Contacts of the helix formed by residues 115 - 124 (chain J) in PDB entry 3TKR
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 115 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D LEU* 4.1 10.6 - - - +
82D ASP 4.6 1.7 + - - -
114J ASP* 1.3 75.6 - - - +
116J GLN* 1.3 61.8 + - - +
117J PHE* 3.2 18.6 + - - +
118J GLU* 3.0 38.0 + - - +
119J HIS* 3.0 26.7 + - - -
141J SER* 3.3 7.0 - - - -
143J LEU* 3.7 25.7 - - - +
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Residues in contact with GLN 116 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54J THR* 4.0 32.1 + - + +
56J VAL* 3.4 13.3 - - + +
61J PHE* 3.5 40.1 - - + -
115J SER* 1.3 77.9 - - - +
117J PHE* 1.3 82.1 + - + +
119J HIS* 3.3 10.5 + - - -
120J LEU 3.0 23.2 + - - -
141J SER* 3.5 17.0 + - - -
143J LEU* 4.5 7.3 - - - +
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Residues in contact with PHE 117 (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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81D LEU* 3.9 17.0 - - + -
82D ASP 4.3 4.5 - - - +
83D PHE* 3.9 21.6 - - - +
84D THR* 3.5 27.8 - - + -
85D PHE* 3.8 29.8 - + - -
223F PRO* 4.5 6.1 - - + -
61J PHE* 3.6 30.7 - + - -
115J SER* 3.1 12.1 - - - +
116J GLN* 1.3 104.5 - - - +
118J GLU* 1.3 57.0 + - - +
120J LEU* 3.4 4.6 + - - +
121J ALA* 3.0 27.9 + - - +
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Residues in contact with GLU 118 (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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82D ASP* 3.6 7.6 - - - +
83D PHE* 3.8 19.7 - - + -
114D ASP* 2.4 35.2 - - - +
118D GLU* 2.8 46.2 - - + +
82J ASP* 3.4 8.5 - - + +
83J PHE* 4.0 3.8 - - + -
114J ASP* 3.7 2.1 - - - +
115J SER* 3.0 36.8 + - - +
117J PHE* 1.3 74.8 - - - +
119J HIS* 1.3 66.6 + - - +
121J ALA* 3.2 6.1 + - - +
122J TRP* 2.9 25.8 + - - +
143J LEU* 5.2 0.5 - - - +
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Residues in contact with HIS 119 (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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56J VAL* 3.6 10.8 - - + -
79J TYR* 3.1 23.5 + + - -
82J ASP* 2.6 27.4 + - - -
111J CYS* 5.4 0.2 - - - -
112J SER* 3.1 19.5 + - - -
114J ASP* 3.8 8.5 - - + -
115J SER 3.0 13.8 + - - -
116J GLN* 3.3 10.5 + - - +
118J GLU* 1.3 75.3 - - - +
120J LEU* 1.3 57.8 + - - +
122J TRP* 3.2 3.7 + - - +
123J ILE* 2.9 34.2 + - - +
139J LEU* 3.3 43.3 - - + +
140J LEU 2.9 25.0 + - - -
141J SER* 3.9 9.7 - - - -
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Residues in contact with LEU 120 (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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223F PRO* 3.6 38.6 - - + -
56J VAL* 4.4 7.0 - - + -
59J GLY* 3.8 33.9 - - - +
61J PHE* 4.0 14.1 - - + -
116J GLN 3.0 15.5 + - - +
117J PHE* 3.7 4.5 - - - +
119J HIS* 1.3 75.7 - - - +
121J ALA* 1.3 60.2 + - - +
123J ILE* 3.3 11.4 + - + +
124J ASN* 3.0 54.0 + - - +
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Residues in contact with ALA 121 (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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83D PHE* 3.7 38.8 - - + -
83J PHE* 4.0 5.2 - - + -
117J PHE 3.0 17.6 + - - +
118J GLU* 3.7 4.3 - - - +
120J LEU* 1.3 75.9 - - - +
122J TRP* 1.3 55.4 + - - +
124J ASN* 3.4 10.8 + - - +
125J THR* 2.7 32.4 + - - -
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Residues in contact with TRP 122 (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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79J TYR* 3.6 5.4 - + - -
82J ASP* 3.2 36.6 - - - +
83J PHE* 3.2 54.3 - + + +
87J CYS* 4.1 6.5 - - + -
88J PRO* 3.5 47.1 - - + -
91J ILE* 3.4 27.8 - - + -
118J GLU 2.9 16.9 + - - +
119J HIS 3.4 4.0 - - - +
121J ALA* 1.3 76.2 - - - +
123J ILE* 1.3 64.9 + - - +
125J THR* 3.1 11.9 + - - -
130J GLY 3.0 19.1 + - - -
131J GLY* 3.6 8.4 - - - -
132J LEU* 3.1 40.4 + - + -
139J LEU* 4.9 2.0 - - + -
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Residues in contact with ILE 123 (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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56J VAL* 3.6 31.4 - - + +
59J GLY* 5.5 6.5 - - - +
119J HIS 2.9 19.9 + - - +
120J LEU* 3.3 13.2 + - + +
122J TRP* 1.3 77.6 - - - +
124J ASN* 1.3 65.6 + - - +
125J THR 3.1 2.1 + - - -
132J LEU* 4.1 6.7 - - + -
133J GLY* 3.2 41.4 + - - +
134J PRO* 4.2 8.5 - - + +
135J ILE* 3.6 31.0 - - + +
139J LEU* 3.8 16.6 - - + -
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Residues in contact with ASN 124 (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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120J LEU* 3.0 42.3 + - - +
121J ALA* 3.6 10.1 - - - +
122J TRP 3.2 0.2 - - - -
123J ILE* 1.3 80.5 - - - +
125J THR* 1.3 59.9 + - - +
126J PRO* 3.9 4.9 - - - +
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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