Contacts of the helix formed by residues 128 - 145 (chain D) in PDB entry 6AH0
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 PRO 128 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D ASP 4.0 0.2 - - - -
127D GLN* 1.3 70.4 - - - +
129D ARG* 1.3 70.5 + - - +
130D ASP 3.1 2.9 - - - -
131D ILE* 2.6 17.7 + - - -
132D LEU 3.2 5.6 + - - -
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Residues in contact with ARG 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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127D GLN 3.4 4.8 + - - -
128D PRO* 1.3 68.0 - - - +
130D ASP* 1.3 52.1 + - - +
132D LEU* 2.6 26.1 + - - +
133D CYS* 3.0 11.4 + - - -
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Residues in contact with ASP 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 PRO 2.8 3.2 + - - -
129D ARG* 1.3 70.8 - - - +
131D ILE* 1.3 57.3 + - - +
133D CYS* 5.6 0.2 - - - +
134D GLY* 2.9 28.9 + - - -
697D ALA* 4.6 10.5 + - - +
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Residues in contact with ILE 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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127D GLN* 5.6 1.6 - - - +
128D PRO 2.6 17.0 + - - -
130D ASP* 1.3 70.0 - - - +
132D LEU* 1.3 63.3 + - - +
135D ALA* 3.0 19.6 + - - -
697D ALA* 4.4 19.2 - - - +
698D ILE* 5.1 2.6 + - - +
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Residues in contact with LEU 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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127D GLN* 4.9 6.6 + - - +
128D PRO 3.2 6.0 + - - -
129D ARG* 2.6 15.1 + - - +
131D ILE* 1.3 72.8 - - - +
133D CYS* 1.3 61.2 + - - +
135D ALA* 3.6 1.0 - - - -
136D ALA* 3.0 17.8 + - - -
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Residues in contact with CYS 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 ARG 3.0 10.7 + - - -
130D ASP* 5.6 0.2 - - - +
132D LEU* 1.3 72.1 - - - +
134D GLY* 1.3 67.4 + - - +
136D ALA* 3.0 4.4 + - - +
137D ASP* 3.0 19.6 + - - -
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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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130D ASP 2.9 18.6 + - - -
131D ILE* 4.2 0.4 - - - -
133D CYS* 1.3 77.7 - - - +
135D ALA* 1.3 61.9 + - - +
137D ASP* 3.1 3.2 + - - -
138D GLU* 3.0 17.0 + - - -
696D LYS* 6.1 1.3 - - - -
697D ALA 5.3 3.6 - - - -
698D ILE* 5.2 9.2 - - - -
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Residues in contact with ALA 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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131D ILE 3.0 17.4 + - - -
132D LEU 3.2 3.8 + - - -
134D GLY* 1.3 74.0 - - - +
136D ALA* 1.3 63.7 + - - +
138D GLU* 2.8 13.8 + - - +
139D VAL 3.0 12.6 + - - -
698D ILE* 5.0 8.7 - - - +
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Residues in contact with ALA 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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117D LEU* 6.5 1.8 - - - +
132D LEU 3.0 10.1 + - - -
133D CYS* 3.0 9.3 + - - +
135D ALA* 1.3 75.0 - - - +
137D ASP* 1.3 62.4 + - - +
139D VAL* 4.0 0.2 - - - -
140D LEU* 3.0 24.3 + - - -
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Residues in contact with ASP 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 CYS 3.0 12.0 + - - -
134D GLY* 3.1 4.9 + - - -
136D ALA* 1.3 73.7 - - - +
138D GLU* 1.3 65.7 + - - +
140D LEU* 4.1 0.6 - - - +
141D ALA* 2.9 18.4 + - - -
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Residues in contact with GLU 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 GLY 3.0 8.9 + - - -
135D ALA* 2.8 14.8 + - - +
137D ASP* 1.3 69.5 - - - +
139D VAL* 1.3 64.6 + - - +
141D ALA* 2.7 14.0 + - - -
142D VAL* 2.9 9.9 + - - -
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Residues in contact with VAL 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 ALA 3.0 13.7 + - - -
136D ALA* 4.0 0.9 - - - +
138D GLU* 1.3 68.2 - - - +
140D LEU* 1.3 64.7 + - - +
142D VAL* 2.7 14.2 + - - +
143D LEU* 3.0 13.2 + - - -
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Residues in contact with LEU 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 ALA 3.0 15.9 + - - -
137D ASP 4.1 0.7 - - - -
139D VAL* 1.3 72.9 - - - +
141D ALA* 1.3 61.5 + - - +
143D LEU* 5.6 0.2 - - - +
144D LYS* 3.2 23.3 + - - +
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Residues in contact with ALA 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 ASP 2.9 11.9 + - - -
138D GLU 2.7 15.7 + - - -
140D LEU* 1.3 74.8 - - - +
142D VAL* 1.3 61.0 + - - +
144D LYS* 3.9 4.0 + - - -
145D ASN 4.4 4.2 + - - -
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Residues in contact with VAL 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 GLU 2.9 7.7 + - - -
139D VAL* 2.7 14.2 + - - +
141D ALA* 1.3 72.6 - - - +
143D LEU* 1.3 65.2 + - - +
145D ASN* 3.9 5.9 + - - +
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Residues in contact with LEU 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 VAL 3.0 11.9 + - - -
140D LEU* 5.6 0.4 - - - +
142D VAL* 1.3 77.1 - - - +
144D LYS* 1.3 55.5 + - - +
145D ASN 2.8 20.8 + - - +
146D GLU* 3.5 5.0 + - - -
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Residues in contact with LYS 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 LEU 3.2 18.5 + - - -
141D ALA 4.6 1.1 - - - -
142D VAL 3.3 1.6 - - - -
143D LEU* 1.3 75.6 - - - +
145D ASN* 1.3 56.2 + - - +
146D GLU* 2.7 8.9 + - - -
176D GLY 5.6 6.5 - - - -
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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
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141D ALA 4.4 4.8 + - - -
142D VAL 3.9 7.3 + - - +
143D LEU 2.8 7.0 + - - +
144D LYS* 1.3 72.1 - - - +
146D GLU* 1.3 59.9 + - - +
147D LYS 3.2 3.6 - - - +
148D LEU* 3.0 20.7 + - - +
149D ARG 3.2 7.6 + - - +
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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