Contacts of the strand formed by residues 99 - 108 (chain E) in PDB entry 3STJ
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 99 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30E ARG* 6.3 0.9 - - - -
91E SER* 5.9 4.9 - - - -
92E ILE 3.3 6.7 - - - +
93E GLN* 3.8 28.7 + - + +
97E GLY 3.5 8.7 + - - +
98E ARG* 1.3 76.2 - - - +
100E PHE* 1.3 67.1 + - - +
250F SER* 5.6 2.1 - - - -
251F ALA* 3.9 21.8 + - + +
252F ASP* 4.1 20.4 - - - +
255F LYS* 2.7 31.2 + - - +
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Residues in contact with PHE 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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91E SER* 3.3 7.2 - - - -
92E ILE* 2.8 38.2 + - + +
94E LEU* 3.7 34.1 - - + -
98E ARG* 3.5 40.2 - - + -
99E GLU* 1.3 79.0 - - - +
101E ASP* 1.3 62.9 + - - +
118E ILE* 3.5 33.7 - - + -
119E GLN 3.8 4.9 - - - +
120E ASN 3.4 22.4 - - - -
121E PRO* 4.1 1.1 - - + -
122E SER* 4.0 17.0 - - - -
124E LEU* 4.0 7.0 - - + -
255F LYS* 6.1 3.8 - - - -
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Residues in contact with ASP 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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89E LYS* 5.5 5.4 - - - +
90E ILE 3.3 19.0 + - - +
91E SER* 5.0 4.6 - - - -
100E PHE* 1.3 79.1 - - - +
102E ALA* 1.3 61.1 + - - +
118E ILE* 3.5 5.2 - - - -
119E GLN* 2.8 43.8 + - + -
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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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90E ILE* 2.9 38.7 + - + +
92E ILE* 3.6 31.6 - - + -
101E ASP* 1.3 78.3 - - - +
103E LYS* 1.3 67.5 + - - +
116E LEU* 4.4 8.7 - - + -
117E GLN 3.3 13.9 - - - +
118E ILE* 4.6 2.0 - - + -
119E GLN* 4.4 1.8 - - - -
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Residues in contact with LYS 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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90E ILE* 5.0 0.4 - - - -
102E ALA* 1.3 77.3 - - - +
104E LEU* 1.3 66.3 + - - +
105E ILE* 3.3 6.2 + - + -
116E LEU* 3.3 5.3 - - - -
117E GLN* 2.9 31.4 + - - +
119E GLN* 3.6 39.1 + - + +
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Residues in contact with LEU 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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84E ILE* 3.9 25.8 - - + +
90E ILE* 4.5 12.1 - - + +
103E LYS* 1.3 73.7 - - - +
105E ILE* 1.3 61.7 + - - +
106E GLY* 3.4 31.0 - - - +
107E SER* 4.4 12.1 - - - +
114E ALA* 4.1 4.5 - - + -
115E LEU 3.5 9.2 - - - +
116E LEU* 3.8 18.7 - - + +
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Residues in contact with ILE 105 (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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76E TYR* 4.3 11.4 - - + -
103E LYS* 3.3 6.7 + - + +
104E LEU* 1.3 78.0 - - - +
106E GLY* 1.3 58.4 + - - +
115E LEU* 2.8 30.2 + - + +
116E LEU 4.1 3.1 - - - -
117E GLN* 3.5 49.4 - - + +
231E LEU 3.5 24.0 - - - +
232E ILE* 4.5 4.9 - - + +
235E GLY* 3.9 14.6 - - - +
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Residues in contact with GLY 106 (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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104E LEU* 3.4 11.9 - - - +
105E ILE* 1.3 82.0 - - - +
107E SER* 1.3 59.0 + - - -
115E LEU* 2.8 30.9 + - - +
231E LEU* 3.6 21.4 - - - +
235E GLY 3.9 8.5 - - - -
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Residues in contact with SER 107 (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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81E ASN* 3.3 24.9 + - - -
84E ILE* 5.1 0.2 - - - -
104E LEU* 4.4 13.9 - - - +
106E GLY* 1.3 75.3 - - - -
108E ASP* 1.3 58.6 + - - +
109E ASP* 4.2 8.4 + - - +
113E ILE 3.3 10.5 - - - -
114E ALA* 4.1 8.7 - - - +
231E LEU* 3.5 11.7 - - - +
235E GLY 4.9 0.6 + - - -
236E GLU* 5.3 1.2 - - - -
237E ILE* 3.7 14.9 - - - +
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Residues in contact with ASP 108 (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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81E ASN* 3.9 4.7 - - - +
107E SER* 1.3 72.6 - - - +
109E ASP* 1.3 57.7 + - - +
110E GLN* 3.2 11.1 + - - +
111E SER* 2.6 30.4 + - - +
112E ASP* 3.0 26.0 + - - -
113E ILE* 2.7 21.0 + - + +
227E LEU* 3.7 3.7 - - + +
231E LEU* 5.6 0.2 - - + -
237E ILE* 3.8 24.2 - - + +
239E ARG* 2.8 45.4 + - - -
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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