Contacts of the strand formed by residues 145 - 155 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E HIS 3.2 13.5 - - - -
12E PHE* 3.5 14.3 - - - -
99E ILE 4.7 0.2 - - - +
100E ALA* 5.2 1.2 - - - -
101E GLN 5.5 0.2 + - - -
139E PHE* 3.6 4.8 + - - -
140E THR* 3.5 26.9 - - - +
144E GLU* 1.3 81.2 - - - +
146E ILE* 1.3 68.3 + - - +
137F LEU* 3.8 10.9 - - - +
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Residues in contact with ILE 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 3.3 5.7 - - - +
10E HIS 3.0 31.2 + - - +
12E PHE* 3.5 32.1 - - + -
18E ILE* 3.8 25.6 - - + -
20E ILE* 4.3 6.3 - - + -
31E LEU* 4.8 7.4 - - + -
39E VAL* 3.5 24.0 - - + +
98E ILE* 3.9 8.3 - - + -
99E ILE 3.4 9.4 - - - +
100E ALA* 3.8 17.0 - - + -
102E ALA 4.1 2.5 - - - +
105E MET* 3.8 14.8 - - + -
140E THR* 4.3 0.4 - - - -
145E GLY* 1.3 74.8 - - - +
147E ALA* 1.3 72.4 + - - +
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Residues in contact with ALA 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8903D GPP 5.0 2.7 - - + -
7E PHE* 4.1 9.4 - - + -
8E ASP 3.3 5.8 - - - +
9E VAL* 3.8 17.9 - - + -
39E VAL* 4.0 1.3 - - - -
98E ILE* 3.9 0.2 - - - -
99E ILE* 2.7 57.5 + - + +
139E PHE* 4.3 3.6 - - + -
140E THR* 3.7 14.5 - - + +
146E ILE* 1.3 79.7 - - - +
148E CYS* 1.3 59.7 + - - +
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Residues in contact with CYS 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PHE* 3.3 7.7 - - - -
8E ASP 2.9 30.5 + - - -
39E VAL* 3.6 28.3 - - + +
40E ALA* 3.4 26.2 - - - -
43E ALA* 3.5 7.4 - - - +
96E VAL* 3.4 24.7 - - - -
97E THR 3.3 13.9 - - - -
98E ILE* 4.1 3.6 - - - -
99E ILE* 4.6 0.9 - - - -
147E ALA* 1.3 77.6 - - - +
149E GLU* 1.3 66.5 + - - +
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Residues in contact with GLU 149 (chain E).
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 26.1 + - + +
7D PHE* 4.1 5.9 - - - -
149D GLU* 2.8 35.9 - - - +
8903D GPP 4.1 6.9 - - - +
5E HIS* 2.7 31.3 + - - +
6E GLY 3.4 3.4 - - - -
7E PHE* 3.6 19.2 - - + -
96E VAL* 3.5 1.0 - - - -
97E THR* 2.7 41.5 + - - +
99E ILE* 4.0 13.4 - - + +
148E CYS* 1.3 77.2 - - - +
150E ALA* 1.3 60.8 + - - +
149F GLU* 2.9 10.6 - - - +
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Residues in contact with ALA 150 (chain E).
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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5D HIS* 5.4 1.1 - - - -
5E HIS* 3.4 6.0 + - - -
6E GLY 2.8 34.8 + - - +
43E ALA* 3.6 30.3 - - + +
44E LEU* 3.7 14.1 - - + +
47E ALA* 3.6 4.0 - - + +
95E ASP 3.3 10.8 - - - +
96E VAL* 4.2 11.2 - - + -
149E GLU* 1.3 76.2 - - - +
151E VAL* 1.3 63.5 + - - +
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Residues in contact with VAL 151 (chain E).
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* 3.7 29.3 - - + +
4D GLY 3.9 0.2 - - - -
5D HIS* 3.6 41.5 - - + +
151D VAL* 4.4 13.0 - - + -
3E ILE* 4.8 1.8 - - + -
4E GLY 3.3 9.9 - - - +
5E HIS* 4.2 11.0 - - + -
44E LEU* 5.2 0.5 - - - +
47E ALA* 4.2 1.3 - - - -
93E ASN 4.4 0.2 - - - +
94E VAL* 3.7 3.5 - - - +
95E ASP* 3.0 48.6 + - + +
150E ALA* 1.3 79.9 - - - +
152E ALA* 1.3 62.8 + - - +
151F VAL* 4.7 6.5 - - + -
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Residues in contact with ALA 152 (chain E).
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* 4.0 4.3 - - - -
2E ARG 3.7 0.6 - - - +
3E ILE* 3.3 8.3 - - - +
4E GLY 2.9 31.0 + - - -
44E LEU* 5.4 0.2 - - + -
47E ALA* 3.8 25.4 - - + +
48E LEU* 3.8 31.2 - - + -
51E ALA* 4.2 3.3 - - + +
93E ASN 3.8 4.9 - - - -
94E VAL* 4.2 5.4 - - + -
151E VAL* 1.3 75.5 - - - +
153E LEU* 1.3 60.6 + - - +
154E LEU 4.2 0.2 - - - -
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Residues in contact with LEU 153 (chain E).
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* 3.4 31.4 - - - +
2D ARG* 3.9 1.3 - - - -
3D ILE* 3.6 32.3 - - + +
153D LEU* 4.0 12.1 - - + -
1E MET* 3.7 20.2 - - + -
2E ARG 3.4 15.5 - - - +
3E ILE* 3.8 26.7 - - + -
91E LEU* 4.2 1.4 - - - +
92E GLY* 2.8 23.2 + - - -
93E ASN* 3.1 19.3 + - - +
152E ALA* 1.3 73.5 - - - +
154E LEU* 1.3 66.0 + - - +
153F LEU* 4.0 11.2 - - + -
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Residues in contact with LEU 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 3.2 6.7 - - - +
2E ARG* 2.8 39.7 + - + +
48E LEU* 3.6 38.8 - - + +
51E ALA* 3.6 17.3 - - + -
52E ALA* 3.8 10.8 - - + +
81E TRP* 3.6 25.4 - - + -
84E ILE* 3.7 20.0 - - + -
89E TYR* 4.2 15.3 - - + -
90E THR 3.4 14.8 - - - +
91E LEU* 4.1 3.8 - - + -
152E ALA* 5.3 0.2 - - + -
153E LEU* 1.3 79.4 - - - +
155E ILE* 1.3 63.2 + - - +
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Residues in contact with ILE 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 3.7 31.2 - - + +
89E TYR* 3.5 4.6 - - - -
90E THR* 2.9 41.3 + - - +
91E LEU 3.5 21.3 - - - +
92E GLY* 3.9 11.4 - - - +
154E LEU* 1.3 77.2 - - - +
156E LYS* 1.3 81.6 + - + +
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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