Contacts of the helix formed by residues 128 - 146 (chain D) in PDB entry 6DWN
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 GLY 128 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D LYS* 4.9 7.3 + - - -
126D ASP* 3.2 9.7 + - - -
127D SER* 1.3 81.5 - - - +
129D PRO* 1.3 76.3 - - - +
130D VAL 3.2 2.2 - - - -
131D TRP* 3.3 3.9 + - - -
132D ALA* 3.3 18.9 + - - +
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Residues in contact with PRO 129 (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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128D GLY* 1.3 83.3 - - - +
130D VAL* 1.3 70.5 + - + +
132D ALA* 3.5 6.5 + - + +
133D ALA* 3.2 23.0 + - - +
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Residues in contact with VAL 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ASP* 3.3 21.8 - - - +
128D GLY 3.2 0.8 - - - -
129D PRO* 1.3 85.6 - - + +
131D TRP* 1.3 64.7 + - - +
133D ALA* 3.5 5.8 + - - +
134D ARG* 3.3 30.8 + - + +
303D SER 6.0 2.5 - - - +
306D LYS* 4.7 14.8 - - + +
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Residues in contact with TRP 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D LYS* 4.1 23.1 - - + -
121D MET* 3.7 25.1 - - + +
126D ASP* 3.5 28.8 + - + +
127D SER* 3.6 21.1 - - - -
128D GLY 3.3 7.9 + - - +
129D PRO 3.3 0.4 - - - -
130D VAL* 1.3 79.0 - - - +
132D ALA* 1.3 91.5 + - + +
134D ARG* 2.9 22.5 + - - +
135D ARG* 2.9 33.9 + - - +
454D LYS* 3.4 43.1 - - + -
455D ARG* 3.0 43.6 - - - +
601D HEM 3.7 5.4 + - - -
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Residues in contact with ALA 132 (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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104D LYS* 6.2 0.7 - - - +
128D GLY 3.3 8.3 + - - +
129D PRO* 4.0 7.4 - - + +
130D VAL 3.5 0.2 - - - -
131D TRP* 1.3 103.6 - - + +
133D ALA* 1.3 62.3 + - - +
135D ARG* 3.4 14.5 + - - +
136D ARG* 3.4 30.5 + - - +
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Residues in contact with ALA 133 (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 PRO 3.2 12.6 + - - +
130D VAL* 3.6 10.5 - - - +
131D TRP 3.1 0.8 - - - -
132D ALA* 1.3 77.6 - - - +
134D ARG* 1.3 63.7 + - + +
135D ARG 3.3 0.5 + - - -
136D ARG* 3.4 11.6 + - - +
137D LEU* 3.3 25.5 + - + +
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Residues in contact with ARG 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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119D GLN 2.9 25.9 + - - -
121D MET* 3.2 51.1 - - + +
124D SER* 4.3 8.9 + - - -
126D ASP* 4.3 9.3 + - - +
130D VAL* 3.3 28.7 - - + +
131D TRP* 2.9 10.6 + - - +
133D ALA* 1.3 76.9 - - + +
135D ARG* 1.3 63.1 + - - +
137D LEU* 3.2 20.1 + - + +
138D ALA 3.2 9.4 + - - -
306D LYS* 3.2 46.0 + - + +
307D ILE* 5.7 3.8 - - + -
309D ASN* 3.3 17.6 + - - -
310D ILE* 3.9 15.3 - - + +
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Residues in contact with ARG 135 (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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121D MET* 3.9 10.2 - - - -
131D TRP* 2.9 36.8 + - + +
132D ALA* 3.5 11.9 - - - +
133D ALA 3.2 0.2 - - - -
134D ARG* 1.3 76.5 - - - +
136D ARG* 1.3 63.7 + - + +
138D ALA* 3.1 7.7 + - - +
139D GLN* 3.0 42.5 + - - +
453D GLY 4.5 0.2 + - - -
454D LYS* 3.0 23.2 + - - +
455D ARG* 3.7 1.2 - - - +
456D LYS* 2.9 48.1 + - - +
457D CYS 4.8 0.2 + - - -
458D ILE* 3.6 17.3 - - + +
601D HEM 2.7 35.5 + - + +
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Residues in contact with ARG 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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132D ALA* 3.4 24.5 + - - +
133D ALA* 3.4 11.2 + - - +
134D ARG 3.3 0.6 - - - -
135D ARG* 1.3 76.6 - - + +
137D LEU* 1.3 57.5 + - - +
139D GLN* 3.5 19.7 - - - +
140D ASN* 2.7 52.1 + - - +
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Residues in contact with LEU 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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133D ALA* 3.3 15.6 + - + +
134D ARG* 3.2 12.6 + - + +
136D ARG* 1.3 77.8 - - - +
138D ALA* 1.3 57.3 + - - +
140D ASN* 4.1 6.9 - - + +
141D GLY* 2.8 27.4 + - - -
281D ILE* 5.8 0.9 - - - +
284D SER* 5.6 1.0 + - - +
285D LEU* 4.4 15.1 - - + +
288D HIS* 3.5 51.6 - - + +
307D ILE* 4.4 18.4 - - + -
310D ILE* 4.1 22.7 - - + -
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Residues in contact with ALA 138 (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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121D MET* 4.3 4.9 - - + -
134D ARG 3.2 5.1 + - - +
135D ARG 3.1 8.7 + - - +
137D LEU* 1.3 76.5 - - - +
139D GLN* 1.3 61.3 + - - +
141D GLY* 3.6 0.6 - - - -
142D LEU* 2.8 37.0 + - - +
281D ILE* 6.3 0.4 - - - -
310D ILE* 4.0 13.6 - - + +
314D LEU* 3.8 24.0 - - + +
458D ILE* 3.3 26.2 - - + -
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Residues in contact with GLN 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 ARG* 3.0 42.9 + - - +
136D ARG* 3.1 30.0 + - - +
138D ALA* 1.3 76.2 - - - +
140D ASN* 1.3 66.6 + - - +
142D LEU* 3.3 8.7 + - - +
143D LYS* 3.0 24.5 + - - +
456D LYS* 5.7 4.9 - - - +
458D ILE* 4.2 21.1 - - + +
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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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136D ARG* 2.7 39.3 + - - +
137D LEU* 4.1 7.6 - - + +
139D GLN* 1.3 72.7 - - - +
141D GLY* 1.3 64.5 + - - +
143D LYS* 3.3 20.0 + - - +
144D SER* 2.9 31.5 + - - +
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Residues in contact with GLY 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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137D LEU 2.8 23.3 + - - -
138D ALA* 3.6 1.3 - - - -
140D ASN* 1.3 74.6 - - - +
142D LEU* 1.3 61.0 + - - +
144D SER* 3.4 9.0 + - - -
145D PHE* 3.4 18.4 + - - -
281D ILE* 3.7 20.6 - - - +
284D SER* 4.5 17.3 - - - -
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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 ALA 2.8 21.2 + - - +
139D GLN* 3.6 4.9 - - - +
141D GLY* 1.3 69.6 - - - +
143D LYS* 1.3 64.5 + - - +
145D PHE 3.0 2.5 + - - -
146D SER* 2.4 33.6 + - - -
147D ILE* 6.2 0.9 - - + -
198D ILE* 5.5 2.0 - - + -
201D ILE* 4.7 7.6 - - + -
281D ILE* 4.2 17.4 - - + +
314D LEU* 4.3 9.9 - - + -
458D ILE* 3.2 47.1 - - + +
459D GLY* 4.1 3.6 - - - -
462D ILE* 3.2 31.2 - - + -
601D HEM 4.2 18.4 - - + -
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Residues in contact with LYS 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 GLN 3.0 16.7 + - - +
140D ASN* 3.3 19.0 + - - +
142D LEU* 1.3 76.0 - - - +
144D SER* 1.3 60.0 - - - +
145D PHE 3.2 0.7 + - - -
146D SER* 4.1 3.1 - - - -
147D ILE* 3.4 28.3 + - + +
148D ALA* 2.9 34.8 + - + +
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Residues in contact with SER 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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140D ASN* 2.9 19.8 + - - +
141D GLY* 3.7 2.2 - - - -
142D LEU 3.1 0.6 - - - -
143D LYS* 1.3 79.1 - - - +
145D PHE* 1.3 86.3 + - - +
146D SER 3.8 0.2 - - - -
148D ALA* 3.4 18.4 - - - +
158D TYR* 3.6 9.0 - - - -
284D SER* 5.9 1.1 - - - -
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Residues in contact with PHE 145 (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 GLY 3.4 12.5 + - - +
142D LEU 3.0 4.3 + - - -
144D SER* 1.3 100.8 - - - +
146D SER* 1.3 58.8 + - - +
158D TYR* 3.3 40.4 - + + +
162D HIS* 5.1 0.2 - - - -
201D ILE* 3.5 38.0 - - + +
278D ILE* 3.3 41.5 - - + -
279D ARG 3.3 31.2 - - - -
280D ASP* 3.5 21.3 - - - -
281D ILE* 4.2 2.2 - - + -
284D SER* 4.2 10.1 - - - -
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Residues in contact with SER 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 2.4 28.8 + - - -
143D LYS 3.7 0.2 + - - -
144D SER 3.8 0.2 - - - -
145D PHE* 1.3 79.2 - - - +
147D ILE* 1.3 74.6 + - - +
148D ALA 3.5 1.2 - - - +
157D CYS* 3.5 6.2 - - - -
158D TYR* 3.6 7.0 + - - +
159D LEU* 3.1 34.9 + - - +
201D ILE* 4.2 15.5 - - - -
462D ILE* 3.3 33.6 - - - +
465D TRP* 5.3 0.3 - - - -
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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
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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