Contacts of the helix formed by residues 130 - 139 (chain J) in PDB entry 6K71
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 130 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48J VAL* 6.3 0.4 - - - -
50J ASP 4.5 9.2 - - - -
51J SER* 4.7 2.2 - - - -
52J PHE* 4.3 17.7 - - - -
129J ARG* 1.3 101.1 + - - +
131J LEU* 1.3 66.1 + - - +
132J GLY 3.1 0.7 - - - -
133J ASP* 2.9 20.6 + - - +
134J VAL* 3.3 11.4 - - - +
267J GLN* 2.3 31.9 + - - -
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Residues in contact with LEU 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48J VAL* 4.9 16.8 - - + +
50J ASP 5.3 0.4 + - - -
51J SER* 4.0 22.3 + - - +
130J SER* 1.3 77.4 + - - +
132J GLY* 1.3 56.2 + - - +
133J ASP 3.6 0.2 - - - -
134J VAL* 3.3 12.4 - - + +
135J LEU* 3.0 35.9 + - + +
150J LEU* 5.2 13.2 - - + -
152J TYR* 4.6 13.7 - - + +
260J PHE* 4.3 8.8 - - + -
267J GLN* 3.3 43.7 - - - +
268J THR* 3.8 16.2 - - + -
269J ARG* 4.1 21.8 - - + +
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Residues in contact with GLY 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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129J ARG* 5.0 2.5 - - - -
130J SER* 3.1 0.6 - - - -
131J LEU* 1.3 76.9 - - - +
133J ASP* 1.3 58.2 + - - +
135J LEU* 3.2 1.0 + - - -
136J ARG* 3.0 51.2 + - - -
260J PHE* 3.9 6.4 - - - -
267J GLN* 3.0 27.3 - - - +
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Residues in contact with ASP 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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127J LEU* 2.9 39.3 - - + +
128J TYR* 3.2 20.0 - - + +
129J ARG* 3.2 23.9 + - - +
130J SER* 2.9 23.1 + - - +
132J GLY* 1.3 71.0 - - - +
134J VAL* 1.3 60.7 + - - +
136J ARG* 3.8 11.6 - - + +
137J ASP* 2.8 29.3 + - - +
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Residues in contact with VAL 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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46J VAL* 4.6 7.9 - - + -
48J VAL* 3.6 29.4 - - + -
94J PHE* 3.5 41.7 - - + -
128J TYR* 5.8 5.6 - - + -
130J SER 3.3 15.7 + - - +
131J LEU* 3.3 14.4 - - + +
132J GLY 3.1 0.4 - - - -
133J ASP* 1.3 80.4 + - - +
135J LEU* 1.3 67.6 + - + +
137J ASP* 3.1 5.7 + - - +
138J VAL* 2.9 25.9 + - + +
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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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46J VAL* 5.4 1.6 - - + -
131J LEU* 3.0 19.0 + - + +
134J VAL* 1.3 78.9 - - + +
136J ARG* 1.3 60.6 + - - +
138J VAL* 3.3 20.9 - - + +
139J ASP* 2.8 33.3 + - - +
148J PHE* 4.6 15.3 - - + -
150J LEU* 4.9 25.8 - - + -
252J CYS* 5.8 1.6 - - - -
256J VAL* 5.3 12.6 - - + +
257J ALA* 5.5 4.8 - - - +
260J PHE* 3.5 54.7 - - + -
261J THR* 5.0 0.2 - - - -
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Residues in contact with ARG 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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132J GLY* 3.0 35.3 + - - +
133J ASP* 4.0 10.5 - - + +
135J LEU* 1.3 76.9 - - - +
137J ASP* 1.3 58.0 + - - +
139J ASP* 2.9 7.6 - - - +
140J ALA* 2.9 31.1 + - - +
260J PHE* 3.0 52.1 + - - -
261J THR* 4.1 19.0 - - + +
263J ASN 3.6 1.2 + - - -
264J PHE* 3.2 50.0 + - + +
266J TYR 3.8 10.7 + - - -
267J GLN* 4.8 4.2 - - - +
430P THR* 4.7 13.0 - - - +
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Residues in contact with ASP 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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94J PHE* 3.5 24.9 - - + -
123J ILE* 4.7 4.2 - - - +
128J TYR* 4.2 17.2 + - + -
133J ASP 2.8 19.7 + - - +
134J VAL* 3.4 6.5 - - - +
136J ARG* 1.3 77.5 - - - +
138J VAL* 1.3 56.7 + - - +
140J ALA* 4.2 4.6 - - - +
141J LYS* 2.7 46.2 + - - +
143J LEU* 4.9 3.5 - - - +
303P LYS* 4.1 24.0 - - - +
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Residues in contact with VAL 138 (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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46J VAL* 4.8 19.1 - - + -
92J PHE* 5.7 3.6 - - + -
94J PHE* 5.4 3.1 - - + -
134J VAL* 2.9 11.7 + - + +
135J LEU* 3.2 39.4 + - + +
137J ASP* 1.3 79.0 - - - +
139J ASP* 1.3 59.2 + - + +
141J LYS* 5.2 0.9 - - - -
142J ALA* 3.3 18.3 - - - +
143J LEU* 4.4 23.1 - - + +
144J VAL* 3.4 23.0 - - + +
148J PHE* 4.5 16.6 - - + -
257J ALA* 5.6 4.5 - - + -
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Residues in contact with ASP 139 (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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135J LEU 2.8 20.5 + - - +
136J ARG* 2.9 14.0 - - - +
138J VAL* 1.3 80.1 - - - +
140J ALA* 1.3 57.7 + - - +
142J ALA* 3.9 11.9 - - - +
144J VAL* 5.1 2.5 - - + -
257J ALA* 2.9 37.8 - - + +
261J THR* 2.4 35.7 + - - +
352P ARG* 4.9 10.6 - - - +
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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