Contacts of the helix formed by residues 114 - 124 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E ILE* 4.0 25.6 - - + -
42I LEU* 3.7 42.5 - - + +
43I LEU* 5.3 8.5 - - + -
46I VAL* 5.3 6.7 - - + -
48I PHE* 4.7 9.6 - - + -
102I LEU* 5.0 9.0 - - + -
104I LEU* 5.5 2.9 - - + -
110I THR* 5.9 0.7 - - + -
112I VAL* 3.3 6.2 + - - +
113I ALA* 1.3 69.4 - - - +
115I HIS* 1.3 61.4 + - - +
116I GLU* 3.2 4.0 - - - -
117I VAL* 3.3 13.4 - - + +
118I VAL* 3.3 26.9 - - + +
131I LEU* 5.9 1.6 - - + -
204I LEU* 3.8 36.8 - - + -
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Residues in contact with HIS 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E SER* 5.9 0.2 - - - -
193E THR 3.8 16.4 - - - +
194E GLN* 3.5 47.2 + - + +
196E MET 5.5 0.7 - - - +
198E ILE* 3.8 21.7 - - + +
46I VAL* 6.2 1.6 - - + -
113I ALA* 3.2 30.7 - - + +
114I LEU* 1.3 78.8 - - - +
116I GLU* 1.3 68.1 + - + +
118I VAL* 3.3 3.8 + - - +
119I ASP* 2.9 47.2 + - - +
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Residues in contact with GLU 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I VAL* 4.4 9.2 - - + +
113I ALA 3.7 15.3 - - - +
114I LEU* 5.2 1.2 - - - -
115I HIS* 1.3 93.0 - - + +
117I VAL* 1.3 75.5 + - - +
119I ASP* 3.2 10.5 + - + +
120I LEU* 2.9 29.8 + - - +
131I LEU* 3.8 12.0 - - - +
266I PHE* 3.1 59.5 - - + +
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Residues in contact with VAL 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I LEU* 3.3 20.0 - - + +
116I GLU* 1.3 91.0 - - - +
118I VAL* 1.3 65.3 + - + +
120I LEU* 3.3 8.2 + - + +
121I PHE* 2.9 27.4 + - - +
129I ALA* 3.9 22.2 - - + +
130I MET 3.8 28.7 - - - +
131I LEU* 4.6 4.7 - - + +
204I LEU* 4.1 28.7 - - + +
206I CYS* 4.6 7.2 - - - -
265I SER* 5.9 0.2 - - - -
266I PHE* 5.2 3.6 - - + +
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Residues in contact with VAL 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E ILE* 3.7 29.4 - - + -
3I PHE* 3.6 22.0 - - + -
102I LEU* 4.5 11.2 - - + -
114I LEU* 3.3 22.2 - - + +
115I HIS 3.3 6.2 + - - +
116I GLU 3.3 0.4 - - - -
117I VAL* 1.3 80.4 - - + +
119I ASP* 1.3 60.7 + - - +
121I PHE* 3.6 5.0 - - - +
122I ARG* 2.9 62.4 + - - +
206I CYS* 5.0 2.2 - - - -
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Residues in contact with ASP 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E SER* 4.0 15.4 + - - +
193E THR* 2.9 30.8 + - - -
198E ILE* 6.0 0.3 - - - +
212E LEU* 3.7 21.1 - - + +
216E GLN* 5.2 8.5 - - - +
115I HIS* 2.9 32.7 + - - +
116I GLU* 3.2 11.2 + - - +
118I VAL* 1.3 78.6 - - - +
120I LEU* 1.3 57.6 + - + +
122I ARG* 4.5 5.7 + - - -
123I ALA* 2.9 36.7 + - - +
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Residues in contact with LEU 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E GLN* 6.1 0.9 - - - +
116I GLU* 2.9 18.5 + - - +
117I VAL* 3.6 11.2 - - + +
118I VAL 3.3 0.2 - - - -
119I ASP* 1.3 76.8 - - - +
121I PHE* 1.3 62.3 + - - +
124I TYR* 3.7 53.1 + - + +
126I ALA* 4.1 6.6 - - - +
129I ALA* 4.8 4.0 - - + -
165I LYS* 3.8 23.8 - - + +
264I TYR* 4.0 21.5 - - + -
265I SER* 4.2 15.7 - - - +
266I PHE* 4.0 33.0 - - + +
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Residues in contact with PHE 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E ARG* 3.7 15.8 + - - -
3I PHE* 3.5 29.8 - + - -
100I ASP* 3.8 13.9 - - - -
117I VAL 2.9 16.4 + - - +
118I VAL* 3.6 9.0 - - - +
119I ASP 3.2 0.2 - - - -
120I LEU* 1.3 77.5 - - - +
122I ARG* 1.3 61.6 + - + +
126I ALA* 3.2 51.8 + - + +
127I SER 3.8 7.9 - - - -
129I ALA* 3.8 17.4 - - + +
206I CYS* 3.2 39.3 - - + -
207I LEU 4.2 12.6 - - - -
208I LYS* 3.6 18.8 - - - -
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Residues in contact with ARG 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E THR* 4.7 8.1 - - - +
196E MET* 6.1 0.6 - - - +
197E SER 4.0 5.9 + - - -
198E ILE* 2.5 31.3 + - - +
200E SER* 3.2 17.5 + - - -
208E VAL* 4.0 21.0 - - - +
209E ARG* 3.0 52.8 + - + +
212E LEU* 3.8 18.8 - - + +
213E GLN* 5.3 0.3 - - - +
2I GLU* 2.4 45.6 + - - +
118I VAL* 2.9 36.3 + - + +
119I ASP* 4.5 9.7 + - - -
121I PHE* 1.3 81.2 - - + +
123I ALA* 1.3 65.3 + - - +
125I ASP* 3.4 2.8 + - - +
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Residues in contact with ALA 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E LEU* 4.0 22.4 - - + +
213E GLN* 3.8 17.6 - - - +
216E GLN* 3.4 35.4 - - - +
218E LEU* 3.3 16.7 - - + +
119I ASP 2.9 18.0 + - - +
122I ARG* 1.3 79.0 - - - +
124I TYR* 1.3 64.5 + - + +
125I ASP* 5.2 0.3 - - - +
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Residues in contact with TYR 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E GLN* 3.9 21.1 + - - -
218E LEU* 3.9 28.8 - - + +
120I LEU* 3.7 38.3 + - + +
122I ARG 3.4 0.2 - - - -
123I ALA* 1.3 80.2 - - + +
125I ASP* 1.3 69.5 + - - +
126I ALA* 3.3 1.0 + - - +
165I LYS* 3.1 31.3 + - + +
262I ASP* 3.5 15.1 - - - +
264I TYR* 3.2 45.8 - + + +
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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