Contacts of the helix formed by residues 131 - 140 (chain D) in PDB entry 1FS2
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 131 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131C LYS* 5.8 0.9 - - - -
129D GLY 5.2 1.6 - - - +
130D LYS* 1.3 76.4 - - - +
132D PRO* 1.3 78.3 - - + +
133D GLU* 3.6 8.7 + - - +
134D GLU* 2.8 44.3 + - - +
135D ILE* 2.8 25.4 + - - +
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Residues in contact with PRO 132 (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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131C LYS* 3.8 31.0 - - + +
134C GLY* 4.2 4.5 - - - -
135C VAL* 3.8 24.1 - - + +
131D THR* 1.3 88.5 - - + +
133D GLU* 1.3 51.0 + - - +
135D ILE* 3.1 6.0 - - + +
136D ARG* 2.7 58.1 + - - +
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Residues in contact with GLU 133 (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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131D THR* 3.1 8.2 - - - +
132D PRO* 1.3 78.0 - - + +
134D GLU* 1.3 66.5 + - - +
136D ARG* 2.5 46.1 + - - +
137D LYS* 2.9 53.9 + - - +
143D ASN* 4.8 2.1 + - - -
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Residues in contact with GLU 134 (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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129D GLY 4.2 2.1 - - - +
130D LYS* 3.2 34.8 - - + +
131D THR* 2.8 47.0 + - - +
133D GLU* 1.3 78.2 - - - +
135D ILE* 1.3 57.1 + - - +
137D LYS* 3.1 12.3 + - + +
138D THR* 2.8 33.9 + - + +
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Residues in contact with ILE 135 (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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131C LYS* 4.8 2.9 - - + +
132C VAL* 4.1 8.3 - - + +
135C VAL* 3.8 31.9 - - + -
139C TRP* 3.9 22.4 - - + -
127D ILE* 3.5 34.5 - - + +
130D LYS* 3.8 20.0 - - + +
131D THR 2.8 26.2 + - - +
132D PRO* 3.1 7.9 - - + +
134D GLU* 1.3 73.9 - - - +
136D ARG* 1.3 68.4 + - - +
137D LYS 3.0 0.3 + - - -
138D THR* 3.3 6.9 + - - -
139D PHE* 2.9 33.5 + - + +
141D ILE* 5.2 0.4 - - + -
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Residues in contact with ARG 136 (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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134C GLY 3.0 25.7 + - - -
135C VAL* 2.9 27.5 + - + +
132D PRO* 2.7 22.7 + - - +
133D GLU* 2.5 64.1 + - - +
135D ILE* 1.3 71.9 - - - +
137D LYS* 1.3 58.6 + - + +
140D ASN* 2.8 26.7 + - - -
141D ILE* 3.0 33.7 + - + +
143D ASN* 3.0 45.3 + - - +
145D PHE* 4.9 1.6 - - - -
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Residues in contact with LYS 137 (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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133D GLU* 2.9 46.3 + - - +
134D GLU* 3.4 10.3 - - + +
135D ILE 3.0 1.0 + - - -
136D ARG* 1.3 75.4 - - + +
138D THR* 1.3 68.3 + - + +
139D PHE 3.3 0.3 + - - -
140D ASN* 3.4 9.9 + - - +
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Residues in contact with THR 138 (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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97D GLN* 2.8 36.8 + - - +
126D MET* 6.3 0.4 - - - -
130D LYS* 3.4 34.9 - - + +
134D GLU* 2.8 20.7 + - + +
135D ILE* 3.3 4.3 + - - -
137D LYS* 1.3 74.0 - - + +
139D PHE* 1.3 84.9 + - - +
140D ASN* 5.2 0.5 - - - +
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Residues in contact with PHE 139 (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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107C VAL 4.1 0.2 - - - +
109C TRP* 3.2 62.9 - + + +
139C TRP* 5.1 7.4 - + + -
97D GLN* 4.6 4.3 - - - -
123D VAL* 3.7 28.7 - - + -
126D MET* 3.6 43.7 - - + -
127D ILE* 4.2 14.6 - - + -
135D ILE* 2.9 23.7 + - + +
138D THR* 1.3 107.0 + - - +
140D ASN* 1.3 71.7 + - - +
141D ILE* 3.1 22.3 + - + -
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Residues in contact with ASN 140 (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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142B LYS* 4.4 19.6 + - - +
106C GLY* 4.0 18.1 - - - -
107C VAL* 3.3 26.8 + - + +
108C SER* 5.3 1.0 - - - +
109C TRP* 5.3 0.4 - - + -
110C ASP* 2.9 12.5 + - - +
97D GLN* 5.9 0.2 - - - +
136D ARG 2.8 11.9 + - - -
137D LYS* 3.4 8.6 + - - +
138D THR 3.5 1.1 - - - +
139D PHE* 1.3 80.0 - - - +
141D ILE* 1.3 59.0 + - - +
142D LYS 4.0 0.3 + - - -
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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