -
146E PRO* 1.3 81.3 - - - +
148E VAL* 1.3 61.5 + - - +
153E ALA* 3.4 16.8 - - - +
286E TYR* 4.7 1.4 + - - -
289E ILE* 3.4 24.6 - - + +
292E GLU* 3.4 35.7 - - + +
293E LEU* 3.8 28.9 - - + +
296E LYS* 3.0 39.0 + - - +
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Residues in contact with VAL 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E LEU* 3.0 32.1 + - + +
147E ASP* 1.3 81.3 - - + +
149E LEU* 1.3 59.5 + - - +
153E ALA* 4.5 1.8 - - - -
157E PHE* 3.8 21.5 - - - -
204E LEU* 5.8 0.9 - - + -
289E ILE* 3.7 29.1 - - + +
293E LEU* 5.1 1.3 - - + -
311E LEU* 4.0 28.0 - - + -
451E LEU* 3.3 33.8 - - + +
452E GLY* 4.7 4.6 - - - -
454E ARG* 5.1 0.3 - - - +
455E LEU* 4.9 10.2 + - + +
601E HEM 5.2 1.8 - - + -
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Residues in contact with LEU 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E ARG* 3.4 29.4 - - - +
145E ASN* 3.1 20.3 + - + +
148E VAL* 1.3 77.2 - - - +
150E SER* 1.3 64.3 + - - +
154E VAL* 5.0 0.2 - - - -
449E GLN* 4.4 13.9 - - + +
450E CYS 3.8 17.9 - - - +
451E LEU* 3.7 12.6 - - + +
453E ARG* 4.2 9.6 - - + +
454E ARG* 2.7 75.8 + - + +
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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
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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