Contacts of the helix formed by residues 73 - 78 (chain B) in PDB entry 1J8H
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 ALA 73 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLU 3.3 13.7 + - - +
70B GLN* 3.2 8.1 + - - +
71B LYS 3.1 0.8 - - - -
72B ARG* 1.3 75.8 - - - +
74B ALA* 1.3 55.0 + - - +
75B VAL 3.3 2.7 - - - -
76B ASP* 3.3 13.6 + - + +
77B THR* 2.7 38.3 + - + +
50D THR 5.5 1.1 - - - +
51D SER* 4.3 18.6 - - - +
52D ALA* 6.2 2.7 - - + +
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 3.6 33.4 - - + -
70B GLN* 3.3 6.3 + - - +
71B LYS* 3.1 19.1 + - - +
73B ALA* 1.3 73.8 - - - +
75B VAL* 1.3 66.5 + - - +
76B ASP 2.9 2.5 - - - -
77B THR* 3.5 9.0 - - - -
78B TYR* 2.8 21.7 + - + +
79B CYS* 3.1 10.9 + - - -
311C GLN* 4.2 14.1 - - - +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 3.9 24.1 - - + +
26B PHE* 3.8 23.1 - - + +
42B SER* 3.8 20.4 - - - +
71B LYS 4.6 0.6 + - - +
72B ARG 4.2 15.2 + - - +
73B ALA 4.7 0.2 - - - -
74B ALA* 1.3 77.3 - - - +
76B ASP* 1.3 73.0 + - - +
79B CYS* 3.4 12.2 - - - +
80B ARG* 3.0 43.1 + - - +
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Residues in contact with ASP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ARG 5.4 0.2 - - - +
73B ALA* 3.3 12.0 + - + +
74B ALA 2.9 1.4 - - - -
75B VAL* 1.3 88.0 - - - +
77B THR* 1.3 64.1 + - + +
78B TYR 3.1 5.3 + - - -
80B ARG* 2.9 38.0 + - - +
81B HIS* 3.6 19.4 + - - +
29D PRO* 5.1 0.9 - - - +
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Residues in contact with THR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLN* 4.6 6.9 + - - -
73B ALA* 2.7 33.8 + - + +
74B ALA* 3.5 5.5 - - - -
76B ASP* 1.3 75.0 - - + +
78B TYR* 1.3 58.8 + - - +
81B HIS* 4.2 1.2 - - - +
309C VAL* 3.7 12.3 - - - +
311C GLN* 5.6 0.5 + - - -
29D PRO* 3.5 31.2 - - + +
31D TYR* 3.2 30.2 + - + +
51D SER* 3.8 25.8 - - - +
96D PRO* 5.6 0.5 - - - +
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Residues in contact with TYR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 5.8 2.2 - - + +
9A GLN* 2.9 36.5 + - - +
24A PHE* 4.1 5.4 - + - -
13B HIS* 3.6 10.8 + - + +
15B CYS* 3.5 31.9 - - - -
26B PHE* 3.7 23.3 - + - -
74B ALA* 2.8 14.3 + - - +
76B ASP 3.1 0.8 - - - -
77B THR* 1.3 81.2 - - - +
79B CYS* 1.3 66.6 + - - +
80B ARG 3.5 0.7 - - - -
81B HIS* 3.3 2.2 + - - +
82B ASN* 2.9 46.0 + - - -
309C VAL* 3.1 27.4 - - + -
310C LYS 4.0 1.8 - - - -
311C GLN* 3.4 44.4 - - + +
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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
------------------------------------------------------------
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