Contacts of the helix formed by residues 115 - 123 (chain B) in PDB entry 1JTY
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 LYS 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B ASN* 5.0 15.5 - - - +
51B LEU* 3.9 19.3 - - + -
52B GLU* 2.7 37.2 + - - +
55B ASN* 5.1 2.4 - - - +
114B GLU* 1.3 100.8 - - - +
116B MET* 1.3 59.1 + - - +
117B ASN 2.9 5.2 - - - -
118B LYS* 2.8 66.5 + - + +
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Residues in contact with MET 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU* 3.5 26.1 - - + +
54B LEU* 4.1 15.3 - - + -
99B ILE* 4.2 17.5 - - + -
102B PHE* 3.6 39.0 - - + -
103B TYR* 4.2 17.3 - - + +
111B SER 2.7 20.6 + - - +
112B ILE* 2.9 29.7 - - + +
115B LYS* 1.3 78.4 - - - +
117B ASN* 1.3 57.6 + - - +
118B LYS 3.3 0.2 - - - -
119B LEU* 3.8 8.4 + - + +
120B GLU* 3.3 19.9 + - - +
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Residues in contact with ASN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLU* 5.4 6.4 - - - +
112B ILE 3.3 4.0 + - - +
113B ASN* 2.8 40.3 - - - +
114B GLU 3.5 4.4 + - - +
115B LYS 2.9 0.8 - - - -
116B MET* 1.3 76.6 - - - +
118B LYS* 1.3 65.8 + - - +
119B LEU 3.3 0.4 - - - -
120B GLU* 3.4 11.2 + - - +
121B ASN* 3.0 39.6 + - - +
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU* 3.6 17.0 + - - +
55B ASN* 2.8 48.4 - - - +
114B GLU 4.1 1.9 + - - +
115B LYS* 2.8 40.5 + - + +
117B ASN* 1.3 80.3 - - - +
119B LEU* 1.3 81.3 + - - +
121B ASN* 3.1 21.5 + - - +
122B LYS* 3.2 12.9 + - - +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU* 3.8 20.6 - - + -
54B LEU* 3.4 36.1 - - + -
55B ASN* 3.5 14.4 - - + +
58B GLU* 3.6 39.7 - - + -
92B TYR* 4.0 13.9 - - + +
115B LYS 3.6 0.6 + - - -
116B MET* 3.9 13.2 - - + +
117B ASN 3.3 0.2 - - - -
118B LYS* 1.3 91.5 - - - +
120B GLU* 1.3 52.2 + - - +
121B ASN 2.7 9.9 + - - -
122B LYS* 3.0 5.5 + - + +
123B TYR* 2.7 36.5 + - + +
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A PHE 5.4 1.6 - - - +
165A GLU* 3.8 38.0 - - + +
166A GLN* 4.6 0.3 - - - +
103B TYR* 5.6 2.5 - - - +
112B ILE 6.1 0.4 - - - +
116B MET* 3.3 13.4 + - + +
117B ASN* 3.5 18.2 - - - +
119B LEU* 1.3 78.6 - - - +
121B ASN* 1.3 63.4 + - - +
123B TYR* 4.0 15.4 - - + +
124B ILE* 3.4 32.7 + - - +
150B LYS* 4.4 20.0 - - - +
154B ASN* 5.3 5.0 + - - +
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Residues in contact with ASN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ASN* 3.0 28.9 + - - +
118B LYS* 3.1 12.2 + - - +
119B LEU 2.7 1.6 + - - -
120B GLU* 1.3 81.1 - - - +
122B LYS* 1.3 64.3 + - - +
123B TYR 3.2 1.1 - - - -
124B ILE* 3.2 12.2 + - - +
125B ASP* 3.1 20.7 + - - +
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Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ASN* 2.8 32.4 + - - +
58B GLU* 3.0 28.9 - - + +
59B SER* 2.9 25.9 + - - +
62B GLN* 3.3 25.4 - - + +
118B LYS* 3.2 10.8 + - - +
119B LEU* 3.0 6.7 + - + +
121B ASN* 1.3 79.6 - - - +
123B TYR* 1.3 62.4 + - - +
125B ASP* 3.1 23.1 + - + +
126B ALA 4.2 0.9 + - - -
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Residues in contact with TYR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A PHE* 5.4 0.4 - - + -
58B GLU* 3.4 17.4 + - + +
82B TYR* 4.3 11.3 + - - -
92B TYR* 4.1 31.2 - + - +
93B TYR* 5.2 10.3 - + - -
96B GLN* 4.8 0.4 - - - -
119B LEU* 2.7 20.0 + - + +
120B GLU* 4.0 15.7 - - + +
122B LYS* 1.3 77.2 - - - +
124B ILE* 1.3 77.3 + - + +
126B ALA* 5.3 1.0 + - - +
127B TYR* 4.3 11.9 - + - -
153B ALA* 2.9 35.9 + - + +
154B ASN* 2.8 33.8 + - - -
157B ASN* 3.3 26.8 + - + +
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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