Contacts of the strand formed by residues 90 - 99 (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 THR 90 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81E TRP* 3.7 10.8 - - + -
85E GLN* 5.6 4.3 - - - +
89E TYR* 1.3 79.0 - - - +
91E LEU* 1.3 63.5 + - - +
154E LEU* 3.4 9.2 - - - +
155E ILE* 2.9 50.2 + - - +
156E LYS* 5.0 3.9 - - + +
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Residues in contact with LEU 91 (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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48E LEU* 3.6 31.4 - - + -
81E TRP* 3.4 23.5 - - + -
90E THR* 1.3 76.2 - - - +
92E GLY* 1.3 76.7 + - - +
93E ASN* 4.2 4.7 - - - +
94E VAL* 3.9 10.3 - - + -
120E LEU* 3.8 18.6 - - + +
122E CYS* 3.4 41.2 - - + +
126E ASP* 4.2 10.5 - - + +
153E LEU 4.6 1.8 - - - +
154E LEU* 4.1 4.9 - - + -
155E ILE* 3.5 12.2 - - - +
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Residues in contact with GLY 92 (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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1D MET 5.4 1.8 - - - -
2D ARG* 4.6 3.4 + - - -
1E MET* 4.5 7.6 - - - -
90E THR 3.7 2.2 + - - -
91E LEU* 1.3 77.6 - - - +
93E ASN* 1.3 63.0 + - - +
126E ASP* 3.4 22.9 - - - +
153E LEU 2.8 19.5 + - - -
155E ILE* 3.9 19.5 - - - +
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Residues in contact with ASN 93 (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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1D MET 4.3 0.3 - - - +
2D ARG* 3.5 41.9 - - - +
3D ILE* 2.8 54.5 + - - +
50D GLY 4.3 1.8 + - - -
51D ALA* 4.1 4.6 + - - +
91E LEU* 4.4 2.2 - - - -
92E GLY* 1.3 77.6 - - - +
94E VAL* 1.3 75.1 + - - +
126E ASP* 3.3 12.6 - - - +
152E ALA* 3.8 0.9 - - - -
153E LEU* 3.1 32.1 + - - +
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Residues in contact with VAL 94 (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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2D ARG* 5.8 0.2 + - - -
3D ILE* 5.2 0.2 - - - -
44E LEU* 3.6 28.0 - - + -
48E LEU* 4.0 10.1 - - + -
91E LEU* 3.9 22.4 - - + -
93E ASN* 1.3 86.5 + - - +
95E ASP* 1.3 62.4 + - - +
96E VAL* 5.1 2.0 - - + -
116E ILE* 4.4 8.7 - - + -
120E LEU* 4.2 4.5 - - + -
126E ASP 2.7 21.2 + - - +
127E VAL* 3.6 29.6 - - + -
128E ASN* 2.9 26.6 + - - +
151E VAL 3.7 3.4 - - - +
152E ALA* 4.2 6.5 - - + -
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Residues in contact with ASP 95 (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* 4.1 9.8 - - - +
4D GLY* 3.4 0.2 - - - -
5D HIS* 2.6 28.6 + - - +
50D GLY* 3.3 20.6 - - - +
94E VAL* 1.3 75.1 - - - +
96E VAL* 1.3 66.8 + - - +
97E THR* 5.2 0.4 - - - -
128E ASN* 2.8 27.3 + - - +
130E LYS* 2.8 23.6 + - - -
149E GLU 4.1 0.2 - - - +
150E ALA* 3.3 3.6 - - - -
151E VAL* 3.0 50.8 + - + +
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Residues in contact with VAL 96 (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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40E ALA* 4.1 18.6 - - + +
44E LEU* 4.0 34.1 - - + -
94E VAL* 5.1 2.7 - - + -
95E ASP* 1.3 80.8 + - - +
97E THR* 1.3 59.6 + - - +
98E ILE* 4.5 1.6 - - + -
116E ILE* 4.8 4.7 - - + -
127E VAL* 5.8 0.2 - - + -
128E ASN 2.7 15.8 + - - +
129E VAL* 3.4 22.2 - - + -
130E LYS* 2.8 35.8 + - - +
148E CYS* 3.4 26.2 - - - -
149E GLU 3.5 3.6 - - - +
150E ALA* 4.2 5.6 - - + -
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Residues in contact with THR 97 (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* 3.1 27.9 + - - +
7D PHE* 4.1 26.9 - - + +
46D ASP* 5.9 0.4 - - - +
96E VAL* 1.3 70.3 - - - +
98E ILE* 1.3 68.2 + - - +
99E ILE* 3.5 5.3 + - + +
130E LYS* 3.0 38.3 + - + -
132E THR* 4.4 13.0 - - + -
148E CYS* 3.3 4.0 - - - -
149E GLU* 2.7 38.2 + - - -
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Residues in contact with ILE 98 (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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20E ILE* 3.8 18.2 - - + -
39E VAL* 4.9 2.2 - - + -
40E ALA* 4.4 3.6 - - + -
96E VAL* 4.5 0.7 - - + -
97E THR* 1.3 72.5 - - - +
99E ILE* 1.3 63.0 + - - +
100E ALA* 3.8 3.0 + - + -
105E MET* 3.9 39.5 - - + -
109E ILE* 4.6 0.9 - - + -
112E MET* 3.8 22.9 - - + -
129E VAL* 3.6 29.4 - - + -
130E LYS 2.8 16.8 + - - +
131E ALA* 3.2 4.8 - - + +
132E THR* 2.9 27.7 + - - +
146E ILE* 3.9 16.8 - - + -
147E ALA 3.9 3.8 - - - +
148E CYS* 4.1 11.9 - - - -
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Residues in contact with ILE 99 (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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7D PHE* 3.8 34.8 - - + -
8903D GPP 5.0 6.1 - - + -
7E PHE* 4.7 3.4 - - + -
97E THR* 3.8 9.4 - - + +
98E ILE* 1.3 73.5 - - - +
100E ALA* 1.3 62.2 + - - +
132E THR* 3.5 10.8 - - + +
134E THR* 3.7 29.8 - - + +
140E THR* 3.6 15.9 - - + +
146E ILE* 3.4 0.7 - - - +
147E ALA* 2.7 54.9 + - + +
149E GLU* 4.0 28.9 - - + +
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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