Contacts of the strand formed by residues 72 - 78 (chain E) in PDB entry 1J0B
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 VAL 72 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70E ALA* 3.5 2.7 - - - +
71E ASP* 1.3 88.2 - - - +
73E VAL* 1.3 79.5 + - - +
74E ILE* 4.8 0.9 - - + -
96E LEU* 4.5 1.4 - - - +
97E ASP* 3.1 20.6 - - + +
99E ILE* 4.1 18.8 - - + -
144E LEU* 3.7 27.4 - - + -
149E ARG* 4.6 7.2 - - + +
150E LYS 3.2 17.2 - - - +
151E PRO* 3.3 20.5 - - + +
152E TYR* 3.1 24.6 + - - +
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Residues in contact with VAL 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E LEU* 4.0 13.7 - - + -
65E ALA* 4.8 7.0 - - + -
72E VAL* 1.3 76.5 - - - +
74E ILE* 1.3 68.3 + - - +
75E THR* 5.6 0.2 - - + -
87E THR* 4.3 12.3 - - + +
91E ALA* 4.3 9.4 - - + -
96E LEU* 3.4 33.2 - - + -
97E ASP 2.8 13.9 + - - +
98E ALA* 3.2 5.4 - - + +
99E ILE* 2.6 33.8 + - - +
100E LEU* 5.5 0.9 - - - +
152E TYR* 3.6 8.3 - - + +
154E ILE* 3.8 29.6 - - + -
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Residues in contact with ILE 74 (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 VAL* 4.8 4.9 - - + -
73E VAL* 1.3 83.8 - - - +
75E THR* 1.3 70.1 + - - +
99E ILE* 3.3 23.3 - - + +
101E VAL* 4.2 8.1 - - + -
137E ALA* 3.4 33.2 - - + +
140E ILE* 3.7 27.4 - - + -
141E ALA* 3.7 27.6 - - + +
144E LEU* 4.2 9.0 - - + -
151E PRO* 4.7 3.4 - - + -
152E TYR 2.9 11.1 + - - +
153E VAL* 4.0 6.5 - - + -
154E ILE 2.9 24.7 + - - -
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Residues in contact with THR 75 (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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73E VAL* 5.6 0.2 - - + -
74E ILE* 1.3 81.5 - - - +
76E VAL* 1.3 72.8 + - - +
83E HIS* 3.2 30.4 + - + +
84E ALA* 4.6 3.4 - - - -
87E THR* 3.9 29.2 - - + -
99E ILE 3.8 2.8 + - - -
100E LEU* 4.1 19.7 - - + +
101E VAL* 3.1 24.6 + - - +
102E LEU* 6.4 0.2 - - + -
134E MET* 5.9 0.2 - - - -
153E VAL* 5.5 0.2 - - - -
154E ILE* 3.3 25.8 + - - +
155E PRO 3.4 1.7 + - - -
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Residues in contact with VAL 76 (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 THR* 1.3 87.0 + - - +
77E GLY* 1.3 59.2 + - - +
83E HIS* 4.1 7.5 - - - -
84E ALA* 5.7 0.7 - - - -
101E VAL* 3.1 29.2 - - + +
102E LEU* 4.7 1.1 - - - -
131E PHE* 4.3 11.7 - - + +
133E LEU* 4.1 21.1 - - + +
134E MET* 3.4 41.1 - - + -
137E ALA* 4.3 5.8 - - + -
154E ILE 4.3 1.0 + - - -
155E PRO 4.4 0.2 + - - -
156E PRO* 4.0 26.2 - - + +
157E GLY 4.1 6.6 + - - -
1051E 5PA 5.0 0.3 - - - +
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Residues in contact with GLY 77 (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 VAL* 1.3 75.9 - - - +
78E ALA* 1.3 72.3 + - - +
81E SER* 3.7 17.0 - - - -
101E VAL 3.4 3.0 + - - -
102E LEU* 3.1 22.8 - - - +
103E ARG* 3.7 3.8 + - - +
133E LEU* 4.0 5.0 - - - +
1051E 5PA 4.1 5.8 - - - -
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Residues in contact with ALA 78 (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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77E GLY* 1.3 80.6 - - - +
79E VAL* 1.3 65.0 + - - +
80E HIS* 3.1 35.7 - - + +
81E SER* 3.3 9.4 - - - -
102E LEU* 3.0 14.3 - - - +
103E ARG* 4.2 28.6 - - - +
256E TYR* 4.3 11.2 + - + +
1051E 5PA 4.4 2.6 + - - -
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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