Contacts of the strand formed by residues 147 - 152 (chain E) in PDB entry 1E50
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 THR 147 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106E MET 3.6 0.9 - - - +
107E ALA* 3.4 5.2 - - - -
108E GLY 3.0 33.3 + - - +
109E ASN* 5.5 2.2 - - - +
145E SER 4.6 2.3 + - - -
146E PHE* 1.3 74.9 - - - +
148E LEU* 1.3 75.3 + - - +
149E THR* 3.8 8.1 + - - +
161E THR* 4.5 6.3 - - + -
162E TYR 3.3 9.0 - - - +
163E HIS* 3.2 45.3 - - + +
164E ARG 3.9 2.1 + - - -
61F GLY 5.3 5.8 - - - +
62F THR* 6.2 2.9 - - - -
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Residues in contact with LEU 148 (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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75E LEU* 3.6 24.0 - - + -
89E PHE* 3.7 24.7 - - + -
105E VAL* 3.5 28.0 - - + -
106E MET 3.3 6.3 - - - +
107E ALA* 4.1 5.2 - - + -
136E PHE* 3.7 29.2 - - + -
146E PHE 4.0 0.6 - - - -
147E THR* 1.3 75.9 - - - +
149E THR* 1.3 62.3 + - - +
150E ILE* 4.0 6.3 - - + -
161E THR* 3.2 5.2 - - - -
162E TYR* 2.8 54.6 + - + -
165E ALA* 3.9 13.7 - - + +
166E ILE* 5.2 0.4 - - + -
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Residues in contact with THR 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E THR 3.7 0.7 - - - +
105E VAL* 3.5 4.9 - - - -
106E MET* 2.8 54.8 + - + +
147E THR* 4.5 7.1 + - - +
148E LEU* 1.3 76.0 + - - +
150E ILE* 1.3 61.2 + - - +
151E THR* 3.9 7.1 + - - +
159E VAL* 3.8 24.2 - - + -
160E ALA 3.7 2.9 - - - -
161E THR* 4.2 10.0 - - + +
62F THR* 5.7 1.0 - - - +
63F ASN* 3.2 32.7 + - - +
64F LEU* 4.5 2.7 - - + -
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Residues in contact with ILE 150 (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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65E THR* 4.2 16.4 - - + -
70E PHE* 5.7 1.1 - - + -
72E CYS* 3.9 31.6 - - + -
89E PHE* 4.6 4.0 - - + -
91E VAL* 3.9 26.0 - - + -
103E VAL* 3.9 23.6 - - + -
104E THR 3.5 4.3 - - - +
105E VAL* 5.0 8.3 - - + -
148E LEU* 4.9 12.3 - - + -
149E THR* 1.3 74.6 - - - +
151E THR* 1.3 64.3 + - - +
152E VAL* 4.1 7.9 + - + +
158E GLN 3.7 0.7 - - - +
159E VAL* 3.2 5.0 - - - +
160E ALA* 2.6 53.2 + - + +
162E TYR* 5.3 3.8 - - + -
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Residues in contact with THR 151 (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 VAL* 3.2 5.5 - - - -
104E THR* 2.9 46.0 + - - -
106E MET* 4.7 1.6 - - - +
149E THR* 3.9 15.8 + - - +
150E ILE* 1.3 76.5 + - - +
152E VAL* 1.3 62.0 + - - +
153E PHE* 3.4 33.0 - - + -
157E PRO* 4.2 14.8 - - + -
158E GLN 3.5 6.7 - - - +
159E VAL* 4.2 11.4 - - + +
65F SER* 4.1 17.6 + - - +
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Residues in contact with VAL 152 (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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70E PHE* 3.3 49.1 - - + -
91E VAL* 4.8 0.4 - - + -
97E VAL* 4.1 9.0 - - + -
101E THR* 3.8 20.6 - - + -
102E LEU 3.6 4.7 - - - +
103E VAL* 4.2 21.8 - - + -
124E MET* 4.5 1.6 - - + -
150E ILE* 4.4 8.1 - - + +
151E THR* 1.3 75.6 - - - +
153E PHE* 1.3 58.8 + - - +
154E THR* 2.9 18.4 + - + -
157E PRO* 3.4 1.2 - - - +
158E GLN* 2.8 37.3 + - + +
160E ALA* 6.4 0.2 - - + -
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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