Contacts of the strand formed by residues 102 - 108 (chain E) in PDB entry 2ODY
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 LEU 102 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100E GLY* 5.0 1.6 - - - -
101E GLN* 1.3 80.5 - - - +
103E GLU* 1.3 61.1 + - - +
104E ARG* 3.4 32.2 + - - +
118E VAL* 3.5 4.1 - - - -
119E TYR* 2.7 45.8 + - + +
120E GLY 4.4 1.6 - - - +
121E GLY* 3.7 30.1 - - - +
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Residues in contact with GLU 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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101E GLN 3.7 4.2 + - - +
102E LEU* 1.3 70.5 - - - +
104E ARG* 1.3 71.3 + - - +
105E TRP* 4.3 16.1 + - - +
116E THR* 3.7 36.0 + - + +
117E PHE 3.8 4.9 - - - +
118E VAL* 5.0 2.2 - - - +
129E TYR 4.7 0.3 - - - +
130E GLU 4.7 7.4 - - - +
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Residues in contact with ARG 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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102E LEU* 3.4 28.7 + - - +
103E GLU* 1.3 84.0 + - - +
105E TRP* 1.3 65.9 + - - +
116E THR* 3.2 7.6 - - - -
117E PHE* 2.8 48.4 + - + +
119E TYR* 3.6 36.4 - - + -
128E ASN* 3.0 39.6 + - - +
129E TYR 3.4 17.3 - - - -
130E GLU* 3.9 30.7 + - - +
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Residues in contact with TRP 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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103E GLU* 4.3 15.6 + - - +
104E ARG* 1.3 80.1 - - - +
106E PHE* 1.3 60.1 + - - +
114E CYS 3.7 18.8 - - - -
115E GLU* 3.2 18.8 - - - -
116E THR* 3.5 31.2 - - + +
117E PHE* 3.8 1.6 - - - -
128E ASN* 3.4 7.3 - - - -
129E TYR* 2.7 42.8 + - - +
130E GLU 3.9 4.9 + - - -
131E SER* 3.4 31.6 - - - +
132E GLU* 3.5 53.4 - - + +
135E CYS* 4.2 10.3 - - + -
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Residues in contact with PHE 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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91E PRO 4.5 0.7 - - - -
92E ALA* 4.8 4.0 - - + -
93E ALA* 3.8 30.3 - - + -
105E TRP* 1.3 72.7 - - - +
107E TYR* 1.3 83.4 + - - +
108E ASN* 3.5 19.4 + - + -
114E CYS* 3.3 1.0 - - - -
115E GLU* 2.9 78.1 + - + -
116E THR 4.0 10.1 - - - -
117E PHE* 3.7 20.4 - + + -
127E ASN* 3.3 33.7 - - - +
129E TYR* 4.7 0.2 - - - -
135E CYS* 3.6 6.5 - - - -
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Residues in contact with TYR 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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85E PHE* 4.1 12.1 - + - -
89E CYS* 3.1 36.0 - - + +
90E GLU 4.8 0.7 - - - +
91E PRO 4.3 1.4 - - - +
106E PHE* 1.3 76.2 - - - +
108E ASN* 1.3 61.6 + - - +
109E VAL* 3.8 26.7 + - + -
112E GLY* 3.4 41.3 + - - -
113E GLU 3.9 8.3 - - - -
114E CYS* 4.1 2.2 - - - -
127E ASN* 2.8 27.6 + - - +
135E CYS* 3.5 7.0 - - - -
139E CYS* 3.6 33.2 - - + -
140E LYS* 3.6 28.4 - - + +
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Residues in contact with ASN 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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106E PHE* 3.5 18.7 + - + +
107E TYR* 1.3 74.4 - - - +
109E VAL* 1.3 58.8 + - - +
110E GLN* 3.0 31.3 + - - +
111E SER* 3.4 17.2 + - - +
112E GLY* 2.8 32.2 + - - -
113E GLU 2.9 18.9 + - - +
115E GLU* 2.9 30.1 + - - +
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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