Contacts of the helix formed by residues 132 - 146 (chain D) in PDB entry 6P7B
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 132 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D ASP* 3.2 9.3 - - - +
12D ASN* 3.2 28.5 - - - +
14D ALA* 3.8 10.5 - - + -
34D LYS* 3.1 33.3 - - - +
127D TYR* 5.7 0.2 - - - -
129D LYS* 3.1 35.6 - - - +
130D LEU 3.6 1.1 + - - -
131D ASP* 1.3 75.9 + - - +
133D ILE* 1.3 80.0 + - - +
134D ALA 3.2 1.1 - - - +
135D ASN 3.4 0.3 + - - -
136D SER* 3.0 28.8 + - - -
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Residues in contact with ILE 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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14D ALA* 4.9 3.6 - - + -
32D ILE* 4.4 22.4 - - + -
33D GLU 5.6 0.4 - - - +
34D LYS* 5.2 2.2 - - + +
109D PHE* 3.8 27.1 - - + -
123D ILE* 6.5 0.7 - - + -
127D TYR* 5.0 26.2 - - + +
128D THR* 5.9 0.7 - - - -
129D LYS* 4.8 19.1 - - + +
130D LEU 5.7 1.1 - - - +
132D ASP* 1.3 93.4 - - - +
134D ALA* 1.3 60.5 + - + +
136D SER* 3.6 7.0 - - - -
137D PHE* 2.9 36.1 + - + +
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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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101D ARG* 5.9 4.7 - - + -
105D SER* 3.2 29.6 - - - +
109D PHE* 3.7 12.1 - - + -
130D LEU 4.8 5.4 - - - +
131D ASP* 4.7 13.5 - - - -
132D ASP 3.2 1.4 - - - +
133D ILE* 1.3 82.3 - - + +
135D ASN* 1.3 59.8 + - - +
138D ASN* 2.7 42.6 + - - +
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Residues in contact with ASN 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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7D ASP* 3.3 29.9 + - + +
11D LYS* 5.1 3.4 - - - +
60D GLU* 4.6 12.1 + - - +
93D PHE* 3.8 34.4 - - - +
131D ASP* 2.9 33.8 + - - +
132D ASP 3.4 2.6 + - - -
134D ALA* 1.3 81.0 - - - +
136D SER* 1.3 58.4 + - - +
138D ASN* 4.0 3.1 + - - +
139D LEU* 2.9 39.5 + - + +
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Residues in contact with SER 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D SER* 2.9 33.5 + - - -
6D VAL 4.6 2.7 - - - -
7D ASP* 3.7 25.9 - - - +
14D ALA* 4.0 10.3 - - - +
15D TYR* 4.6 1.1 - - - -
16D ALA* 4.8 1.6 - - - -
32D ILE* 3.8 14.0 - - - +
132D ASP 3.0 18.4 + - - -
133D ILE* 3.3 9.4 + - - -
135D ASN* 1.3 78.7 - - - +
137D PHE* 1.3 70.2 + - - +
139D LEU* 3.4 2.0 + - - +
140D GLY 3.0 11.1 + - - -
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Residues in contact with PHE 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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5D SER* 4.7 2.5 - - - -
16D ALA* 5.0 3.6 - - + -
18D PHE* 3.5 31.6 - + - -
29D LEU* 3.8 18.8 - - + -
32D ILE* 5.2 9.4 - - + -
108D VAL* 3.4 29.4 - - + -
109D PHE* 3.4 28.7 - + + -
112D LYS 4.8 4.7 - - - -
113D ILE* 3.8 23.6 - - + -
116D TYR* 5.4 3.4 - + - -
133D ILE* 2.9 19.6 + - + +
136D SER* 1.3 80.2 + - - +
138D ASN* 1.3 57.5 + - - +
140D GLY* 3.4 0.9 + - - -
141D LEU* 2.8 55.5 + - + +
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Residues in contact with ASN 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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104D GLN* 4.5 17.9 - - - +
105D SER* 4.3 8.5 + - - +
108D VAL* 3.5 29.3 - - - +
109D PHE* 4.7 1.9 - - - -
134D ALA* 2.7 43.0 + - - +
135D ASN* 4.0 3.7 + - - +
137D PHE* 1.3 74.6 - - - +
139D LEU* 1.3 60.2 + - - +
141D LEU* 4.1 3.3 - - - +
142D SER* 2.9 33.8 + - - -
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Residues in contact with LEU 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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5D SER* 4.5 2.7 - - - -
6D VAL 4.1 13.2 - - - +
7D ASP* 5.3 1.3 - - - -
58D ILE* 4.1 14.9 - - + +
59D LEU* 4.0 5.4 - - - -
60D GLU* 3.7 45.3 - - + +
89D ARG* 4.0 32.1 + - + +
90D ASN 5.4 2.7 - - - +
92D THR* 5.0 12.3 - - + +
135D ASN* 2.9 27.4 + - + +
136D SER 3.7 3.6 - - - +
138D ASN* 1.3 77.5 - - - +
140D GLY* 1.3 62.9 + - - +
142D SER* 3.4 3.9 + - - -
143D TYR* 3.0 24.1 + - - +
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Residues in contact with GLY 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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3D ILE* 5.3 2.2 - - - -
5D SER* 3.5 23.6 - - - -
18D PHE* 4.2 10.8 - - - -
58D ILE* 5.1 2.9 - - - -
136D SER 3.0 11.5 + - - -
137D PHE 3.8 1.3 - - - -
139D LEU* 1.3 77.8 - - - +
141D LEU* 1.3 57.2 + - - +
143D TYR* 3.3 7.2 + - - +
144D MET* 2.9 35.6 + - - +
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Residues in contact with LEU 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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18D PHE* 4.3 4.0 - - + -
27D ILE* 4.9 0.9 - - + -
108D VAL* 4.0 22.0 - - + -
112D LYS* 3.7 28.9 - - + +
116D TYR* 4.5 10.8 - - + -
137D PHE* 2.8 55.8 + - + +
138D ASN* 4.1 3.8 - - - +
140D GLY* 1.3 72.3 - - - +
142D SER* 1.3 57.3 + - - +
144D MET* 3.3 18.0 + - + +
145D GLU* 2.8 56.1 + - + +
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Residues in contact with SER 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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89D ARG* 3.1 17.1 + - - -
92D THR* 5.9 3.3 - - - +
138D ASN 2.9 20.5 + - - -
139D LEU* 3.8 2.7 - - - -
141D LEU* 1.3 74.7 - - - +
143D TYR* 1.3 59.9 + - - +
145D GLU* 4.0 4.3 - - - +
146D SER* 2.9 33.3 + - - -
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Residues in contact with TYR 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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3D ILE* 3.6 34.1 - - + -
56D VAL* 4.2 18.2 - - + +
58D ILE* 3.9 34.8 - - + -
87D ILE* 4.9 8.5 - - + +
89D ARG* 3.2 32.6 - - - +
139D LEU 3.0 17.8 + - - +
140D GLY 3.6 3.4 - - - +
142D SER* 1.3 76.8 - - - +
144D MET* 1.3 58.1 + - + +
146D SER* 3.1 3.6 + - - -
147D LEU* 3.0 50.9 + - + +
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Residues in contact with MET 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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3D ILE* 3.6 22.2 - - + -
18D PHE* 3.8 29.8 - - + -
20D TYR* 3.4 52.3 + - + -
27D ILE* 3.4 40.2 - - + -
140D GLY 2.9 20.2 + - - +
141D LEU* 3.8 13.0 - - + +
143D TYR* 1.3 76.4 - - + +
145D GLU* 1.3 64.9 + - + +
147D LEU* 3.2 22.6 + - - +
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Residues in contact with GLU 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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27D ILE* 4.3 12.2 - - - +
112D LYS* 3.3 35.1 + - - +
116D TYR* 4.5 0.5 + - - -
141D LEU* 2.8 43.7 + - + +
142D SER* 4.0 4.7 - - - +
144D MET* 1.3 73.5 - - - +
146D SER* 1.3 59.6 + - - +
147D LEU* 3.1 3.7 + - - -
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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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89D ARG* 3.8 11.0 + - - -
142D SER* 2.9 25.8 + - - -
143D TYR* 3.1 11.8 + - - -
145D GLU* 1.3 75.0 - - - +
147D LEU* 1.3 61.1 + - - +
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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