Contacts of the helix formed by residues 120 - 135 (chain D) in PDB entry 1KD1
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 ASP 120 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2821A C 4.6 1.4 + - - -
119D HIS* 1.3 83.3 + - - +
121D PRO* 1.3 62.7 - - - +
122D ASP* 3.4 8.5 + - - +
123D ALA* 2.5 49.1 + - + +
124D ALA* 3.3 15.1 + - - +
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Residues in contact with PRO 121 (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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100D VAL* 4.0 20.6 - - + +
101D TRP 4.0 10.3 - - - +
103D ASP* 5.2 9.2 - - - +
119D HIS* 3.0 36.8 - - + +
120D ASP* 1.3 82.0 - - - +
122D ASP* 1.3 66.7 + - - +
124D ALA* 3.2 5.0 + - - +
125D GLU* 2.9 28.9 + - - +
183D GLU* 5.2 8.1 - - - +
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Residues in contact with ASP 122 (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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120D ASP* 3.3 5.7 - - - +
121D PRO* 1.3 85.3 - - - +
123D ALA* 1.3 52.5 + - - +
125D GLU* 2.9 12.9 + - - +
126D GLU* 2.6 38.6 + - - +
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Residues in contact with ALA 123 (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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120D ASP* 2.5 36.7 + - + +
122D ASP* 1.3 72.8 - - - +
124D ALA* 1.3 57.5 + - - +
126D GLU* 3.1 12.3 + - - +
127D GLN* 2.8 31.0 + - - +
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Residues in contact with ALA 124 (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 THR* 4.1 21.3 + - + -
99D GLU 3.3 28.5 - - - +
100D VAL* 3.6 7.6 - - + -
119D HIS* 4.5 2.5 - - + -
120D ASP 3.3 8.5 + - - +
121D PRO 3.2 10.0 + - - +
122D ASP 3.1 0.2 - - - -
123D ALA* 1.3 77.7 - - - +
125D GLU* 1.3 66.2 + - - +
127D GLN* 3.1 4.7 + - - +
128D ILE* 3.0 28.8 + - + +
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Residues in contact with GLU 125 (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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100D VAL* 3.8 11.8 - - + +
121D PRO 2.9 14.0 + - - +
122D ASP* 3.2 14.2 - - - +
124D ALA* 1.3 77.4 - - - +
126D GLU* 1.3 64.0 + - - +
128D ILE* 3.3 7.5 + - + +
129D ARG* 2.6 66.2 + - + +
175D LEU* 5.5 0.7 - - + -
179D LEU* 3.4 26.8 - - + +
183D GLU* 4.7 9.5 - - - +
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Residues in contact with GLU 126 (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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122D ASP 2.6 17.3 + - - +
123D ALA* 3.3 14.6 - - - +
125D GLU* 1.3 72.9 - - - +
127D GLN* 1.3 64.6 + - - +
129D ARG* 2.9 9.9 + - + +
130D ASP* 2.8 42.2 + - - +
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Residues in contact with GLN 127 (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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2820A A 4.5 2.1 + - - -
97D LEU* 3.7 24.2 + - + +
98D THR* 2.7 39.4 + - - +
123D ALA 2.8 16.3 + - - +
124D ALA* 3.5 8.7 - - - +
126D GLU* 1.3 72.1 - - - +
128D ILE* 1.3 58.0 + - - +
130D ASP* 3.4 11.0 + - - +
131D ALA* 3.0 26.3 + - - +
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Residues in contact with ILE 128 (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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84D LEU* 3.7 24.0 - - + +
86D ALA* 3.3 34.8 - - + +
97D LEU* 4.5 4.0 - - + -
98D THR* 4.3 15.5 - - - +
100D VAL* 4.3 11.9 - - + -
124D ALA 3.0 14.9 + - - +
125D GLU* 3.5 9.4 - - + +
127D GLN* 1.3 75.2 - - - +
129D ARG* 1.3 60.4 + - + +
131D ALA* 3.2 8.4 + - - +
132D HIS* 2.9 26.0 + - - +
137D LEU* 4.4 10.2 - - + +
140D LEU* 5.0 2.0 - - + -
175D LEU* 3.9 27.4 - - + -
179D LEU* 6.0 0.7 - - + -
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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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125D GLU* 2.6 61.6 + - + +
126D GLU* 2.9 7.3 + - + +
128D ILE* 1.3 74.1 - - + +
130D ASP* 1.3 62.0 + - - +
132D HIS* 3.3 10.5 + - + +
133D GLU* 2.9 36.2 + - + +
172D SER* 5.1 1.2 + - - +
175D LEU* 3.7 22.9 - - + +
176D ASP* 2.6 33.3 + - - -
179D LEU* 3.3 12.9 - - - +
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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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126D GLU* 2.8 42.1 + - - +
127D GLN* 3.7 9.7 - - - +
129D ARG* 1.3 73.7 - - - +
131D ALA* 1.3 67.2 + - - +
133D GLU* 2.9 33.3 + - - +
134D ALA* 2.9 14.3 + - - +
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Residues in contact with ALA 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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88D GLU* 5.7 0.9 - - + -
97D LEU* 3.5 25.6 - - + -
127D GLN 3.0 14.9 + - - +
128D ILE 3.4 8.7 - - - +
130D ASP* 1.3 76.9 - - - +
132D HIS* 1.3 56.8 + - - +
134D ALA* 3.1 8.2 + - - +
135D GLY 2.8 23.9 + - - -
136D ASP* 3.1 17.5 + - + +
137D LEU* 4.3 12.1 - - + +
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Residues in contact with HIS 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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128D ILE 2.9 16.3 + - - +
129D ARG* 3.6 9.6 - - - +
130D ASP 3.1 0.2 - - - -
131D ALA* 1.3 79.0 - - - +
133D GLU* 1.3 62.0 + - + +
135D GLY* 3.1 13.3 + - - +
137D LEU* 3.6 30.4 - - + +
171D VAL* 3.0 29.9 - - + +
172D SER* 2.9 33.0 + - - -
175D LEU* 4.8 8.7 - - + -
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Residues in contact with GLU 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* 2.9 25.2 + - + +
130D ASP* 2.9 29.0 + - - +
132D HIS* 1.3 78.0 - - + +
134D ALA* 1.3 61.7 + - - +
135D GLY* 3.4 0.5 + - - -
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Residues in contact with ALA 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 10.9 + - - +
131D ALA* 3.6 8.3 - - - +
133D GLU* 1.3 77.5 - - - +
135D GLY* 1.3 61.5 + - - +
136D ASP* 3.4 23.6 - - - +
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Residues in contact with GLY 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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89D ASP* 5.1 2.8 - - - +
131D ALA 2.8 6.9 + - - -
132D HIS* 3.1 16.3 + - - -
133D GLU 3.2 0.6 - - - -
134D ALA* 1.3 80.7 - - - +
136D ASP* 1.3 61.4 + - - +
137D LEU 3.5 2.9 - - - -
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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