Contacts of the helix formed by residues 153 - 161 (chain A) in PDB entry 1FO4
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 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A ASN 4.3 0.9 - - - -
147A LEU* 3.7 8.7 - - - +
148A CYS* 3.0 47.9 + - + -
151A THR* 2.9 13.1 + - - -
152A GLY* 1.3 83.2 - - - +
154A ARG* 1.3 65.0 + - - +
155A PRO* 3.4 4.0 - - - -
156A ILE* 3.1 18.0 + - - +
157A LEU* 3.2 12.9 + - + +
1200A VAL* 4.7 3.8 - - + -
1229A ILE* 4.7 0.2 - - - +
1230A PRO* 2.5 37.4 + - + -
1231A ALA* 3.4 24.8 - - - -
1232A PHE* 3.3 55.0 - + + -
1235A ILE* 3.8 17.7 - - + -
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Residues in contact with ARG 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A SER 4.4 6.5 + - - -
109A HIS* 6.0 0.4 - - - +
152A GLY 2.8 10.3 + - - +
153A TYR* 1.3 72.6 - - - +
155A PRO* 1.3 92.0 + - + +
157A LEU* 3.3 4.7 + - - +
158A GLN* 2.8 60.1 + - - +
195A LEU* 4.3 13.9 - - - +
196A PHE* 4.6 5.9 - - - -
556A ASN* 3.6 29.1 + - - +
558A GLN* 3.7 30.6 + - - +
1192A ILE* 4.5 2.0 - - - +
1196A GLU* 2.7 54.8 + - - +
1235A ILE* 3.8 10.4 - - + +
1239A PHE* 4.0 22.0 - - + -
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Residues in contact with PRO 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A SER* 3.4 20.7 - - - +
109A HIS* 3.4 27.4 - - + +
110A GLY* 4.0 2.7 - - - -
151A THR* 3.9 26.2 - - - +
153A TYR 3.4 2.0 - - - -
154A ARG* 1.3 117.5 - - + +
156A ILE* 1.3 58.2 - - - +
158A GLN* 3.9 0.6 - - + +
159A GLY* 2.8 29.1 + - - -
1193A GLY* 6.4 2.0 - - - -
1196A GLU* 3.9 13.2 - - - +
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Residues in contact with ILE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ILE* 4.1 8.7 - - + +
108A SER* 5.9 0.7 - - - -
110A GLY* 3.3 33.4 - - - +
116A CYS* 5.1 1.1 - - - -
120A ILE* 3.8 33.7 - - + -
143A PHE* 4.9 0.7 - - + -
148A CYS* 4.5 7.2 - - + -
151A THR* 3.7 19.7 - - - +
153A TYR* 3.1 9.7 + - - +
155A PRO* 1.3 77.2 - - - +
157A LEU* 1.3 62.9 + - - +
159A GLY* 4.0 0.7 - - - -
160A PHE* 3.1 51.3 + - + -
1232A PHE* 3.8 23.3 - - + -
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A VAL 5.9 0.2 - - - +
139A ILE* 4.4 9.6 - - + +
140A GLU* 4.0 43.1 - - + +
143A PHE* 4.2 10.8 - - + -
153A TYR 3.2 7.2 + - - +
154A ARG* 3.7 6.3 - - - +
156A ILE* 1.3 79.8 - - - +
158A GLN* 1.3 57.0 + - - +
160A PHE* 3.2 5.3 + - - +
161A ARG* 2.8 48.1 + - - +
554A PRO* 6.2 2.0 - - + -
556A ASN* 5.7 0.2 - - - +
1232A PHE* 3.8 36.6 - - + +
1235A ILE* 4.6 18.2 - - + -
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Residues in contact with GLN 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG* 2.8 54.2 + - - +
155A PRO 3.9 2.7 - - - +
157A LEU* 1.3 76.2 - - - +
159A GLY* 1.3 63.5 + - - +
161A ARG* 3.3 37.2 + - - +
162A THR* 4.0 5.0 + - - +
196A PHE* 4.0 23.7 - - + -
556A ASN* 3.9 23.0 + - - +
558A GLN* 3.2 18.0 + - - -
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Residues in contact with GLY 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG* 4.4 9.0 - - - +
105A ILE* 6.0 0.2 - - - -
108A SER* 3.2 29.6 - - - -
155A PRO 2.8 18.1 + - - -
156A ILE 4.0 0.9 - - - -
158A GLN* 1.3 74.0 - - - +
160A PHE* 1.3 57.8 + - - +
161A ARG 3.3 0.5 + - - -
162A THR* 2.6 32.4 + - - +
196A PHE* 4.1 6.3 - - - -
201A PHE* 4.6 0.3 - - - -
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Residues in contact with PHE 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A VAL* 3.5 35.4 - - + -
104A ARG* 4.6 2.9 - - + -
105A ILE* 3.7 32.5 - - + -
120A ILE* 3.9 8.3 - - + -
121A VAL* 5.0 0.7 - - - -
124A MET* 3.7 27.8 - - + -
139A ILE* 3.4 17.1 - - + +
143A PHE* 3.5 33.9 - + - -
156A ILE* 3.1 33.7 + - + +
157A LEU 3.2 3.3 + - - +
159A GLY* 1.3 74.3 - - - +
161A ARG* 1.3 61.7 + - - +
162A THR 3.0 5.8 - - - -
163A PHE* 3.1 37.8 + + - +
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Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A VAL* 4.2 28.1 - - + +
139A ILE* 4.2 8.3 - - - -
157A LEU* 2.8 37.0 + - - +
158A GLN* 3.3 31.2 - - - +
159A GLY 3.1 0.6 - - - -
160A PHE* 1.3 77.0 - - - +
162A THR* 1.3 56.5 + - + +
163A PHE 3.0 1.1 - - - -
164A ALA* 3.0 27.5 + - + +
165A LYS* 5.8 0.3 - - - +
554A PRO* 3.7 35.1 + - - +
556A ASN* 3.3 33.3 - - - +
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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