Contacts of the helix formed by residues 110 - 122 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C ILE* 5.4 0.8 - - - +
108C VAL 3.3 6.0 + - - +
109C HIS* 1.3 93.8 + - - +
111C LEU* 1.3 64.9 + - - +
112C GLU* 3.7 14.3 + - - +
113C ASP* 2.9 42.9 + - - +
114C PHE* 3.6 2.8 + - - +
68D GLU* 5.9 0.2 - - - -
126D PHE* 4.8 0.5 - - - -
130D ARG* 4.0 4.3 - - - +
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Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C THR* 1.3 72.2 - - - +
112C GLU* 1.3 72.1 + - - +
114C PHE* 3.2 7.0 + - + +
115C GLN* 3.0 30.4 + - + +
66D THR* 4.2 20.0 - - - +
68D GLU* 4.6 12.9 + - + +
123D ILE* 3.8 31.2 - - + +
126D PHE* 5.0 6.1 - - + -
127D ASN* 3.7 35.0 - - + +
130D ARG* 3.7 26.6 - - - +
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Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C THR* 3.8 13.1 - - - +
111C LEU* 1.3 98.6 + - - +
113C ASP* 1.3 58.4 + - - +
115C GLN* 3.7 6.8 - - - +
116C ARG* 3.0 29.3 + - - +
68D GLU* 4.9 8.0 - - - +
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Residues in contact with ASP 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C VAL* 5.0 2.4 - - + +
98C ILE* 3.9 22.6 - - + +
109C HIS* 3.9 16.7 - - + -
110C THR* 2.9 28.6 + - - +
111C LEU 3.4 0.2 - - - -
112C GLU* 1.3 74.8 - - - +
114C PHE* 1.3 66.4 + - - +
116C ARG* 3.3 25.5 + - - +
117C VAL* 3.5 26.0 + - - +
167C ALA* 4.7 0.3 - - - +
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Residues in contact with PHE 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C HIS* 3.6 12.7 - + + -
110C THR 3.6 3.9 + - - +
111C LEU* 3.2 9.3 + - + +
113C ASP* 1.3 76.1 - - - +
115C GLN* 1.3 64.6 + - - +
116C ARG 3.4 0.5 + - - -
117C VAL* 3.4 5.0 + - - +
118C ILE* 3.2 41.9 + - + +
166C ALA 4.0 7.0 - - - -
167C ALA* 3.6 33.3 - - + +
170C ALA* 3.9 19.3 - - + -
122D LEU* 4.4 6.3 - - + -
123D ILE* 4.1 27.6 - - + -
126D PHE* 3.4 65.3 - + + -
178D MET* 4.0 6.7 - - - -
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Residues in contact with GLN 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C LEU* 3.0 18.8 + - + +
112C GLU* 3.7 8.1 - - - +
114C PHE* 1.3 77.7 - - - +
116C ARG* 1.3 62.4 + - - +
118C ILE* 3.3 6.4 + - - +
119C ASN* 2.8 64.1 + - - +
115D GLN* 3.4 12.7 - - - +
119D ASN* 3.5 7.2 + - - +
123D ILE* 3.1 45.8 - - + +
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Residues in contact with ARG 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ILE* 4.0 23.6 - - + +
95C ALA 5.0 2.0 + - - -
96C VAL* 3.9 23.5 - - - +
112C GLU 3.0 17.8 + - - +
113C ASP* 3.3 31.0 + - - +
114C PHE 3.3 0.2 - - - -
115C GLN* 1.3 77.5 - - - +
117C VAL* 1.3 61.3 + - - +
119C ASN* 3.4 9.3 + - + +
120C VAL* 3.2 29.1 + - + +
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Residues in contact with VAL 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ILE* 4.2 22.4 - - + +
95C ALA* 5.4 0.2 - - - -
96C VAL* 4.0 35.0 - - + +
113C ASP 3.5 13.9 + - - +
114C PHE 3.4 7.0 + - - +
116C ARG* 1.3 74.0 - - + +
118C ILE* 1.3 65.4 + - - +
120C VAL* 4.3 0.2 - - - -
121C ASN* 3.1 44.4 + - - +
167C ALA* 3.9 30.3 - - + +
168C TYR* 4.0 7.2 - - + +
171C SER* 4.1 1.6 - - - +
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Residues in contact with ILE 118 (chain C).
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* 3.2 34.5 + - + +
115C GLN* 3.7 8.1 - - - +
117C VAL* 1.3 74.8 - - - +
119C ASN* 1.3 65.0 + - - +
122C LEU* 3.0 28.7 + - + +
123C ILE* 3.0 17.3 + - + -
167C ALA 4.1 4.7 - - - +
170C ALA* 4.0 8.5 - - + -
171C SER* 3.8 32.8 - - - +
118D ILE* 3.7 29.6 - - + -
122D LEU* 4.0 18.6 - - + -
123D ILE* 4.4 9.9 - - + -
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Residues in contact with ASN 119 (chain C).
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* 3.6 17.3 - - + +
115C GLN* 2.8 57.0 + - - +
116C ARG* 3.6 8.4 - - - +
117C VAL 3.3 0.2 - - - -
118C ILE* 1.3 76.9 - - - +
120C VAL* 1.3 58.6 + - + +
123C ILE* 3.3 25.0 - - + +
124C GLY 2.9 25.8 + - - -
115D GLN* 3.4 6.1 + - - +
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Residues in contact with VAL 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C VAL* 3.9 7.7 - - + +
66C THR* 4.0 13.0 - - + -
92C ALA 4.6 3.6 - - - +
93C GLY* 4.3 8.1 - - - +
94C ILE* 3.9 22.9 - - + -
116C ARG* 3.2 20.7 + - + +
119C ASN* 1.3 79.2 - - + +
121C ASN* 1.3 75.2 + - - +
124C GLY* 3.6 14.7 - - - -
125C THR* 4.1 1.2 + - - -
301C NAD 3.8 43.5 - - + +
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Residues in contact with ASN 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ALA 4.8 5.2 - - - +
93C GLY* 3.3 9.4 - - - -
94C ILE* 3.0 43.9 + - - +
117C VAL* 3.1 20.6 + - - +
120C VAL* 1.3 81.0 - - - +
122C LEU* 1.3 59.7 + - - +
125C THR* 3.1 26.0 + - - -
168C TYR* 3.8 11.9 - - - -
171C SER* 3.1 26.7 + - - +
172C LYS* 3.8 17.7 + - + +
175C ILE* 3.6 10.5 - - - +
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Residues in contact with LEU 122 (chain C).
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* 3.0 19.3 + - + +
121C ASN* 1.3 74.9 - - - +
123C ILE* 1.3 67.9 + - + +
124C GLY 3.3 0.9 - - - -
125C THR* 3.4 2.8 + - - -
126C PHE* 3.2 21.1 + - - +
170C ALA 4.8 1.8 - - - +
171C SER* 3.9 16.4 - - - +
174C GLY* 3.6 41.3 - - - +
175C ILE* 3.7 7.4 - - + +
178C MET* 4.0 19.9 - - + +
114D PHE* 4.5 6.7 - - + -
118D ILE* 4.0 24.0 - - + -
122D LEU* 4.3 17.5 - - + -
170D ALA* 4.2 6.1 - - + +
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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