Contacts of the helix formed by residues 128 - 132 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ASP* 5.2 0.7 - - - +
93D ILE* 4.2 3.8 - - - +
94D ALA* 4.0 25.7 - - + +
125D LYS* 3.1 36.8 + - + +
126D SER 4.2 1.8 - - - -
127D ASP* 1.3 93.3 - - - +
129D ARG* 1.3 62.9 + - - +
130D HIS* 3.2 21.5 - - + -
131D LEU* 3.1 26.3 + - + -
132D ARG* 3.4 10.2 + - - -
156D LEU* 6.2 0.2 - - + -
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Residues in contact with ARG 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1504B PRO* 3.2 19.9 - - - +
1670B HIS* 4.9 6.0 + - - -
1674B CYS* 3.4 60.8 - - - +
1677B GLY* 3.9 5.3 - - - -
1678B MET 5.7 1.3 + - - +
1680B PRO* 5.3 9.1 - - - +
1683B ILE* 4.0 15.0 - - - +
93D ILE* 5.2 1.8 - - - -
126D SER 3.3 19.4 + - - +
127D ASP* 2.9 26.7 + - - +
128D LEU* 1.3 76.2 - - - +
130D HIS* 1.3 61.2 + - - +
131D LEU 3.1 1.4 + - - -
132D ARG* 3.5 19.8 + - - +
157D ASP* 5.3 2.4 + - - -
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Residues in contact with HIS 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1504B PRO* 4.3 9.2 - - - +
1509B TYR* 5.3 1.6 + - - -
1561B ARG* 3.5 21.0 + - - +
1677B GLY* 3.2 28.2 - - - +
1678B MET 3.8 12.3 - - - +
1679B ASP* 3.6 20.4 - - - +
1680B PRO* 3.6 24.6 - - + +
1830B ASN* 3.7 21.8 + - + +
127D ASP 4.8 2.3 + - - -
128D LEU* 4.0 21.2 - - + -
129D ARG* 1.3 78.5 + - - +
131D LEU* 1.3 95.5 + - + +
132D ARG 3.6 0.4 - - - -
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Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1504B PRO* 5.0 0.2 - - - -
1561B ARG* 3.5 26.2 - - - +
1830B ASN* 4.1 2.7 - - + +
1831B PRO 3.8 14.8 - - - +
1832B SER* 3.7 21.3 - - - -
1833B SER 5.6 1.5 + - - +
1834B LEU* 3.6 16.8 - - - +
94D ALA* 3.4 24.7 - - + +
128D LEU* 3.1 28.3 + - + +
130D HIS* 1.3 110.0 - - + +
132D ARG* 1.3 64.3 + - - +
133D ALA 3.3 2.4 + - - -
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Residues in contact with ARG 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1502B LEU 3.8 20.9 - - - -
1503B ILE* 3.6 17.8 - - + +
1504B PRO* 3.7 21.3 - - + +
1834B LEU* 4.0 8.3 - - - +
93D ILE* 3.6 32.9 - - + +
126D SER* 5.1 5.7 + - - -
128D LEU 3.4 4.9 + - - -
129D ARG* 3.5 17.9 + - - +
130D HIS 3.6 0.6 - - - -
131D LEU* 1.3 77.8 - - - +
133D ALA* 1.3 61.4 + - - +
134D VAL 3.1 29.6 + - - +
135D PRO* 4.5 0.9 - - - -
136D THR* 3.1 12.9 + - - +
152D GLU* 2.8 43.6 + - - -
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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