Contacts of the helix formed by residues 129 - 139 (chain q) 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 PRO 129 (chain q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46q TRP* 4.6 17.0 - - + -
118q LEU* 4.8 12.8 - - + +
121q ILE 3.8 8.1 - - - +
122q ASN* 3.3 34.5 - - + -
127q GLN 3.2 5.3 - - - -
128q ASN* 1.3 73.7 - - - +
130q ILE* 1.3 61.2 + - - +
131q GLN 3.2 0.4 - - - -
132q VAL* 2.9 9.9 + - + +
133q VAL* 2.8 27.6 + - - +
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Residues in contact with ILE 130 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47q SER* 6.2 0.4 - - - -
48q PHE 3.4 24.2 - - - +
49q GLU* 5.3 2.0 - - - -
50q GLU 5.6 0.4 - - - +
128q ASN 2.4 15.7 + - - +
129q PRO* 1.3 71.5 - - - +
131q GLN* 1.3 49.8 + - - +
133q VAL* 2.9 10.5 + - - +
134q VAL* 2.6 34.8 + - - +
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Residues in contact with GLN 131 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48q PHE 4.3 0.2 + - - -
50q GLU* 3.4 32.7 - - + +
53q VAL* 5.5 5.1 - - + +
127q GLN* 3.4 16.8 - - - +
128q ASN* 3.5 8.9 + - + -
129q PRO 3.2 0.4 - - - -
130q ILE* 1.3 74.4 - - - +
132q VAL* 1.3 54.2 + - - +
133q VAL 3.2 0.2 - - - -
134q VAL* 4.1 8.5 - - + -
135q ASP* 2.6 42.1 + - + +
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Residues in contact with VAL 132 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121q ILE* 4.6 9.4 - - + +
122q ASN* 6.1 0.4 - - - -
127q GLN* 3.6 22.3 + - + +
129q PRO* 2.9 21.5 + - + +
131q GLN* 1.3 77.9 - - - +
133q VAL* 1.3 48.8 + - - +
135q ASP* 3.3 4.5 - - - -
136q ALA* 2.5 36.4 + - - +
198q LEU 4.9 1.0 - - - +
202q ALA* 4.4 21.2 - - + +
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Residues in contact with VAL 133 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94q THR* 5.4 11.7 - - - -
129q PRO 2.8 11.5 + - - +
130q ILE* 2.9 13.7 + - - +
132q VAL* 1.3 74.5 - - - +
134q VAL* 1.3 66.4 + - - +
136q ALA* 3.0 18.6 - - - +
137q ILE* 3.1 10.0 + - - +
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Residues in contact with VAL 134 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50q GLU* 5.8 4.0 - - + +
53q VAL* 4.9 13.5 - - + +
130q ILE 2.6 18.6 + - - +
131q GLN* 4.1 7.9 - - - -
133q VAL* 1.3 66.8 - - - +
135q ASP* 1.3 50.6 + - - +
136q ALA 2.6 6.5 + - - -
137q ILE* 3.0 5.9 + - - +
138q THR* 2.6 36.9 + - - -
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Residues in contact with ASP 135 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53q VAL* 5.1 12.9 - - + +
127q GLN* 6.5 0.2 - - + -
131q GLN 2.6 26.9 + - - +
132q VAL* 3.3 5.2 - - - +
134q VAL* 1.3 70.3 - - - +
136q ALA* 1.3 59.9 + - - +
138q THR* 3.2 17.5 - - - -
139q ASN* 4.0 5.4 + - - +
201q ALA 3.8 9.9 - - - +
202q ALA* 4.9 3.2 - - + -
205q SER* 4.5 8.7 - - - -
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Residues in contact with ALA 136 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132q VAL 2.5 21.4 + - - +
133q VAL* 3.0 13.9 - - - +
134q VAL 2.6 4.6 + - - -
135q ASP* 1.3 71.9 - - - +
137q ILE* 1.3 56.3 + - - +
138q THR* 2.7 13.3 + - - -
139q ASN 3.9 0.7 + - - +
140q THR* 2.9 25.7 + - - -
175q LEU* 6.4 1.8 - - + -
198q LEU* 4.4 22.2 - - + +
201q ALA* 3.9 14.0 - - + +
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Residues in contact with ILE 137 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133q VAL 3.1 8.4 + - - +
134q VAL* 3.0 6.7 + - - +
136q ALA* 1.3 76.6 - - - +
138q THR* 1.3 63.1 + - - +
140q THR* 4.3 14.1 + - - -
141q GLY* 4.6 1.0 + - - -
167q ARG 5.1 2.9 - - - +
168q VAL* 4.9 19.2 - - + +
171q ALA* 5.0 8.1 - - + +
172q ILE* 5.4 9.6 - - + -
175q LEU* 6.3 2.9 - - + -
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Residues in contact with THR 138 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53q VAL* 5.4 10.5 - - - -
54q LYS* 6.0 2.9 - - - -
55q ASP 6.2 0.9 - - - -
134q VAL 2.6 17.7 + - - -
135q ASP* 3.2 19.1 - - - -
136q ALA 2.7 2.2 + - - -
137q ILE* 1.3 81.5 - - - +
139q ASN* 1.3 55.9 + - - -
140q THR* 2.7 15.8 + - - -
141q GLY* 4.0 3.8 + - - -
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Residues in contact with ASN 139 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135q ASP 4.0 6.5 + - - +
136q ALA 3.9 2.9 + - - +
138q THR* 1.3 76.4 - - - +
140q THR* 1.3 62.7 + - - +
201q ALA 4.9 4.7 - - - +
205q SER* 5.0 16.3 - - - -
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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