Contacts of the helix formed by residues 128 - 132 (chain A) in PDB entry 5JCZ
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 LEU 128 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ASP* 5.3 0.9 - - - +
93A ILE* 4.0 5.6 - - - +
94A ALA* 4.0 23.1 - - + -
125A LYS* 3.0 38.9 + - + +
126A SER 4.2 1.1 - - - -
127A ASP* 1.3 94.1 - - - +
129A ARG* 1.3 63.7 + - - +
130A HIS* 3.2 21.3 - - + -
131A LEU* 3.0 26.2 + - + -
132A ARG 3.4 8.0 + - - -
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 5.0 2.0 - - - -
126A SER 3.2 20.3 + - - +
127A ASP* 3.1 26.8 + - - +
128A LEU* 1.3 76.0 - - - +
130A HIS* 1.3 61.8 + - - +
131A LEU 3.1 1.1 + - - -
132A ARG* 3.5 19.1 + - - +
157A ASP* 5.3 3.4 + - - -
1504C PRO* 3.2 19.8 - - - +
1670C HIS* 5.1 3.8 + - - -
1674C CYS* 3.4 61.0 - - - +
1677C GLY* 4.0 5.3 - - - -
1678C MET 5.4 2.3 + - - +
1680C PRO* 5.1 11.7 - - - +
1683C ILE* 4.0 16.2 - - - +
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Residues in contact with HIS 130 (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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127A ASP 4.8 2.1 + - - -
128A LEU* 4.0 21.6 - - + -
129A ARG* 1.3 78.6 + - - +
131A LEU* 1.3 96.3 + - + +
132A ARG 3.6 0.7 - - - -
1504C PRO* 4.2 9.6 - - - +
1509C TYR* 5.4 1.0 + - - -
1561C ARG* 3.4 21.9 + - - +
1677C GLY* 3.2 27.6 - - - +
1678C MET 3.8 13.4 + - - +
1679C ASP* 3.7 7.9 - - - +
1680C PRO* 3.6 28.1 - - + +
1830C ASN* 3.6 30.6 + - + +
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA* 3.4 24.3 - - + +
128A LEU* 3.0 27.6 + - + +
130A HIS* 1.3 110.8 - - + +
132A ARG* 1.3 64.2 + - - +
133A ALA 3.3 2.6 + - - -
1504C PRO* 5.1 0.2 - - - -
1561C ARG* 3.6 25.1 - - - +
1830C ASN* 4.1 2.7 - - + +
1831C PRO 3.7 22.4 - - - +
1832C SER* 3.9 14.3 - - - -
1833C SER 5.4 1.5 + - - +
1834C LEU* 3.8 12.5 - - - +
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Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 3.6 32.3 - - + +
94A ALA* 4.4 0.7 - - - +
126A SER* 5.1 5.7 + - - -
128A LEU 3.4 4.9 + - - -
129A ARG* 3.5 16.6 + - - +
130A HIS 3.6 1.0 + - - -
131A LEU* 1.3 76.9 - - - +
133A ALA* 1.3 60.7 + - - +
134A VAL 3.0 30.4 + - - +
135A PRO* 4.4 0.9 - - - -
136A THR* 3.1 13.4 + - - +
152A GLU* 2.8 42.6 + - - -
1502C LEU 3.6 22.2 - - - +
1503C ILE* 3.8 15.3 - - + +
1504C PRO* 3.6 21.6 - - + +
1509C TYR* 6.1 0.2 - - - -
1834C LEU* 3.7 9.0 - - - +
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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