Contacts of the helix formed by residues 131 - 139 (chain k) in PDB entry 5JPQ
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 SER 131 (chain k).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15232 G 1.6 65.9 - - - -
129k ASP* 3.1 6.8 - - - +
130k ILE* 1.3 74.3 - - - +
132k HIS* 1.3 49.2 - - - +
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Residues in contact with HIS 132 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14792 A 5.4 7.9 - - - +
15232 G 1.2 85.4 + - - +
128k ILE* 5.3 4.9 - - + -
129k ASP* 3.0 21.5 + - + +
131k SER* 1.3 68.9 - - - +
133k LEU* 1.3 51.9 + - - +
136k LYS* 2.8 16.6 + - + +
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Residues in contact with LEU 133 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15232 G 0.9 52.9 + - + +
129k ASP 3.7 4.8 + - - +
130k ILE* 3.5 14.0 + - - +
132k HIS* 1.3 59.7 - - - +
134k LYS* 1.3 60.8 + - - +
136k LYS* 3.2 6.8 + - - +
137k PHE 3.1 17.3 + - - -
162k ARG* 5.2 14.4 - - + -
163k LEU* 5.5 9.0 - - + -
166k ALA* 3.9 13.9 - - + +
167k LEU* 6.1 0.3 - - - +
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Residues in contact with LYS 134 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15232 G 2.2 54.3 + - + +
133k LEU* 1.3 69.4 - - - +
135k ALA* 1.3 60.5 + - - +
137k PHE* 3.1 10.3 + - - +
138k LYS* 3.1 20.8 + - - +
166k ALA* 4.6 3.8 - - - -
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Residues in contact with ALA 135 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15232 G 1.8 61.4 + - + +
15252 A 5.9 2.2 - - - +
134k LYS* 1.3 77.2 - - - +
136k LYS* 1.3 58.6 + - - +
138k LYS* 3.2 9.3 + - - +
139k ALA* 3.1 20.8 + - - +
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Residues in contact with LYS 136 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132k HIS* 2.8 14.5 + - + +
133k LEU* 3.7 9.2 - - - +
134k LYS 3.2 0.2 - - - -
135k ALA* 1.3 73.0 - - - +
137k PHE* 1.4 64.1 + - - +
138k LYS 3.1 1.8 - - - -
139k ALA* 2.8 28.5 - - - +
140k TYR* 4.5 0.3 - - - -
142k ALA* 6.0 3.8 - - + -
143k GLN* 3.9 21.4 - - + +
167k LEU* 6.4 1.8 - - + -
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Residues in contact with PHE 137 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133k LEU 3.1 6.5 + - - -
134k LYS* 3.4 9.4 - - - +
136k LYS* 1.4 76.3 - - - +
138k LYS* 1.3 61.9 + - - +
139k ALA 4.5 1.4 - - - -
140k TYR* 4.6 3.8 + - - +
143k GLN* 5.9 0.2 - - - -
166k ALA* 2.9 52.2 - - + +
167k LEU* 5.4 1.5 - - - +
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Residues in contact with LYS 138 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134k LYS 3.1 8.1 + - - +
135k ALA* 3.3 11.7 - - - +
136k LYS 3.1 0.2 - - - -
137k PHE* 1.3 82.7 - - - +
139k ALA* 1.4 60.4 + - + +
140k TYR* 3.5 3.3 + - - +
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Residues in contact with ALA 139 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135k ALA 3.1 11.0 + - - +
136k LYS* 2.8 20.9 + - - +
138k LYS* 1.4 75.2 - - + +
140k TYR* 1.3 61.5 + - - +
141k GLU* 3.4 6.2 + - + +
142k ALA* 3.5 13.5 + - + +
143k GLN 3.3 12.8 + - - -
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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