Contacts of the helix formed by residues 96 - 104 (chain E) in PDB entry 5X11
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 96 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94E VAL 4.2 1.3 - - - +
95E LYS* 1.3 76.2 - - - +
97E GLU* 1.3 63.6 + - - +
98E PHE* 3.0 21.5 + - - +
99E MET* 3.1 23.7 + - - +
100E LEU* 3.4 10.6 + - - +
124E ARG* 4.3 4.9 + - - -
168E TYR* 2.9 30.9 + - - -
33F PHE* 2.9 34.5 + - + +
34F TRP* 4.1 1.9 - - - -
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Residues in contact with GLU 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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96E ASP* 1.3 69.3 + - - +
98E PHE* 1.3 68.5 + - - +
100E LEU* 3.2 16.2 + - + +
101E LYS* 3.3 18.5 + - - +
1F MET* 5.1 6.2 - - - +
3F VAL* 3.5 31.8 - - + +
34F TRP* 4.5 14.4 - - + -
83F TRP* 3.1 37.5 + - + -
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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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96E ASP* 3.0 9.0 + - - +
97E GLU* 1.3 78.3 - - - +
99E MET* 1.3 63.5 + - - +
101E LYS* 2.9 41.6 + - + +
102E ALA* 2.9 11.7 + - + -
116E LEU* 4.1 15.7 - - + -
117E PHE* 3.8 41.3 - + - -
120E GLN* 3.5 49.8 - - + +
124E ARG* 5.3 0.9 - - - +
168E TYR* 3.7 17.0 - - - +
171E TRP* 4.2 8.1 - + - -
172E LEU* 3.7 18.6 - - + -
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Residues in contact with MET 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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96E ASP* 3.1 26.6 + - - +
98E PHE* 1.3 77.7 - - - +
100E LEU* 1.3 64.0 + - - +
102E ALA* 3.2 18.2 - - + +
103E TYR* 3.1 20.4 + - - +
168E TYR* 4.0 7.2 - - + +
171E TRP* 3.5 44.4 - - + -
30F LEU* 5.1 0.9 - - - +
33F PHE* 3.8 49.7 - - + +
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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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96E ASP 3.4 9.0 + - - +
97E GLU* 3.2 10.6 + - - +
99E MET* 1.3 77.7 - - - +
101E LYS* 1.3 61.5 + - - +
103E TYR* 3.2 16.2 + - - +
104E PHE* 3.2 43.8 - - + -
3F VAL* 3.9 24.7 - - + -
7F ALA* 3.9 28.5 - - + +
26F PHE* 5.2 0.2 - - + -
30F LEU* 4.1 18.8 - - + -
33F PHE* 4.9 1.5 - - - +
34F TRP* 4.0 25.1 - - + -
83F TRP* 3.5 23.6 - - + -
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Residues in contact with LYS 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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97E GLU* 3.3 14.1 + - - +
98E PHE* 2.9 28.6 + - + +
100E LEU* 1.3 74.2 - - - +
102E ALA* 1.3 63.7 + - - +
104E PHE* 2.8 17.3 + - - +
105E ILE* 3.3 9.4 + - - -
108E LEU* 5.6 4.6 - - + +
116E LEU* 6.4 1.3 - - + -
83F TRP* 2.9 57.6 + - + +
84F LEU* 3.3 32.0 + - + +
86F ARG* 2.7 30.1 + - - +
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Residues in contact with ALA 102 (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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98E PHE* 2.9 9.4 + - + +
99E MET* 3.2 40.8 - - + +
101E LYS* 1.3 74.6 - - - +
103E TYR* 1.3 61.9 + - - +
105E ILE* 3.2 27.3 + - - +
117E PHE* 4.5 26.0 - - + -
171E TRP* 4.7 2.9 - - + -
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Residues in contact with TYR 103 (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 MET 3.1 8.9 + - - +
100E LEU 3.3 11.2 - - - +
101E LYS 3.1 0.4 - - - -
102E ALA* 1.3 79.9 - - - +
104E PHE* 1.3 79.9 + + - +
105E ILE* 3.3 5.9 + - - +
106E SER 4.8 0.3 + - - -
11F LEU* 4.1 13.0 - - + -
13F ARG* 3.7 23.1 + - - -
25F TYR* 4.0 19.0 - + - -
29F GLU* 2.7 40.2 + - + -
30F LEU* 3.7 42.0 - - + +
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Residues in contact with PHE 104 (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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100E LEU* 3.2 47.3 + - + -
101E LYS* 2.8 10.0 + - - +
103E TYR* 1.3 97.5 - + - +
105E ILE* 1.3 59.8 + - - +
106E SER* 2.9 8.5 + - - -
107E SER* 3.1 17.5 + - - -
108E LEU 4.4 0.3 + - - -
6F TYR 4.1 6.5 - - - -
7F ALA 3.4 21.8 - - - -
10F GLY* 3.3 31.0 - - - -
11F LEU* 3.6 9.9 - - + -
13F ARG* 3.4 30.7 + - - +
30F LEU* 4.6 0.9 - - + -
80F LEU* 4.7 1.3 - - + -
83F TRP* 4.3 14.4 - + - -
84F LEU* 4.2 17.9 - - + +
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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