Contacts of the helix formed by residues 131 - 137 (chain J) in PDB entry 6QX2
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 ILE 131 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101J TYR* 4.1 24.0 - - + +
102J PRO 3.6 13.0 - - - +
103J LEU* 4.1 14.1 - - + -
129J THR* 3.1 14.6 - - - +
130J LYS* 1.3 76.0 - - - +
132J THR* 1.3 61.2 - - - +
134J GLU* 3.0 25.8 + - + +
135J LEU 3.5 3.5 + - - -
164J PHE* 3.5 33.6 - - + -
188J LEU* 4.1 10.8 - - + -
476J ILE* 6.0 0.2 - - + -
480J PHE* 3.7 48.5 - - + -
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Residues in contact with THR 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J LEU* 4.0 23.3 - - + -
103J LEU* 2.6 49.3 + - - +
128J MET* 3.8 20.0 - - + -
129J THR* 3.0 14.1 + - - -
131J ILE* 1.3 74.5 - - - +
133J LEU* 1.3 65.3 + - - +
135J LEU* 3.1 18.2 + - + +
136J LEU* 3.2 24.6 + - + +
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Residues in contact with LEU 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54J ASN* 5.4 2.7 - - - +
59J THR* 4.3 10.5 - - + -
60J PRO* 4.0 30.1 - - + -
128J MET* 3.6 25.6 - - + -
129J THR 3.7 1.8 + - - +
130J LYS* 3.2 20.4 - - + +
131J ILE 3.2 0.2 - - - -
132J THR* 1.3 78.6 - - - +
134J GLU* 1.3 57.1 + - - +
136J LEU* 3.2 5.8 + - + +
137J ARG* 2.7 37.2 + - - +
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Residues in contact with GLU 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J LYS 4.6 0.7 - - - +
131J ILE* 3.0 13.2 + - - +
133J LEU* 1.3 81.4 - - - +
135J LEU* 1.3 62.9 + - - +
136J LEU 3.4 0.2 + - - -
137J ARG* 2.7 41.8 + - - -
163J ARG* 3.0 38.5 + - + +
164J PHE* 3.9 14.8 - - + -
476J ILE* 3.6 14.8 - - + +
479J ARG* 3.3 29.7 + - - -
480J PHE* 3.7 26.0 - - + -
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Residues in contact with LEU 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J ASP* 4.5 5.8 - - + +
42J LEU* 4.5 5.6 - - + -
50J LEU* 3.6 28.3 - - + -
103J LEU* 3.8 26.5 - - + -
131J ILE 3.5 1.9 + - - +
132J THR* 3.1 13.5 + - + +
134J GLU* 1.3 77.0 - - - +
136J LEU* 1.3 58.8 + - + +
160J LEU* 3.5 15.6 - - + +
161J PRO* 3.4 11.1 - - - +
162J ALA* 3.0 44.6 + - + +
164J PHE* 3.6 23.8 - - + +
166J ASN* 3.9 24.0 - - + +
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Residues in contact with LEU 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J LEU* 3.7 18.6 - - + +
51J TYR* 4.4 5.2 - - - -
54J ASN* 3.7 38.1 - - + +
128J MET* 3.7 20.2 - - - -
132J THR* 3.2 24.6 + - + +
133J LEU* 3.2 5.6 + - + +
135J LEU* 1.3 77.3 - - + +
137J ARG* 1.3 67.6 + - - +
138J ASP 3.2 0.5 + - - -
139J ILE* 3.0 43.7 + - + +
160J LEU* 3.9 25.4 - - + -
161J PRO* 4.2 3.4 - - - -
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Residues in contact with ARG 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J LEU* 2.7 15.8 + - + +
134J GLU* 2.7 39.9 + - - +
135J LEU 3.5 1.8 - - - -
136J LEU* 1.3 73.8 - - - +
138J ASP* 1.3 82.6 + - - +
161J PRO* 3.2 22.5 - - - +
163J ARG* 3.5 26.6 - - + +
366J ARG* 4.0 4.9 - - - +
472J GLU* 3.3 38.8 + - - +
475J GLU* 4.4 9.3 + - - -
476J ILE* 4.0 15.8 - - - +
479J ARG* 4.9 1.2 - - - +
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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