Contacts of the strand formed by residues 113 - 122 (chain E) in PDB entry 3F5O
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 113 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84E VAL* 4.6 2.0 - - + -
109E GLN* 3.5 1.4 - - - -
110E GLY* 2.8 31.7 + - - +
112E THR* 1.3 90.1 - - - +
114E ALA* 1.3 57.7 + - - +
115E PHE* 3.9 20.5 - - + -
135E THR* 4.1 13.9 - - + -
136E LYS 3.4 12.6 - - - +
137E HIS* 4.2 9.2 - - + +
138E LEU* 4.2 3.8 - - - -
84G VAL* 3.8 24.0 - - + -
113G LEU* 4.3 21.5 - - + -
137G HIS* 4.1 12.3 - - + +
150G COA 3.2 39.9 + - + +
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Residues in contact with ALA 114 (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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72E LEU* 3.6 38.1 - - + -
108E LYS 3.5 5.8 - - - -
109E GLN* 3.8 11.9 - - + -
113E LEU* 1.3 74.5 - - - +
115E PHE* 1.3 64.2 + - - +
116E THR* 5.2 0.9 - - - -
134E HIS 3.9 0.4 - - - +
135E THR* 3.3 6.8 - - - +
136E LYS* 2.8 35.7 + - + +
138E LEU* 4.1 13.5 - - + -
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Residues in contact with PHE 115 (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 VAL* 3.7 2.6 - - - +
107E LEU* 2.7 28.3 + - + -
108E LYS* 2.9 31.8 + - + +
113E LEU* 3.9 26.9 - - + -
114E ALA* 1.3 74.4 - - - +
116E THR* 1.3 64.0 + - - +
133E ARG* 5.9 1.3 - - + -
134E HIS 3.7 3.1 - - - -
135E THR* 3.5 15.9 - - + +
84G VAL* 3.7 23.1 - - + -
150G COA 3.5 27.4 - - - -
89H THR* 3.2 34.1 - - + -
90H TYR 3.8 10.5 - - - -
91H MET* 3.4 31.2 - - + -
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Residues in contact with THR 116 (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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68E SER* 3.1 36.4 + - - +
72E LEU* 3.9 26.6 - - + +
105E HIS 3.3 11.9 + - - -
106E VAL* 4.1 6.2 - - - +
107E LEU* 4.2 5.1 - - - +
114E ALA 5.3 0.2 - - - -
115E PHE* 1.3 79.4 + - - +
117E SER* 1.3 58.3 + - - +
118E VAL* 4.9 0.7 - - + -
133E ARG* 3.2 8.3 - - - +
134E HIS* 3.0 56.8 + - + +
136E LYS* 5.6 0.4 - - + -
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Residues in contact with SER 117 (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 ALA* 3.4 0.2 - - - -
105E HIS* 2.9 53.9 + - - +
107E LEU* 4.0 18.3 - - - +
116E THR* 1.3 73.4 - - - +
118E VAL* 1.3 68.0 + - - +
119E ASP* 4.7 1.7 + - - -
131E GLN* 4.3 14.7 + - - +
132E GLY 3.4 11.9 + - - -
133E ARG* 4.4 0.7 - - - +
131H GLN* 4.0 15.6 + - - -
133H ARG* 5.5 0.3 + - - -
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Residues in contact with VAL 118 (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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63E LEU 4.9 0.2 - - - +
64E VAL* 3.6 32.1 - - + +
68E SER* 3.6 28.9 - - - +
102E ILE* 3.5 32.3 - - + -
103E THR 3.3 9.6 - - - +
104E ALA* 3.7 9.2 - - + -
105E HIS* 5.7 0.2 - - - -
116E THR* 4.9 0.7 - - + -
117E SER* 1.3 82.5 + - - +
119E ASP* 1.3 68.1 + - - +
120E LEU* 4.2 10.6 - - + +
131E GLN* 3.3 5.5 - - - +
132E GLY 2.9 32.9 + - - +
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Residues in contact with ASP 119 (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 VAL 3.6 1.6 - - - +
102E ILE* 3.5 2.3 - - - -
103E THR* 2.9 40.8 + - + +
105E HIS* 6.2 0.2 - - - -
117E SER* 4.7 2.4 + - - -
118E VAL* 1.3 74.0 - - - +
120E LEU* 1.3 62.0 + - - +
121E THR* 4.9 5.9 - - - +
128E LEU* 3.8 19.7 - - + +
130E ALA 3.6 3.4 - - - -
131E GLN* 2.8 35.6 - - - +
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Residues in contact with LEU 120 (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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55E LEU* 4.3 8.1 - - + -
60E THR* 4.0 23.6 - - + +
63E LEU* 3.9 27.6 - - + -
64E VAL* 4.0 27.1 - - + -
100E ILE* 3.9 15.3 - - + -
101E VAL 3.2 4.9 - - - +
102E ILE* 4.0 14.8 - - + -
118E VAL* 4.2 9.2 - - + +
119E ASP* 1.3 75.3 - - - +
121E THR* 1.3 57.6 + - - +
128E LEU* 3.5 4.5 - - - +
129E ILE* 2.6 43.9 + - + -
130E ALA* 2.8 21.7 + - + +
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Residues in contact with THR 121 (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 ILE* 3.3 5.5 - - - +
101E VAL* 2.8 59.6 + - + +
103E THR* 5.4 2.2 - - - +
119E ASP* 4.9 5.9 - - - +
120E LEU* 1.3 78.6 + - - +
122E ASN* 1.3 63.3 + - - +
126E GLY* 3.3 21.9 + - - +
127E LYS 3.4 5.6 + - - -
128E LEU* 4.0 12.0 - - - +
129E ILE* 3.6 4.7 - - - +
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Residues in contact with ASN 122 (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 GLU* 2.6 46.5 + - - +
99E ASP 4.0 2.2 - - - -
121E THR* 1.3 72.5 - - - +
123E LYS* 1.3 58.6 + - - +
124E ALA* 2.8 33.2 + - - +
125E THR* 2.9 33.1 + - - +
126E GLY* 2.7 33.4 + - - -
127E LYS* 2.8 16.3 + - + +
129E ILE* 3.7 5.1 - - + +
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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