Contacts of the helix formed by residues 96 - 100 (chain A) in PDB entry 3JYT
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 HIS 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A ILE 4.8 1.6 - - - +
95A PRO* 1.3 75.8 - - - +
97A PRO* 1.3 81.9 - - + +
98A ALA* 3.6 21.3 - - + +
99A GLY* 2.4 22.0 + - - +
100A LEU* 3.8 0.4 + - - -
229A TRP* 4.5 2.2 - - - -
232A TYR* 3.0 23.0 + + - -
239A TRP* 4.2 11.5 - + - -
269A GLN* 2.6 25.0 + - - -
350A LYS* 3.6 40.6 - - + +
382A ILE* 4.0 17.9 - - + +
136B ASN* 2.6 20.7 + - - +
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Residues in contact with PRO 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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95A PRO 4.4 0.2 - - - +
96A HIS* 1.3 100.1 - - + +
98A ALA* 1.3 53.3 + - - +
99A GLY 2.6 0.9 + - - -
100A LEU* 2.6 56.4 + - + +
229A TRP* 3.9 7.4 - - + -
232A TYR* 3.2 43.1 - - + -
234A LEU* 4.3 6.3 - - + -
239A TRP* 3.6 35.9 - - + -
318A TYR* 4.0 4.0 - - - -
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Residues in contact with ALA 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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96A HIS* 2.7 23.5 + - + +
97A PRO* 1.3 76.6 - - - +
99A GLY* 1.3 50.6 + - - +
100A LEU 3.4 1.6 - - - -
239A TRP* 3.9 1.8 - - - +
317A VAL 4.0 12.8 - - - -
319A TYR* 3.6 5.0 - - - +
349A LEU* 3.3 38.7 - - + +
350A LYS* 4.2 1.8 - - + -
382A ILE* 4.9 0.4 - - + -
383A TRP* 2.7 44.1 + - + -
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Residues in contact with GLY 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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96A HIS 2.4 24.6 + - - -
97A PRO 2.6 0.6 + - - -
98A ALA* 1.3 67.8 - - - +
100A LEU* 1.3 60.2 + - - -
101A LYS* 3.8 6.8 + - - +
181A TYR* 3.3 12.6 + - - -
319A TYR* 4.5 4.7 - - - +
382A ILE* 3.8 17.4 - - - +
383A TRP* 3.7 13.1 - - - -
135B ILE* 6.0 1.9 - - - +
136B ASN* 3.8 15.0 - - - +
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Residues in contact with LEU 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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96A HIS 4.2 0.9 - - - +
97A PRO* 2.6 41.3 + - + +
99A GLY* 1.3 73.7 - - - +
101A LYS* 1.3 65.7 + - - +
181A TYR* 3.8 29.8 - - + -
188A TYR* 4.0 27.8 - - + +
229A TRP* 3.5 32.1 - - + -
234A LEU* 4.0 17.3 - - + -
318A TYR* 3.7 15.9 - - + +
319A TYR* 2.9 24.8 + - - +
560A SO4 4.4 1.8 - - - +
136B ASN* 4.6 0.2 - - - +
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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