Contacts of the helix formed by residues 114 - 124 (chain J) in PDB entry 6O81
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 LEU 114 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198F ILE* 4.0 26.2 - - + -
42J LEU* 3.7 43.2 - - + +
43J LEU* 5.3 7.9 - - + -
46J VAL* 5.3 6.5 - - + -
48J PHE* 4.7 9.2 - - + -
102J LEU* 5.0 9.0 - - + -
104J LEU* 5.5 2.5 - - + -
110J THR* 5.9 0.4 - - + -
112J VAL* 3.3 6.6 + - - +
113J ALA* 1.3 69.0 - - - +
115J HIS* 1.3 61.4 + - - +
116J GLU* 3.2 5.6 - - - +
117J VAL* 3.3 13.2 - - + +
118J VAL* 3.3 27.3 - - + +
131J LEU* 5.9 2.0 - - + -
204J LEU* 3.8 38.1 - - + -
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Residues in contact with HIS 115 (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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193F THR* 3.6 17.5 - - - +
194F GLN* 3.4 48.8 + - + +
196F MET 5.4 1.3 - - - +
198F ILE* 3.7 23.2 - - + +
46J VAL* 6.2 0.7 - - + -
113J ALA* 3.2 28.9 + - + +
114J LEU* 1.3 78.1 - - - +
116J GLU* 1.3 69.0 + - + +
118J VAL* 3.3 3.5 + - - +
119J ASP* 2.9 44.0 + - - +
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Residues in contact with GLU 116 (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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112J VAL* 4.4 8.8 - - + +
113J ALA 3.7 14.9 - - - +
114J LEU* 4.8 1.3 - - - -
115J HIS* 1.3 93.2 - - + +
117J VAL* 1.3 75.1 + - - +
119J ASP* 3.2 9.9 + - - +
120J LEU* 2.9 30.1 + - - +
131J LEU* 3.8 12.5 - - - +
266J PHE* 3.1 59.0 - - + +
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Residues in contact with VAL 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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114J LEU* 3.3 20.0 - - + +
116J GLU* 1.3 91.9 - - - +
118J VAL* 1.3 63.1 + - + +
120J LEU* 3.3 8.6 + - + +
121J PHE* 2.9 26.5 + - - +
129J ALA* 3.9 22.2 - - + +
130J MET* 3.8 28.7 - - - +
131J LEU* 4.6 6.3 - - + +
204J LEU* 4.1 26.7 - - + +
206J CYS* 4.6 7.9 - - - -
264J TYR 6.3 0.2 - - - -
266J PHE* 5.2 3.1 - - + +
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Residues in contact with VAL 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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198F ILE* 3.7 30.1 - - + -
3J PHE* 3.6 22.2 - - + -
102J LEU* 4.5 10.5 - - + -
114J LEU* 3.3 22.0 - - + +
115J HIS 3.3 6.5 + - - +
116J GLU 3.3 0.2 - - - -
117J VAL* 1.3 81.2 - - + +
119J ASP* 1.3 60.0 + - - +
121J PHE* 3.3 5.4 + - - +
122J ARG* 2.9 62.0 + - - +
206J CYS* 5.0 3.6 - - - -
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Residues in contact with ASP 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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191F SER* 4.5 9.1 + - - -
193F THR* 2.8 34.3 + - - +
198F ILE* 6.0 0.2 - - - +
212F LEU* 3.7 19.5 - - + +
216F GLN* 5.2 9.0 - - - +
115J HIS* 2.9 34.5 + - - +
116J GLU* 3.2 10.9 + - - +
118J VAL* 1.3 78.8 - - - +
120J LEU* 1.3 56.1 + - - +
122J ARG* 4.5 5.4 + - - -
123J ALA* 2.9 36.4 + - - +
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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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216F GLN* 6.0 1.8 - - - +
116J GLU* 2.9 18.2 + - - +
117J VAL* 3.7 11.7 - - + +
119J ASP* 1.3 76.9 - - + +
121J PHE* 1.3 61.7 + - - +
124J TYR* 3.7 52.4 + - + +
126J ALA* 4.1 6.6 - - - +
129J ALA* 4.8 4.3 - - + -
165J LYS* 3.8 26.0 - - + +
264J TYR* 4.0 21.7 - - + -
265J SER 4.2 14.6 - - - +
266J PHE* 4.0 32.5 - - + +
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Residues in contact with PHE 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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209F ARG* 3.7 14.0 + - - -
3J PHE* 3.5 30.1 - + - -
100J ASP* 3.8 13.7 - - - -
117J VAL 2.9 16.6 + - - +
118J VAL* 3.6 8.3 - - - +
119J ASP 3.3 0.2 - - - -
120J LEU* 1.3 79.0 - - - +
122J ARG* 1.3 64.1 + - + +
126J ALA* 3.2 52.2 + - + +
127J SER 3.8 8.3 - - - -
128J LEU 4.3 0.2 - - - -
129J ALA* 3.8 17.2 - - + +
206J CYS* 3.3 37.9 - - + -
207J LEU 4.2 12.3 - - - -
208J LYS* 3.6 18.8 - - - -
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Residues in contact with ARG 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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193F THR* 4.5 13.5 - - - +
197F SER 4.3 6.5 + - - -
198F ILE* 2.4 36.0 + - - +
200F SER* 3.2 20.0 + - - -
208F VAL* 4.1 15.6 - - + +
209F ARG* 2.9 51.9 + - + +
212F LEU* 3.8 19.5 - - + -
213F GLN* 5.2 0.2 - - - +
2J GLU* 2.4 39.2 + - - +
118J VAL* 2.9 37.0 + - + +
119J ASP* 4.5 9.3 + - - -
121J PHE* 1.3 82.0 - - + +
123J ALA* 1.3 64.3 + - - +
125J ASP* 3.4 3.1 + - - +
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Residues in contact with ALA 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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209F ARG 4.8 0.2 - - - -
212F LEU* 3.9 23.1 - - + +
213F GLN* 3.6 19.9 - - - +
216F GLN* 3.5 34.3 - - - +
218F LEU* 3.3 15.8 - - + +
119J ASP 2.9 19.8 + - - +
122J ARG* 1.3 77.3 - - - +
124J TYR* 1.3 64.6 + - + +
125J ASP 3.7 0.2 + - - -
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Residues in contact with TYR 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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216F GLN* 3.7 22.2 + - - +
218F LEU* 3.9 31.4 - - + +
120J LEU* 3.7 38.1 + - + +
123J ALA* 1.3 82.0 - - + +
125J ASP* 1.3 69.5 + - - +
126J ALA* 3.3 0.8 + - - +
165J LYS* 3.1 30.9 + - + +
262J ASP* 3.5 14.7 - - - +
264J TYR* 3.2 46.2 - + + +
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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