Contacts of the helix formed by residues 133 - 149 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D CYS* 3.6 20.4 - - - +
110D ARG* 3.3 33.5 + - - +
111D MET 5.4 0.2 - - - -
112D ILE* 5.1 12.3 - - - +
131D LEU 4.2 1.5 + - - -
132D LEU* 1.3 76.2 - - - +
134D GLY* 1.3 67.2 + - - +
135D PRO* 4.0 0.3 - - - +
136D GLU* 4.1 6.8 + - - +
137D TRP* 3.6 9.6 + - - -
448D ARG* 2.8 31.7 + - - +
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Residues in contact with GLY 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D HIS* 3.8 33.1 + - - +
108D PRO 5.3 0.6 + - - -
109D CYS* 5.1 1.9 - - - -
133D ASN* 1.3 75.3 - - - +
135D PRO* 1.3 77.9 - - - +
137D TRP* 3.0 14.9 + - - +
138D ARG 3.1 9.5 + - - -
448D ARG* 5.2 0.2 - - - +
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Residues in contact with PRO 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D HIS* 4.0 28.3 - - + +
133D ASN 4.6 0.2 - - - +
134D GLY* 1.3 83.5 - - - +
136D GLU* 1.3 57.4 + - - +
138D ARG* 3.3 3.7 + - + +
139D PHE* 2.9 30.0 + - - +
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Residues in contact with GLU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D LYS* 3.5 34.6 + - - +
127D CYS 5.1 0.3 - - - +
132D LEU* 3.3 30.9 - - + +
133D ASN 4.1 4.2 + - - +
134D GLY 3.2 0.4 - - - -
135D PRO* 1.3 76.7 - - - +
137D TRP* 1.3 65.7 + - - +
139D PHE* 3.3 5.9 + - + +
140D ASN* 3.2 40.4 + - - +
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Residues in contact with TRP 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU 3.5 23.8 - - - -
107D HIS* 4.4 4.0 - - + -
108D PRO* 3.7 15.5 - - + -
129D VAL* 3.3 41.8 - - + +
132D LEU* 3.6 16.9 - - + +
133D ASN* 3.6 19.7 + - - -
134D GLY 3.0 15.1 + - - +
136D GLU* 1.3 79.7 - - - +
138D ARG* 1.3 87.0 + - + +
140D ASN* 3.4 0.3 + - - +
141D ARG* 2.8 43.4 + - + +
447D MET* 3.6 39.0 - - + -
448D ARG* 3.5 35.3 - - + +
601D HEM 3.1 18.6 + - - -
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Residues in contact with ARG 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D LEU* 3.8 43.5 + - - +
107D HIS* 3.8 15.8 + - + +
134D GLY 3.1 6.2 + - - +
135D PRO* 3.8 6.7 - - + +
137D TRP* 1.3 100.6 - - + +
139D PHE* 1.3 61.1 + - - +
141D ARG* 4.2 2.5 - - + -
142D LEU* 2.9 65.5 + - + +
447D MET* 5.5 9.9 - - - +
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Residues in contact with PHE 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D PRO 2.9 17.3 + - - +
136D GLU* 3.7 9.0 - - + +
137D TRP 3.3 0.2 - - - -
138D ARG* 1.3 77.7 - - - +
140D ASN* 1.3 66.3 + - - +
142D LEU* 5.8 0.7 - - - -
143D ARG* 3.1 79.0 + - - +
298D GLU 4.2 10.5 - - - -
299D LEU* 4.1 14.1 - - + -
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Residues in contact with ASN 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D CYS 4.9 2.8 + - - +
129D VAL* 4.3 3.4 - - + -
132D LEU* 3.7 23.5 - - + +
136D GLU* 3.2 30.4 + - - +
137D TRP 3.8 6.3 - - - +
139D PHE* 1.3 80.1 - - - +
141D ARG* 1.3 68.0 + - - +
143D ARG* 3.0 12.6 + - - +
144D LEU* 3.0 28.1 + - + +
299D LEU* 3.7 21.6 - - - +
303D ALA* 4.0 10.8 - - - +
307D ASN* 2.8 25.9 + - - +
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Residues in contact with ARG 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D VAL* 3.9 10.5 - - + +
137D TRP* 2.8 44.4 + - + +
138D ARG* 3.8 4.0 - - - +
140D ASN* 1.3 72.7 - - - +
142D LEU* 1.3 68.2 + - + +
144D LEU* 2.9 15.7 + - - +
145D ASN* 2.8 46.5 + - - +
149D LEU* 3.6 20.0 - - - +
447D MET* 3.2 22.4 + - + +
448D ARG 3.4 0.8 + - - -
449D GLN* 2.8 33.5 + - - +
451D LEU* 3.8 16.6 - - - +
601D HEM 2.7 45.3 + - - +
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Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D ARG* 2.9 63.8 + - + +
141D ARG* 1.3 80.2 - - + +
143D ARG* 1.3 73.3 + - + +
145D ASN* 4.7 12.2 - - - +
146D PRO* 3.4 21.1 - - - +
447D MET* 5.2 11.7 - - - -
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Residues in contact with ARG 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D PHE* 3.1 80.4 + - - +
140D ASN 3.0 5.3 + - - +
142D LEU* 1.3 91.9 - - - +
144D LEU* 1.3 60.8 + - - +
146D PRO* 4.0 7.3 - - - +
147D ASP* 4.5 4.7 - - - +
293D LEU* 3.6 18.2 - - - +
296D LYS* 6.1 0.2 - - - +
298D GLU* 3.9 44.1 + - + +
299D LEU* 3.9 17.4 - - + +
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Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D VAL* 3.9 19.1 - - + -
140D ASN* 3.0 26.8 + - + +
141D ARG* 2.9 6.5 + - - +
143D ARG* 1.3 78.6 - - - +
145D ASN* 1.3 66.1 + - - +
146D PRO 3.2 2.3 - - - -
147D ASP* 3.4 3.5 + - - +
148D VAL* 3.1 33.0 + - + +
293D LEU* 4.0 28.0 - - + +
299D LEU* 4.2 6.7 - - + -
307D ASN* 3.3 49.8 - - + +
311D LEU* 5.4 1.8 - - + -
451D LEU* 4.1 20.4 - - + -
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Residues in contact with ASN 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D ARG* 2.8 61.0 + - - +
142D LEU* 4.7 12.6 - - - +
144D LEU* 1.3 76.6 - - - +
146D PRO* 1.3 73.4 - - + +
149D LEU* 3.0 29.5 + - + +
150D SER* 3.0 10.6 + - - +
447D MET* 5.1 10.1 + - - +
451D LEU* 3.3 11.1 - - - +
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Residues in contact with PRO 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D LEU 3.4 19.5 - - - +
143D ARG* 4.0 7.2 - - - +
144D LEU 3.4 4.3 - - - -
145D ASN* 1.3 96.1 - - + +
147D ASP* 1.3 60.1 + - - +
150D SER* 2.5 32.8 + - - -
152D LYS* 5.3 0.3 - - - +
153D ALA* 3.3 7.3 + - - +
296D LYS* 4.4 17.3 - - - +
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Residues in contact with ASP 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ARG 4.5 4.7 - - - +
144D LEU 3.4 2.0 + - - +
145D ASN 3.2 0.2 - - - -
146D PRO* 1.3 77.5 - - - +
148D VAL* 1.3 61.8 + - - +
153D ALA* 3.1 19.1 - - - +
286D TYR* 4.6 2.4 + - - -
289D ILE* 3.6 25.5 - - + +
292D GLU* 3.6 34.3 - - + +
293D LEU* 4.0 23.6 - - + +
296D LYS* 2.9 40.8 + - - +
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Residues in contact with VAL 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D LEU* 3.1 30.5 + - + +
147D ASP* 1.3 80.0 - - + +
149D LEU* 1.3 58.4 + - - +
150D SER 4.0 0.2 - - - -
153D ALA* 4.3 1.3 - - - -
157D PHE* 3.8 21.1 - - - -
204D LEU* 6.1 0.2 - - + -
289D ILE* 3.8 28.4 - - + +
293D LEU* 5.0 2.7 - - + -
311D LEU* 4.0 28.5 - - + -
451D LEU* 3.2 39.4 - - + +
452D GLY* 4.6 4.3 - - - -
454D ARG* 5.1 0.2 - - - +
455D LEU* 4.9 9.3 + - + +
601D HEM 5.7 0.9 - - + -
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Residues in contact with LEU 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D ARG* 3.6 27.1 - - - +
145D ASN* 3.0 18.4 + - + +
148D VAL* 1.3 77.6 - - - +
150D SER* 1.3 61.5 - - - +
154D VAL* 4.9 0.2 - - - -
449D GLN* 3.9 17.5 - - - +
450D CYS 4.0 12.3 - - - +
451D LEU* 3.6 19.7 - - + +
453D ARG* 4.2 11.0 - - + +
454D ARG* 2.6 76.2 + - + +
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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
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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