Contacts of the helix formed by residues 95 - 100 (chain A) in PDB entry 2JPH
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 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASP 3.6 4.3 - - - +
34A CYS* 3.9 8.3 - - + -
35A ASP* 2.9 27.6 - - - +
36A THR* 5.4 0.4 - - + -
37A ILE* 4.3 7.0 - - - +
77A LEU* 4.9 1.6 - - - +
93A LEU 3.8 5.1 + - - +
94A ASN* 1.3 79.2 - - - +
96A LEU* 1.3 64.6 + - - +
97A GLN* 3.1 42.9 - - - +
98A HIS* 3.2 25.0 + - - +
99A TYR* 3.8 4.2 + - - +
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.7 28.7 - - + -
31A VAL* 3.7 16.8 - - + -
32A LEU 3.1 24.0 - - - +
33A ASP* 3.7 20.9 - - + +
35A ASP* 2.7 20.1 + - - +
37A ILE* 4.9 0.4 - - - +
67A TRP* 3.6 33.4 - - + -
77A LEU* 5.4 0.4 - - - -
95A THR* 1.3 73.2 - - - +
97A GLN* 1.3 55.3 + - - +
99A TYR* 3.1 5.3 + - - +
100A LYS* 2.8 28.6 + - - -
101A VAL* 3.3 34.3 + - + +
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Residues in contact with GLN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLU 5.6 0.6 + - - -
33A ASP* 2.6 65.3 + - - +
34A CYS* 3.2 17.7 - - - +
95A THR* 3.1 23.8 + - - +
96A LEU* 1.3 77.2 - - - +
98A HIS* 1.3 59.5 + - - +
100A LYS* 2.7 48.6 + - + +
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Residues in contact with HIS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A VAL* 3.8 21.1 - - + -
83A THR* 5.2 0.7 - - + -
92A ARG* 4.8 19.3 + - - -
94A ASN* 2.8 28.4 + - - +
95A THR* 3.2 21.6 + - - +
96A LEU 3.1 0.6 - - - -
97A GLN* 1.3 83.6 - - - +
99A TYR* 1.3 60.6 + - - +
100A LYS* 3.5 8.5 + - - +
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Residues in contact with TYR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A TRP* 3.4 40.8 - + + -
69A SER* 2.9 32.7 + - - -
71A VAL* 6.0 0.5 - - - +
72A ALA* 3.6 25.0 + - + +
73A GLY 3.6 0.9 - - - -
74A HIS 3.5 11.3 + - - -
75A LEU* 3.4 45.2 + - + +
77A LEU* 4.1 20.0 - - + -
95A THR 3.8 0.6 + - - -
96A LEU 3.1 9.2 + - - +
98A HIS* 1.3 78.2 - - - +
100A LYS* 1.3 70.5 + - - +
101A VAL* 3.6 10.4 - - + -
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASP* 5.8 1.1 - - - +
71A VAL* 4.7 8.1 - - - +
96A LEU 2.8 9.4 + - - -
97A GLN* 2.7 38.2 + - + +
98A HIS* 4.2 8.3 + - - +
99A TYR* 1.3 82.7 - - - +
101A VAL* 1.3 63.3 + - - +
102A PRO* 3.8 3.3 - - - +
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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