Contacts of the helix formed by residues 95 - 100 (chain F) in PDB entry 1JB0
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 ASN 95 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A GLY 6.0 0.2 - - - -
42A PRO* 2.9 33.7 - - + +
43A GLN* 4.0 6.5 - - - -
716A ALA* 3.2 32.7 + - - +
717A ILE* 3.6 24.3 - - - +
93F GLU* 3.2 0.8 - - - +
94F ALA* 1.3 82.1 - - - +
96F GLU* 1.3 64.1 + - - +
98F GLU 3.2 6.8 + - - -
99F ILE* 3.8 3.9 + - - +
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Residues in contact with GLU 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PRO* 5.4 4.5 - - + +
93F GLU* 3.2 31.6 + - + +
95F ASN* 1.3 79.5 - - - +
97F LYS* 1.3 59.1 + - + +
98F GLU 3.2 0.4 - - - -
99F ILE* 3.5 11.0 - - + +
100F ILE* 2.9 53.3 + - + +
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Residues in contact with LYS 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F TYR* 2.7 33.3 + - - +
88F VAL* 3.2 38.1 - - + -
91F SER* 4.8 6.3 + - - +
93F GLU* 2.9 27.2 + - + +
94F ALA 3.7 0.9 - - - -
95F ASN 3.2 0.4 - - - -
96F GLU* 1.3 77.3 - - + +
98F GLU* 1.3 60.5 + - - +
99F ILE 3.5 0.2 - - - -
100F ILE 3.4 12.4 - - - +
101F ILE* 3.6 5.4 - - - +
102F ASP* 3.6 32.0 + - + -
105F LEU* 4.9 5.3 - - - +
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Residues in contact with GLU 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715A PRO* 3.6 6.2 - - - +
716A ALA* 2.8 28.1 + - - +
717A ILE* 3.0 37.3 + - + +
1139A CLA 3.2 55.7 - - + +
84F TYR* 5.2 2.7 - - + -
85F LEU* 3.5 22.8 - - + +
88F VAL* 5.6 3.6 - - + +
89F ARG* 6.1 0.3 - - - -
94F ALA* 3.2 21.8 + - - +
95F ASN 3.2 6.0 + - - +
97F LYS* 1.3 79.9 - - - +
99F ILE* 1.3 61.1 + - - +
101F ILE* 3.6 8.2 - - - +
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Residues in contact with ILE 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PRO* 4.6 5.8 - - + -
42A PRO* 3.3 33.7 - - + -
47A TRP* 3.9 17.0 - - + -
48A ILE* 4.6 5.2 - - + -
717A ILE* 3.4 25.1 - - + -
1101A CLA 3.8 23.9 - - + +
1139A CLA 4.0 12.8 - - + -
95F ASN 4.0 3.4 - - - +
96F GLU* 3.5 14.8 - - + +
98F GLU* 1.3 80.3 - - - +
100F ILE* 1.3 74.2 - - + +
101F ILE* 3.6 1.3 - - - -
10J THR* 3.4 3.5 - - - -
11J ALA* 2.6 37.3 + - - +
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Residues in contact with ILE 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA 3.6 24.5 - - - +
31A PRO* 3.7 20.9 - - + -
96F GLU* 2.9 44.6 + - + +
97F LYS* 3.4 13.7 - - - +
99F ILE* 1.3 89.5 - - + +
101F ILE* 1.3 62.9 + - - +
102F ASP* 3.6 1.0 + - - +
6J THR* 3.6 36.8 - - + +
9J SER* 3.8 10.3 - - - +
10J THR* 4.3 4.5 - - + +
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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