Contacts of the strand formed by residues 143 - 147 (chain E) in PDB entry 3J7Y
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 ALA 143 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132E TYR* 3.9 28.0 - - + +
133E THR 3.5 5.4 - - - -
134E SER* 3.9 12.3 - - - +
135E LYS* 3.9 8.3 - - + +
142E MET* 1.3 78.7 - - - +
144E THR* 1.3 60.0 + - - +
180E ASN* 3.7 1.0 - - - -
181E ILE* 2.8 45.2 + - + +
183E ASP* 4.8 13.0 - - + +
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Residues in contact with THR 144 (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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3206A C 5.3 3.1 - - - +
131E LYS 4.2 0.2 - - - +
132E TYR* 3.4 6.9 - - - -
133E THR* 2.6 64.8 + - - -
142E MET* 3.7 11.6 + - + +
143E ALA* 1.3 82.2 - - - +
145E LEU* 1.3 64.7 + - - +
146E SER 4.3 0.4 + - - -
178E ILE* 3.6 16.5 - - + +
179E PHE 3.2 7.4 - - - +
180E ASN* 3.4 25.6 - - - +
181E ILE* 3.9 2.4 - - - +
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Residues in contact with LEU 145 (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 VAL* 3.3 35.2 - - + -
129E VAL* 3.8 21.1 - - + -
131E LYS 3.7 0.7 - - - -
132E TYR* 3.6 35.9 - - + -
144E THR* 1.3 74.5 - - - +
146E SER* 1.3 61.6 + - - +
147E VAL* 3.5 8.8 + - + -
177E LYS 3.7 0.2 - - - +
178E ILE* 3.3 3.0 - - - -
179E PHE* 2.8 45.1 + - + +
181E ILE* 3.4 24.7 - - + +
186E ALA* 4.7 3.8 - - - -
187E ILE* 3.4 21.8 - - + +
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Residues in contact with SER 146 (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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129E VAL* 3.7 3.8 - - - +
130E LEU* 2.8 25.1 + - - +
131E LYS* 2.8 50.7 + - - +
144E THR 4.3 0.4 - - - -
145E LEU* 1.3 71.3 - - - +
147E VAL* 1.3 60.2 + - - +
176E VAL* 3.7 20.9 - - - -
177E LYS 3.6 5.8 - - - -
178E ILE* 4.1 15.1 - - - +
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Residues in contact with VAL 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E VAL* 3.7 20.9 - - + -
98E GLY 4.4 2.2 - - - +
100E ILE* 3.8 11.7 - - + +
127E CYS* 4.4 8.5 - - + -
128E HIS 3.7 7.9 - - - +
129E VAL* 4.4 6.7 - - + -
130E LEU* 4.2 2.9 - - - -
145E LEU* 4.1 4.5 - - + +
146E SER* 1.3 79.0 - - - +
148E GLY* 1.3 71.4 + - - +
176E VAL* 3.3 3.1 - - - -
177E LYS 2.8 32.2 + - - +
179E PHE* 3.4 35.4 - - + -
193E LEU* 3.6 23.6 - - + -
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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