Contacts of the helix formed by residues 110 - 122 (chain D) in PDB entry 1E3S
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 THR 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C PHE* 4.7 0.9 - - - -
130C ARG* 4.0 5.4 - - - +
98D ILE* 5.4 0.6 - - - +
108D VAL 3.4 6.7 + - - +
109D HIS* 1.3 93.6 + - - +
111D LEU* 1.3 65.3 + - - +
112D GLU* 3.7 15.2 + - - +
113D ASP* 3.0 39.2 + - - +
114D PHE* 3.5 7.1 + - - +
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Residues in contact with LEU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C THR 4.1 20.2 - - - +
68C GLU* 4.0 26.4 + - + +
123C ILE* 3.8 31.0 - - + +
126C PHE* 4.9 6.5 - - + -
127C ASN* 3.9 35.0 - - + +
130C ARG* 3.8 20.7 - - - +
110D THR* 1.3 74.1 - - - +
112D GLU* 1.3 65.1 + - - +
114D PHE* 3.3 6.6 + - + +
115D GLN* 3.0 30.9 + - + +
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Residues in contact with GLU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C GLU* 3.6 20.7 - - - +
110D THR* 3.3 13.2 - - - +
111D LEU* 1.3 90.4 + - - +
113D ASP* 1.3 58.2 + - - +
115D GLN* 3.5 6.7 + - - +
116D ARG* 3.0 29.6 + - - +
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Residues in contact with ASP 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D VAL* 5.1 2.9 - - + +
98D ILE* 3.7 23.0 - - + +
109D HIS* 3.8 16.1 - - + -
110D THR* 3.0 28.9 + - - +
112D GLU* 1.3 73.2 - - - +
114D PHE* 1.3 67.0 + - - +
116D ARG* 3.3 25.6 + - - +
117D VAL* 3.5 26.2 + - - +
167D ALA* 4.7 0.7 - - - +
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Residues in contact with PHE 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C LEU* 4.3 6.1 - - + -
123C ILE* 4.1 26.2 - - + -
126C PHE* 3.4 63.0 - + + -
178C MET* 4.0 7.4 - - - -
109D HIS* 3.5 14.1 - + + -
110D THR 3.5 1.5 + - - +
111D LEU* 3.3 10.1 + - + +
113D ASP* 1.3 78.4 - - - +
115D GLN* 1.3 62.8 + - - +
116D ARG 3.3 0.3 + - - -
117D VAL* 3.4 4.5 + - - +
118D ILE* 3.1 41.3 + - + +
166D ALA 4.1 2.7 - - - -
167D ALA* 3.7 32.5 - - + +
170D ALA* 3.8 24.0 - - + -
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Residues in contact with GLN 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C GLN* 3.4 15.4 - - - +
119C ASN* 3.4 5.9 + - - +
123C ILE* 2.9 46.4 - - + +
111D LEU* 3.0 19.1 + - + +
112D GLU* 3.9 7.6 - - - +
114D PHE* 1.3 77.1 - - - +
116D ARG* 1.3 56.7 + - - +
118D ILE* 3.3 6.3 + - - +
119D ASN* 2.9 66.2 + - - +
123D ILE* 4.8 0.2 - - - +
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Residues in contact with ARG 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ILE* 3.8 24.1 - - + +
95D ALA 5.1 2.4 + - - -
96D VAL* 3.8 24.7 - - - +
112D GLU 3.0 18.1 + - - +
113D ASP* 3.3 30.4 + - - +
114D PHE 3.3 0.2 - - - -
115D GLN* 1.3 75.1 - - - +
117D VAL* 1.3 61.7 + - - +
119D ASN* 3.3 9.5 + - + +
120D VAL* 3.2 30.2 + - + +
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Residues in contact with VAL 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ILE* 4.2 22.0 - - + +
95D ALA 5.0 0.2 - - - -
96D VAL* 4.0 36.1 - - + +
113D ASP 3.5 13.4 + - - +
114D PHE 3.4 7.5 + - - +
116D ARG* 1.3 74.3 - - + +
118D ILE* 1.3 66.8 + - - +
121D ASN* 3.2 48.5 + - - +
167D ALA* 3.8 24.7 - - + +
168D TYR* 3.9 13.2 - - + +
171D SER* 4.1 1.1 - - - +
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Residues in contact with ILE 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ILE* 3.7 30.5 - - + -
122C LEU* 4.0 17.5 - - + -
123C ILE* 4.4 8.7 - - + -
114D PHE* 3.1 35.6 + - + +
115D GLN* 3.6 9.0 - - - +
117D VAL* 1.3 74.8 - - - +
119D ASN* 1.3 63.5 + - - +
122D LEU* 3.0 28.2 + - + -
123D ILE* 3.1 16.9 + - + -
167D ALA 4.1 4.9 - - - +
170D ALA* 4.0 8.3 - - + -
171D SER* 3.8 33.4 - - - +
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Residues in contact with ASN 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C GLN* 3.5 6.8 + - - +
66D THR* 3.6 16.4 - - + +
115D GLN* 2.9 54.4 + - - +
116D ARG* 3.6 8.2 - - + +
117D VAL 3.3 0.2 - - - -
118D ILE* 1.3 76.8 - - - +
120D VAL* 1.3 58.8 + - + +
123D ILE* 3.3 23.7 - - + +
124D GLY 2.9 25.6 + - - -
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Residues in contact with VAL 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D VAL* 3.9 7.4 - - + +
66D THR* 3.9 13.5 - - + -
92D ALA 4.6 3.3 - - - +
93D GLY* 4.3 9.4 - - - +
94D ILE* 3.9 21.8 - - + -
116D ARG* 3.2 19.9 + - + +
119D ASN* 1.3 79.3 - - + +
121D ASN* 1.3 73.6 + - - +
124D GLY* 3.5 14.6 - - - -
125D THR* 4.1 1.4 + - - -
301D NAD 3.7 43.7 - - + +
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Residues in contact with ASN 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ALA 4.8 5.9 - - - +
93D GLY* 3.2 9.4 - - - -
94D ILE* 3.0 47.0 + - - +
117D VAL* 3.2 21.1 + - - +
120D VAL* 1.3 76.9 - - - +
122D LEU* 1.3 58.3 + - - +
125D THR* 3.2 25.7 + - - -
168D TYR* 3.9 11.9 - - - -
171D SER* 3.1 26.0 + - - +
172D LYS* 3.9 17.9 + - + +
175D ILE* 3.7 10.1 - - - +
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Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C PHE* 4.5 7.4 - - + -
118C ILE* 4.0 24.0 - - + -
122C LEU* 4.3 17.5 - - + -
170C ALA* 4.3 4.7 - - + +
118D ILE* 3.0 21.3 + - + +
121D ASN* 1.3 76.1 - - - +
123D ILE* 1.3 66.1 + - + +
124D GLY 3.3 1.1 - - - -
125D THR* 3.3 2.1 + - - -
126D PHE* 3.2 21.0 + - - +
171D SER* 3.9 18.4 - - - +
174D GLY* 3.6 41.1 - - - +
175D ILE* 3.7 11.2 - - + +
178D MET* 4.2 16.3 - - + +
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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