Contacts of the strand formed by residues 97 - 101 (chain I) 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 ASP 97 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71I ASP 2.8 19.6 + - - +
72I VAL* 3.8 11.4 - - + -
73I VAL* 2.7 28.5 + - - +
91I ALA* 3.7 3.6 - - - +
92I LYS* 4.8 13.4 + - - +
96I LEU* 1.3 74.8 - - - +
98I ALA* 1.3 71.9 + - - +
149I ARG* 3.3 19.2 + - - +
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Residues in contact with ALA 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I VAL* 4.2 0.8 - - - +
73I VAL* 3.3 9.0 - - + +
88I GLY* 4.0 28.0 - - - +
91I ALA* 4.2 7.9 - - + -
92I LYS* 5.5 7.3 - - + +
97I ASP* 1.3 87.5 + - - +
99I ILE* 1.3 68.8 + - - +
100I LEU* 4.3 4.5 - - + -
120I ILE* 4.3 11.9 - - + -
121I GLU* 3.5 23.2 + - - +
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Residues in contact with ILE 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I VAL* 3.5 25.6 - - + -
73I VAL 3.2 5.7 + - - +
74I ILE* 3.8 16.6 - - + +
75I THR* 3.5 24.3 + - - +
98I ALA* 1.3 81.5 - - - +
100I LEU* 1.3 67.5 + - - +
101I VAL* 3.8 5.5 + - + +
121I GLU* 3.6 22.2 - - + +
123I ARG* 3.5 48.0 - - + +
140I ILE* 4.6 2.2 - - + -
144I LEU* 3.5 24.0 - - + -
149I ARG* 5.8 2.5 - - - +
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Residues in contact with LEU 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I THR* 3.7 8.7 - - + +
84I ALA* 3.5 34.1 - - + +
85I PHE 4.0 3.4 - - - +
88I GLY* 4.7 2.2 - - - -
98I ALA* 4.3 5.6 - - + -
99I ILE* 1.3 82.8 - - - +
101I VAL* 1.3 61.5 + - - +
102I LEU* 3.6 21.1 + - + +
115I ASP* 3.1 40.8 - - - +
120I ILE* 3.5 26.7 - - + -
121I GLU 3.2 9.3 + - - +
122I THR* 3.7 2.9 - - - +
123I ARG* 3.0 31.6 + - - +
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Residues in contact with VAL 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I ILE* 4.5 8.7 - - + -
75I THR 3.3 15.2 + - - +
76I VAL* 3.6 4.4 - - - +
77I GLY 3.2 18.6 + - - +
99I ILE* 4.5 4.9 - - + +
100I LEU* 1.3 73.2 - - - +
102I LEU* 1.3 58.9 + - - +
123I ARG* 3.7 4.3 - - + -
125I TYR* 3.5 20.6 - - + -
133I LEU* 3.3 42.6 - - + +
136I TYR* 4.2 6.3 - - + -
137I ALA* 4.3 16.2 - - + +
140I ILE* 3.8 24.9 - - + -
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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