Contacts of the strand formed by residues 92 - 101 (chain E) in PDB entry 3T0E
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 GLU 92 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1E LYS* 3.7 46.4 + - + +
2E LYS* 4.4 11.1 - - - +
15E THR 5.6 1.6 - - - +
28E TRP* 6.3 0.2 - - - -
81E THR* 3.7 20.3 - - + +
82E TYR 3.7 13.7 - - - +
83E ILE* 4.8 8.4 - - + +
90E LYS 3.1 6.5 + - - +
91E GLU* 1.3 78.1 - - - +
93E VAL* 1.3 81.2 + - - +
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Residues in contact with VAL 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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2E LYS* 3.4 27.8 + - + +
4E VAL* 4.1 19.7 - - + -
14E LEU* 4.0 33.4 - - + -
15E THR 5.6 4.5 - - - +
28E TRP* 4.4 9.9 - - + -
81E THR* 3.6 7.1 - - - +
82E TYR* 3.0 50.7 + - + +
92E GLU* 1.3 83.6 - - - +
94E GLN* 1.3 68.8 + - - +
95E LEU* 6.3 0.2 - - + -
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Residues in contact with GLN 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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2E LYS 3.2 6.2 + - - +
3E VAL* 3.2 26.5 - - + +
4E VAL* 2.7 33.8 + - - +
14E LEU* 6.5 0.2 - - - -
80E ASP* 3.2 19.1 + - - +
81E THR* 3.3 21.2 + - + +
82E TYR 4.5 0.2 - - - +
93E VAL* 1.3 82.9 - - - +
95E LEU* 1.3 62.2 + - - +
96E LEU* 3.8 26.3 + - + +
123E GLY 5.5 2.8 + - - -
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Residues in contact with LEU 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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4E VAL* 3.3 16.6 - - + +
5E LEU* 4.9 2.7 - - - +
6E GLY 5.0 1.8 - - - +
12E VAL* 3.5 35.4 - - + -
14E LEU* 3.9 10.1 - - + -
71E ILE* 4.4 13.5 - - + -
74E LEU* 3.3 30.3 - - + -
78E ASP 4.0 15.7 - - - +
79E SER* 3.1 7.3 - - - -
80E ASP 2.8 34.8 + - - +
82E TYR* 4.6 13.0 - - + -
93E VAL* 5.4 0.2 - - - +
94E GLN* 1.3 74.8 - - - +
96E LEU* 1.3 67.0 + - - +
97E VAL* 4.1 9.6 - - + -
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Residues in contact with LEU 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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3E VAL* 4.3 7.6 - - + -
4E VAL 3.3 5.1 + - - -
5E LEU* 3.3 46.9 - - + +
6E GLY 3.3 4.0 + - - +
79E SER* 3.5 4.5 - - - -
80E ASP 5.7 0.2 - - - +
94E GLN* 3.8 38.4 - - + +
95E LEU* 1.3 82.4 - - - +
97E VAL* 1.3 61.8 + - - +
98E PHE* 4.1 19.6 - - + -
121E PRO* 4.3 15.7 - - + -
122E PRO 5.3 2.2 - - - +
123E GLY 4.3 16.4 - - - +
124E SER* 4.9 2.9 - - - -
163E GLN* 4.9 9.9 - - + -
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Residues in contact with VAL 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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6E GLY 3.2 16.4 - - - +
8E LYS* 4.8 6.7 - - + +
74E LEU* 3.5 33.4 - - + -
75E LYS 3.2 7.9 - - - +
76E ILE* 3.2 40.0 - - + +
79E SER* 2.8 28.2 + - - +
95E LEU* 4.1 11.0 - - + -
96E LEU* 1.3 75.4 - - - +
98E PHE* 1.3 75.0 + - - +
121E PRO* 3.2 13.7 - - - +
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Residues in contact with PHE 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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5E LEU* 4.9 7.6 - - + -
6E GLY 3.6 6.3 + - - -
7E LYS* 3.7 5.3 - - - -
8E LYS* 2.9 25.9 + - - +
76E ILE* 4.1 6.3 - - - -
96E LEU* 4.1 28.3 - - + -
97E VAL* 1.3 84.6 - - - +
99E GLY* 1.3 60.0 + - - +
118E LEU* 4.1 11.9 - - + -
119E GLU 3.3 10.3 - - - +
120E SER* 4.2 2.9 - - - -
121E PRO* 3.3 28.0 - - + -
124E SER* 4.2 3.6 - - - -
126E PRO* 4.0 29.6 - - + -
161E VAL* 4.1 22.9 - - + -
163E GLN* 4.4 20.6 - - + -
168E VAL* 4.6 14.1 - - + -
170E PHE* 3.8 12.5 - - + -
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Residues in contact with GLY 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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8E LYS* 4.6 11.0 - - - -
98E PHE* 1.3 76.8 - - - +
100E LEU* 1.3 62.8 + - - +
101E THR* 4.3 1.8 - - - -
117E THR 3.7 0.7 - - - +
118E LEU* 3.4 5.1 - - - +
119E GLU* 2.7 48.4 + - - +
170E PHE* 3.8 9.2 - - - -
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Residues in contact with LEU 100 (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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99E GLY* 1.3 73.6 - - - +
101E THR* 1.3 67.6 + - - +
116E LEU* 4.3 15.5 - - + +
117E THR 3.3 9.4 - - - +
118E LEU* 3.2 44.6 - - + +
128E VAL* 4.7 11.2 - - + -
144E LEU* 5.6 1.1 - - + -
159E CYS* 3.4 39.5 - - + -
161E VAL* 5.2 2.7 - - + -
170E PHE* 3.6 36.9 - - + -
172E ILE* 5.7 10.2 - - + +
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Residues in contact with THR 101 (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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99E GLY 5.5 0.7 - - - -
100E LEU* 1.3 82.6 - - - +
102E ALA* 1.3 66.6 + - - +
116E LEU* 3.6 7.1 - - - -
117E THR* 2.9 53.4 + - - -
119E GLU* 5.8 3.6 - - - +
172E ILE* 6.4 0.7 - - - -
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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