Contacts of the helix formed by residues 114 - 124 (chain F) in PDB entry 5EIG
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 TYR 114 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62E ARG* 3.0 11.0 + - - -
91F LEU* 4.3 7.0 - - + -
113F VAL* 1.3 76.3 - - - +
115F GLY* 1.3 73.8 + - - +
116F GLY* 3.4 27.4 - - - -
117F THR* 2.9 27.0 + - - +
118F ASN 3.2 7.8 + - - -
157F GLU* 3.0 10.1 + - - +
161F ASN* 4.1 6.3 - - - +
212F 5OW 3.2 104.4 - + + +
355F THR 4.4 10.8 - - - -
356F HIS* 3.8 9.4 - + - -
501F SO4 2.8 26.9 + - - -
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Residues in contact with GLY 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F VAL 3.4 3.5 + - - -
114F TYR* 1.3 80.3 - - - +
116F GLY* 1.3 55.4 + - - +
118F ASN* 3.3 9.4 + - - +
119F ARG* 2.8 31.8 + - - +
355F THR 4.3 10.1 + - - -
356F HIS* 3.6 19.3 + - - -
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Residues in contact with GLY 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E SER 5.1 0.5 - - - +
91F LEU* 3.8 12.1 - - - +
114F TYR* 3.2 24.6 - - - -
115F GLY* 1.3 73.4 - - - +
117F THR* 1.3 60.3 + - - +
119F ARG* 3.6 28.4 + - - +
120F TYR* 3.0 28.6 + - - +
501F SO4 5.1 0.4 + - - -
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Residues in contact with THR 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F LEU* 4.0 10.1 - - - +
94F THR* 4.4 12.5 + - + -
109F CYS* 4.7 0.2 - - - -
113F VAL* 4.3 12.6 - - + -
114F TYR* 2.9 26.8 + - - +
116F GLY* 1.3 72.3 - - - +
118F ASN* 1.3 66.5 + - - +
120F TYR* 3.4 4.5 + - - +
121F PHE* 3.2 43.9 + - + -
155F TRP* 3.7 29.5 + - + +
157F GLU* 4.9 0.3 + - - -
187F ASP* 4.6 5.0 + - - -
207F MET* 6.1 0.2 - - - +
212F 5OW 4.5 6.9 + - - -
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Residues in contact with ASN 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F ASP 4.5 7.9 + - - -
113F VAL* 3.9 17.5 + - + +
114F TYR 3.2 7.8 + - - +
115F GLY* 3.3 13.5 - - - +
117F THR* 1.3 80.6 - - - +
119F ARG* 1.3 61.8 + - - +
122F ARG* 3.0 40.5 + - - +
134F PHE* 3.7 32.4 - - - -
363F ASP* 4.6 16.0 + - - +
367F LEU* 5.9 2.2 - - - +
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Residues in contact with ARG 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E PHE* 4.0 20.6 - - + -
241E ASN* 3.5 28.7 + - - +
242E SER* 3.7 20.8 + - - +
91F LEU* 4.1 6.5 - - - +
115F GLY 2.8 16.9 + - - +
116F GLY* 3.6 22.2 + - - +
118F ASN* 1.3 78.3 + - - +
120F TYR* 1.3 56.8 + - - +
122F ARG* 5.0 3.6 - - - +
123F GLN* 3.0 55.5 + - - +
124F VAL* 3.9 1.0 + - - +
501F SO4 2.9 39.6 + - - -
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Residues in contact with TYR 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E HIS* 4.9 3.1 + - - -
242E SER* 4.5 12.6 - - - +
243E LEU* 4.1 15.3 - - + -
91F LEU* 5.3 3.4 - - + -
94F THR* 4.1 12.8 - - + -
95F VAL* 3.6 41.4 + - + +
98F THR* 3.2 44.3 - - + +
99F HIS* 4.4 5.4 + - - -
116F GLY 3.0 16.1 + - - +
117F THR* 3.4 4.9 + - - +
118F ASN 3.3 0.2 - - - -
119F ARG* 1.3 78.3 - - - +
121F PHE* 1.3 76.2 + + - +
124F VAL* 3.0 34.5 + - + +
125F ALA* 2.8 37.8 + - + +
130F LEU* 5.5 0.2 - - - +
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Residues in contact with PHE 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F THR* 4.3 6.5 - - + -
98F THR* 3.7 23.1 - - - -
107F ILE* 3.9 25.4 - - + -
109F CYS* 3.7 31.9 - - + -
117F THR* 3.2 34.7 + - + +
118F ASN 4.1 1.8 - - - +
120F TYR* 1.3 91.6 - + - +
122F ARG* 1.3 62.7 + - - +
125F ALA* 4.0 3.6 - - + -
126F SER* 3.3 21.3 + - - -
132F ILE* 3.3 41.8 - - + +
134F PHE* 4.4 3.8 - + + -
153F LEU* 4.6 1.8 - - + -
155F TRP* 4.0 28.5 - + + -
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Residues in contact with ARG 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F ASN* 3.0 32.3 + - - +
119F ARG* 4.5 2.4 - - - +
121F PHE* 1.3 78.2 - - - +
123F GLN* 1.3 91.7 + - - +
126F SER* 2.6 22.3 + - - -
132F ILE* 5.0 2.2 - - - -
134F PHE* 4.2 19.1 - - + -
363F ASP* 5.1 10.2 + - - -
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Residues in contact with GLN 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E PHE* 4.3 20.4 - - + -
119F ARG* 3.0 39.4 + - - +
122F ARG* 1.3 114.6 + - - +
124F VAL* 1.3 66.3 + - + +
126F SER* 4.0 3.4 - - - -
127F GLU* 3.9 14.4 - - - +
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Residues in contact with VAL 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E HIS* 3.7 32.5 - - + +
238E PHE* 4.0 25.1 - - + -
239E LEU* 4.2 14.1 - - + -
242E SER* 4.7 6.5 - - - -
243E LEU* 4.2 4.9 - - + -
119F ARG 4.5 5.4 - - - +
120F TYR* 3.0 29.5 + - + +
122F ARG 3.8 0.2 - - - -
123F GLN* 1.3 84.2 - - - +
125F ALA* 1.3 68.1 + - - +
126F SER 3.1 1.3 - - - -
127F GLU* 3.2 15.3 + - - +
128F PHE* 3.3 17.3 - - + -
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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