Contacts of the helix formed by residues 198 - 208 (chain E) in PDB entry 4P9U
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 ASN 198 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115E TYR* 6.3 1.6 - - + -
193E ALA 3.6 5.7 - - - +
194E PHE 4.6 3.6 - - - +
196E SER* 3.2 16.6 + - - +
197E GLY* 1.3 78.9 - - - +
199E GLN* 1.3 67.7 + - - +
200E ILE* 3.2 17.1 + - - +
201E TYR* 3.5 35.4 + - + -
100F ASP* 3.3 43.1 + - - +
103F ALA* 3.7 11.7 - - - +
104F ALA* 3.6 14.8 - - - +
107F ASN* 4.9 1.0 - - - +
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Residues in contact with GLN 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E PHE* 3.6 18.2 - - + -
197E GLY 4.1 2.2 - - - +
198E ASN* 1.3 74.0 + - - +
200E ILE* 1.3 54.7 + - - +
202E GLY* 2.7 26.5 + - - -
203E LEU* 2.9 25.1 + - + +
75F MET* 3.6 30.7 - - - +
83F LEU* 3.2 27.9 - - + +
86F LEU* 5.4 2.4 - - - +
97F ILE* 5.4 4.0 - - - +
100F ASP* 3.9 14.7 + - + +
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Residues in contact with ILE 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E ASN* 3.2 10.0 + - - +
199E GLN* 1.3 77.7 - - - +
201E TYR* 1.3 58.2 + - + +
203E LEU* 3.7 3.8 - - - +
204E ILE* 2.9 47.0 + - + +
80F LEU* 3.7 20.4 - - + -
83F LEU* 3.6 24.7 - - + -
100F ASP* 3.8 7.4 - - + +
101F LEU* 3.7 27.1 - - + +
104F ALA* 3.7 30.7 - - + -
108F ILE* 6.3 0.9 - - + -
204F ILE* 5.2 3.4 - - + -
208F LEU* 4.0 19.7 - - + -
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Residues in contact with TYR 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E ILE* 4.8 9.8 - - + +
111E ILE* 3.2 21.5 - - + +
112E PHE* 3.8 27.8 - + + -
115E TYR* 5.4 3.6 - + - -
193E ALA* 3.4 18.2 - - + +
196E SER* 3.8 9.0 - - - -
198E ASN* 3.7 38.1 - - + -
199E GLN 3.2 0.8 - - - -
200E ILE* 1.3 78.0 - - + +
202E GLY* 1.3 59.1 + - - +
204E ILE* 3.7 17.5 - - + +
205E PHE* 3.1 31.4 + - - -
104F ALA* 3.8 12.7 + - + -
107F ASN* 2.7 41.9 + - - +
108F ILE* 4.2 15.2 - - + +
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Residues in contact with GLY 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E GLN* 4.2 1.0 - - - +
193E ALA* 3.6 12.9 + - - -
194E PHE* 3.5 26.3 - - - -
199E GLN 2.7 14.6 + - - -
201E TYR* 1.3 72.8 - - - +
203E LEU* 1.3 54.1 + - - -
204E ILE 3.1 0.2 - - - -
205E PHE* 3.2 6.7 + - - +
206E ASN* 2.7 39.2 + - - -
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Residues in contact with LEU 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E LEU* 4.9 0.2 - - - +
194E PHE* 4.0 10.3 - - + -
199E GLN* 2.9 47.5 + - + +
200E ILE* 3.7 2.5 - - - +
202E GLY* 1.3 73.3 - - - +
204E ILE* 1.3 60.4 + - - +
206E ASN* 3.3 11.2 + - - +
207E GLY* 2.9 26.3 + - - -
75F MET* 4.5 13.0 - - - -
78F SER 3.3 24.2 - - - +
79F GLY* 3.3 24.8 - - - +
80F LEU* 3.7 26.7 + - + +
82F ILE* 3.9 15.7 - - + -
83F LEU* 4.9 9.2 - - + -
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Residues in contact with ILE 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E LEU* 3.8 16.3 - - + +
108E ILE* 4.4 26.2 - - + -
200E ILE* 2.9 34.2 + - + +
201E TYR* 3.7 19.7 - - + +
202E GLY 3.1 0.2 - - - -
203E LEU* 1.3 78.2 - - - +
205E PHE* 1.3 67.0 + - + +
207E GLY* 3.2 3.8 + - - -
208E LEU* 3.1 36.7 + - + +
80F LEU* 4.2 17.9 - - + -
108F ILE* 5.8 4.7 - - + -
200F ILE* 5.1 2.9 - - + -
204F ILE* 3.6 27.6 - - + -
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Residues in contact with PHE 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E ARG* 4.0 19.5 - - + -
108E ILE* 4.7 11.4 - - + -
112E PHE* 3.6 32.5 - + - -
186E TYR* 3.2 18.7 + + + -
189E PHE* 3.4 32.3 - + + -
190E GLN* 3.7 21.5 - - + -
193E ALA* 3.7 11.0 - - + -
201E TYR 3.1 21.1 - - - -
202E GLY 3.2 7.4 + - - +
204E ILE* 1.3 79.3 - - + +
206E ASN* 1.3 66.4 + - - +
208E LEU* 3.2 7.7 + - + +
209E LYS 3.1 18.4 + - - -
212E TYR* 3.8 29.3 - + - -
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Residues in contact with ASN 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E TYR* 3.5 9.3 + - - -
190E GLN* 3.0 15.5 + - - +
194E PHE* 3.1 28.9 - - - -
202E GLY 2.7 26.0 + - - -
203E LEU* 3.5 9.6 - - - +
205E PHE* 1.3 75.7 - - - +
207E GLY* 1.3 61.6 + - - +
209E LYS* 3.6 14.8 - - - +
75F MET 3.4 6.8 + - - -
76F GLU 3.0 26.1 - - - +
77F THR* 4.7 8.2 - - - +
78F SER 3.2 23.8 - - - +
79F GLY* 5.2 0.2 - - - -
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Residues in contact with GLY 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E LEU* 3.8 25.1 - - - +
81E HIS* 4.0 13.2 - - - +
203E LEU 2.9 13.8 + - - -
204E ILE 3.2 3.8 + - - -
205E PHE 3.2 0.4 - - - -
206E ASN* 1.3 77.4 - - - +
208E LEU* 1.3 59.4 + - - +
209E LYS 3.3 3.5 + - - -
210E LYS* 4.9 4.3 + - - +
79F GLY* 4.8 10.3 - - - -
80F LEU 5.9 0.2 - - - -
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Residues in contact with LEU 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E LEU* 3.4 34.5 - - + +
83E LEU* 3.6 26.9 - - + -
101E LEU* 3.9 17.9 - - + -
104E ALA* 5.7 1.3 - - + -
204E ILE* 3.1 33.3 + - + +
205E PHE* 3.2 8.2 + - + +
207E GLY* 1.3 75.5 - - - +
209E LYS* 1.3 57.9 + - - +
210E LYS 3.3 2.5 - - - -
211E LEU* 3.3 15.2 + - + +
212E TYR* 2.8 30.9 + - + +
200F ILE* 3.8 23.8 - - + -
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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