Contacts of the strand formed by residues 145 - 155 (chain D) in PDB entry 2AMT
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 145 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D HIS 3.3 12.3 - - - -
12D PHE* 3.4 17.6 - - - -
99D ILE 4.6 0.3 - - - +
100D ALA* 5.0 1.2 - - - -
102D ALA* 5.5 0.3 - - - +
139D PHE* 3.5 5.6 + - - -
140D THR* 3.6 25.0 - - - +
144D GLU* 1.3 81.5 - - - +
146D ILE* 1.3 66.6 + - - +
147D ALA 4.2 0.2 - - - -
137E LEU* 4.0 9.1 - - - +
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Residues in contact with ILE 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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9D VAL* 3.4 3.3 - - - +
10D HIS 3.0 29.6 + - - -
12D PHE* 3.4 32.1 - - + -
18D ILE* 4.7 2.0 - - + -
20D ILE* 4.7 4.5 - - + -
31D LEU* 3.9 19.1 - - + -
39D VAL* 3.4 26.5 - - + +
98D ILE* 3.9 11.4 - - + -
99D ILE 3.6 7.9 - - - +
100D ALA* 3.2 29.2 - - + -
102D ALA* 3.4 9.6 - - + -
103D PRO* 4.4 1.3 - - + -
105D MET* 4.3 9.0 - - + -
139D PHE* 5.2 0.2 - - - -
140D THR* 4.4 0.4 - - - -
145D GLY* 1.3 73.5 - - - +
147D ALA* 1.3 72.2 + - - +
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Residues in contact with ALA 147 (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 PHE* 4.2 13.7 - - + -
8D ASP 3.4 5.8 - - - +
9D VAL* 3.8 18.8 - - + -
39D VAL* 4.7 0.2 - - - -
98D ILE 3.9 0.2 - - - -
99D ILE* 2.8 43.4 + - + +
139D PHE* 4.4 3.8 - - + -
140D THR* 3.7 19.5 - - + +
146D ILE* 1.3 80.6 - - - +
148D CYS* 1.3 62.2 + - - +
8903D GPP 4.8 2.9 - - + -
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Residues in contact with CYS 148 (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 PHE* 3.3 9.9 - - - -
8D ASP 2.8 34.3 + - - +
39D VAL* 3.6 27.8 - - + +
40D ALA* 3.5 18.8 - - - +
43D ALA* 3.5 7.2 - - + +
96D VAL* 3.4 33.0 - - - -
97D THR 3.5 12.1 - - - -
98D ILE* 4.2 4.9 - - + -
99D ILE* 4.6 1.6 - - - -
147D ALA* 1.3 77.9 - - - +
149D GLU* 1.3 65.0 + - - +
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Residues in contact with GLU 149 (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 HIS* 3.1 22.8 + - + +
6D GLY 3.4 3.1 - - - +
7D PHE* 3.6 5.6 - - + -
43D ALA* 4.6 0.2 - - - -
95D ASP 4.7 0.2 - - - -
96D VAL* 3.6 0.7 - - - -
97D THR* 2.7 43.0 + - - +
99D ILE* 4.3 6.5 - - + +
148D CYS* 1.3 77.9 - - - +
150D ALA* 1.3 60.9 + - - +
8903D GPP 3.3 21.7 - - - +
149E GLU* 2.8 40.3 - - - +
5F HIS* 2.8 45.1 + - + +
149F GLU* 3.0 4.6 - - - +
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Residues in contact with ALA 150 (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 HIS* 3.4 5.3 - - - -
6D GLY 2.7 35.6 + - - +
43D ALA* 3.6 30.7 - - + +
44D LEU* 3.8 12.6 - - + +
47D ALA* 3.4 4.3 - - + +
95D ASP 3.3 11.4 - - - +
96D VAL* 4.4 10.8 - - + -
149D GLU* 1.3 78.0 - - - +
151D VAL* 1.3 65.0 + - - +
5F HIS* 5.5 0.7 - - - -
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Residues in contact with VAL 151 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D ILE* 4.6 1.8 - - + -
4D GLY 3.2 11.7 - - - +
5D HIS* 4.1 15.3 - - + -
44D LEU* 5.3 0.2 - - - +
47D ALA* 4.2 1.3 - - - -
94D VAL* 3.5 3.8 - - - +
95D ASP* 3.0 43.0 + - + +
150D ALA* 1.3 80.1 - - - +
152D ALA* 1.3 61.2 + - - +
151E VAL* 4.4 12.8 - - + -
3F ILE* 3.7 28.6 - - + +
4F GLY 4.1 0.2 - - - -
5F HIS* 3.5 38.3 - - + +
151F VAL* 4.6 6.3 - - + -
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Residues in contact with ALA 152 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D ARG 3.5 0.9 - - - +
3D ILE* 3.4 7.4 - - - +
4D GLY 2.9 30.6 + - - -
44D LEU* 5.3 0.4 - - + -
47D ALA* 3.8 26.7 - - + +
48D LEU* 3.9 17.3 - - + -
51D ALA* 4.3 2.4 - - + +
93D ASN 3.6 5.2 - - - -
94D VAL* 3.9 17.9 - - + -
151D VAL* 1.3 75.8 - - - +
153D LEU* 1.3 60.9 + - - +
154D LEU* 4.1 0.4 - - + -
3F ILE* 4.0 3.8 - - - -
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Residues in contact with LEU 153 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MET 4.0 15.3 - - - +
2D ARG 3.4 20.0 - - - +
3D ILE* 3.9 17.5 - - + -
91D LEU* 4.2 1.9 - - - +
92D GLY* 2.8 27.1 + - - -
93D ASN* 2.9 24.8 + - - +
152D ALA* 1.3 72.7 - - - +
154D LEU* 1.3 65.4 + - - +
155D ILE* 6.1 0.9 - - + -
153E LEU* 4.0 14.4 - - + -
1F MET* 3.4 37.0 - - + +
2F ARG* 4.0 1.3 - - - -
3F ILE* 3.7 18.6 - - + +
153F LEU* 4.2 12.8 - - + -
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Residues in contact with LEU 154 (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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1D MET 2.7 29.1 + - - -
2D ARG* 2.8 21.9 + - + -
48D LEU* 3.7 25.6 - - + +
51D ALA* 3.6 26.5 - - + -
52D ALA 3.8 7.4 - - - +
81D TRP* 3.5 31.4 - - + -
84D ILE* 3.7 21.8 - - + -
89D TYR* 3.8 22.2 - - + -
90D THR 3.5 10.5 - - - +
91D LEU* 4.2 2.0 - - + -
152D ALA 5.5 0.2 - - - -
153D LEU* 1.3 78.6 - - - +
155D ILE* 1.3 58.2 + - - +
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Residues in contact with ILE 155 (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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1D MET* 4.1 14.6 - - + +
2D ARG* 5.6 0.2 - - - -
89D TYR* 3.4 6.7 - - - -
90D THR* 3.0 38.0 + - - +
91D LEU 3.8 8.7 - - - +
92D GLY* 3.8 26.5 - - - +
153D LEU* 6.1 0.4 - - + -
154D LEU* 1.3 79.0 - - - +
156D LYS* 1.3 88.1 + - + +
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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