Contacts of the helix formed by residues 128 - 144 (chain D) in PDB entry 1DVM
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 128 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125D ASP* 3.2 34.7 - - + +
126D PHE 2.9 2.0 - - - -
127D SER* 1.3 82.9 - - - +
129D VAL* 1.3 64.9 + - - +
130D GLU 3.4 2.5 - - - -
131D ARG* 3.1 45.7 + - + +
132D ALA* 3.0 19.3 + - - +
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Residues in contact with VAL 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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126D PHE 3.5 7.1 + - - +
127D SER 3.7 2.0 - - - -
128D GLU* 1.3 73.6 - - - +
130D GLU* 1.3 68.2 + - - +
132D ALA* 3.7 3.7 - - - +
133D ARG* 3.0 65.2 + - - +
157D VAL* 3.3 13.8 - - - +
158D GLN* 3.8 4.0 - - + +
159D GLN* 3.5 42.0 - - + +
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Residues in contact with GLU 130 (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 GLU 3.4 0.8 - - - -
129D VAL* 1.3 81.2 - - - +
131D ARG* 1.3 65.1 + - + +
133D ARG* 3.6 26.2 + - - +
134D PHE* 3.1 24.3 + - - +
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Residues in contact with ARG 131 (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 GLU* 3.1 44.6 + - + +
130D GLU* 1.3 78.0 - - + +
132D ALA* 1.3 53.2 + - - +
134D PHE* 3.0 9.6 + - - +
135D ILE* 2.7 51.5 + - + +
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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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124D VAL* 3.6 30.0 - - + +
125D ASP 3.7 9.4 + - - +
126D PHE* 4.1 22.9 - - + -
128D GLU 3.0 13.6 + - - +
129D VAL* 3.7 3.8 - - - +
131D ARG* 1.3 79.0 - - - +
133D ARG* 1.3 58.2 + - - +
135D ILE* 3.2 5.9 + - - +
136D ILE* 3.0 33.8 + - - +
157D VAL* 4.8 1.3 - - + -
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Residues in contact with ARG 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 VAL* 3.0 36.5 + - - +
130D GLU* 3.6 23.9 + - - +
132D ALA* 1.3 76.2 - - - +
134D PHE* 1.3 61.2 + - - +
136D ILE* 3.6 11.8 + - - +
137D ASN* 2.7 37.0 + - - +
154D THR* 3.1 38.8 + - - +
155D GLY* 3.4 23.8 + - - -
157D VAL* 2.7 32.9 + - + +
158D GLN* 4.4 4.6 - - - +
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Residues in contact with PHE 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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130D GLU 3.1 20.5 + - - +
131D ARG* 3.0 10.7 + - - +
133D ARG* 1.3 73.4 - - - +
135D ILE* 1.3 68.5 + - + +
137D ASN* 3.0 12.1 + - + +
138D ASP* 2.8 59.4 + - + +
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Residues in contact with ILE 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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98D PHE* 4.3 16.4 - - + -
101D ARG* 5.9 4.0 - - - +
123D GLN 6.0 0.7 - - - +
124D VAL* 4.4 18.2 - - + -
131D ARG* 2.7 35.2 + - + +
132D ALA* 3.3 13.5 - - - +
134D PHE* 1.3 86.2 - - + +
136D ILE* 1.3 55.5 + - - +
138D ASP* 3.9 5.0 - - - +
139D TRP* 3.1 27.3 + - + +
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Residues in contact with ILE 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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98D PHE* 3.8 47.9 - - + -
124D VAL* 5.1 1.3 - - + -
126D PHE* 4.3 21.3 - - + -
132D ALA* 3.0 23.6 + - + +
133D ARG* 3.8 10.3 - - - +
134D PHE 3.1 0.4 - - - -
135D ILE* 1.3 76.5 - - + +
137D ASN* 1.3 64.4 + - - +
139D TRP* 3.5 4.0 + - - +
140D VAL* 3.1 21.2 + - + +
151D LEU* 4.8 3.1 - - + -
154D THR* 4.3 15.3 - - + -
157D VAL* 4.9 7.6 - - + -
164D VAL* 4.8 11.0 - - + -
166D VAL* 4.2 21.3 - - + -
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Residues in contact with ASN 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 ARG* 2.7 25.3 + - - +
134D PHE* 3.0 11.2 + - + +
136D ILE* 1.3 74.4 - - - +
138D ASP* 1.3 66.2 + - - +
140D VAL* 3.0 17.4 + - - +
141D LYS* 3.0 11.3 + - - +
149D SER 3.2 21.6 - - - +
150D HIS* 4.3 14.2 + - - +
151D LEU* 2.8 39.0 + - - +
154D THR* 3.6 16.6 + - - +
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Residues in contact with ASP 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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134D PHE* 2.8 41.9 + - + +
135D ILE* 3.9 7.0 - - - +
137D ASN* 1.3 78.2 - - - +
139D TRP* 1.3 56.1 + - - +
141D LYS* 3.3 24.4 + - - +
142D THR* 2.9 48.3 + - - +
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Residues in contact with TRP 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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94D THR* 2.9 25.6 + - + -
95D ASP 3.9 5.8 + - - -
96D ALA* 3.8 26.2 - - + +
98D PHE* 4.1 15.7 - + + -
122D LYS* 3.3 45.3 - - + -
135D ILE* 3.1 19.1 + - + +
136D ILE 3.6 6.1 - - - +
137D ASN 3.2 0.4 - - - -
138D ASP* 1.3 76.7 + - - +
140D VAL* 1.3 65.1 + - + +
142D THR* 3.0 17.5 + - - -
143D HIS* 3.0 60.4 + + - +
166D VAL* 6.1 0.4 - - + -
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Residues in contact with VAL 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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94D THR* 4.1 10.1 - - + -
136D ILE 3.1 18.2 - - - +
137D ASN* 3.0 7.8 + - - +
139D TRP* 1.3 78.3 - - + +
141D LYS* 1.3 58.8 + - - +
143D HIS 3.2 1.6 + - - -
144D THR* 2.5 37.0 + - + +
148D ILE* 3.2 37.9 - - + +
149D SER 4.9 0.7 - - - +
151D LEU* 4.1 13.7 - - + -
166D VAL* 4.1 24.9 - - + -
168D ALA* 3.6 20.0 - - + -
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Residues in contact with LYS 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 ASN 3.0 12.3 + - - +
138D ASP* 3.5 26.5 + - - +
140D VAL* 1.3 76.4 - - - +
142D THR* 1.3 64.4 + - + +
144D THR 3.3 0.3 + - - -
146D GLY* 2.6 42.8 + - - +
148D ILE 3.0 13.8 + - - -
149D SER* 3.9 23.1 - - - +
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Residues in contact with THR 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 ASP* 2.9 31.9 + - - +
139D TRP* 3.0 8.8 + - - -
141D LYS* 1.3 82.2 - - + +
143D HIS* 1.3 84.8 + - - +
144D THR 3.3 3.8 + - - -
145D LYS* 3.5 11.6 + - - +
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Residues in contact with HIS 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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92D SER* 4.8 1.3 - - - -
93D THR 3.1 24.9 + - - +
94D THR* 3.2 25.4 - - - +
139D TRP* 3.0 59.6 + + - +
140D VAL 3.5 2.2 - - - -
142D THR* 1.3 102.6 + - - +
144D THR* 1.3 58.6 + - - +
145D LYS 3.5 0.9 - - - -
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Residues in contact with THR 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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92D SER* 3.5 24.7 + - - +
94D THR* 4.0 9.0 - - + +
140D VAL* 2.5 28.5 + - + +
141D LYS 3.4 2.9 + - - -
142D THR 3.3 0.2 - - - -
143D HIS* 1.3 81.4 - - - +
145D LYS* 1.3 58.5 + - - +
146D GLY 2.9 4.0 - - - -
147D MET* 2.7 34.4 + - - +
148D ILE* 2.9 42.0 + - + -
168D ALA 3.9 21.3 - - - +
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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
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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