Contacts of the helix formed by residues 153 - 161 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B ASN 4.2 0.2 - - - -
147B LEU* 3.5 9.5 - - - +
148B CYS* 3.0 48.8 + - + -
151B THR* 3.0 12.5 + - - -
152B GLY* 1.3 82.0 - - - +
154B ARG* 1.3 63.7 + - - +
155B PRO* 3.4 4.0 - - - -
156B ILE* 3.1 16.9 + - + +
157B LEU* 3.3 12.8 + - + +
1200B VAL* 4.8 4.0 - - + -
1229B ILE* 4.7 0.3 - - - +
1230B PRO* 2.6 35.8 + - + -
1231B ALA* 3.4 25.4 - - - -
1232B PHE* 3.3 56.1 - + + -
1235B ILE* 3.8 17.3 - - + -
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Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B SER 4.3 6.3 + - - -
109B HIS* 6.0 0.4 - - - +
152B GLY 2.7 11.1 + - - +
153B TYR* 1.3 71.5 - - - +
155B PRO* 1.3 96.2 - - + +
157B LEU* 3.4 4.5 + - - +
158B GLN* 2.9 57.6 + - - +
195B LEU* 4.3 14.1 - - - +
196B PHE* 4.4 9.5 - - - -
556B ASN* 3.7 27.5 + - - +
558B GLN* 3.4 31.4 + - - +
1192B ILE* 4.5 1.8 - - - +
1193B GLY* 6.0 0.2 - - - -
1196B GLU* 2.6 47.5 + - - +
1235B ILE* 3.9 10.0 - - + +
1239B PHE* 3.9 22.7 - - + -
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Residues in contact with PRO 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B SER* 3.4 27.5 - - - +
109B HIS* 3.5 20.9 - - + +
110B GLY* 4.1 3.4 - - - -
151B THR* 3.8 26.0 - - - +
153B TYR 3.5 1.6 - - - -
154B ARG* 1.3 118.9 + - + +
156B ILE* 1.3 55.0 + - - +
158B GLN* 4.0 0.4 - - + +
159B GLY* 2.8 31.5 + - - -
1193B GLY* 6.2 2.2 - - - -
1196B GLU* 3.8 13.2 - - - +
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Residues in contact with ILE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ILE* 4.1 10.7 - - + +
108B SER* 5.8 0.2 - - - -
110B GLY* 3.4 32.3 - - - +
116B CYS* 5.2 0.7 - - - -
120B ILE* 3.9 29.6 - - + -
143B PHE* 4.6 0.9 - - + -
148B CYS* 4.6 5.4 - - + -
151B THR* 3.7 19.7 - - - +
153B TYR* 3.1 10.4 + - - +
155B PRO* 1.3 77.3 - - + +
157B LEU* 1.3 57.5 - - - +
159B GLY* 3.8 0.3 - - - -
160B PHE* 2.9 58.7 + - + -
1232B PHE* 3.6 26.9 - - + -
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ILE* 4.3 9.9 - - + +
140B GLU* 4.1 37.9 - - + +
143B PHE* 4.0 18.4 - - + -
153B TYR 3.3 7.4 + - - +
154B ARG* 4.0 5.8 - - - +
156B ILE* 1.3 79.9 - - - +
158B GLN* 1.3 57.4 + - - +
160B PHE* 3.7 2.9 - - - +
161B ARG* 2.8 48.6 + - - +
554B PRO* 6.1 2.7 - - + -
1232B PHE* 3.7 44.4 - - + +
1235B ILE* 4.7 11.9 - - + -
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Residues in contact with GLN 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ARG* 2.9 33.2 + - - +
155B PRO 4.0 2.5 - - - +
157B LEU* 1.3 76.6 - - - +
159B GLY* 1.3 66.2 + - - +
161B ARG* 3.2 39.7 - - - +
162B THR* 3.9 7.4 + - - +
196B PHE* 4.2 18.0 - - + -
556B ASN* 3.5 31.9 + - - +
558B GLN* 3.0 30.5 + - - +
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Residues in contact with GLY 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ARG* 4.3 9.1 - - - +
105B ILE* 6.0 0.4 - - - -
108B SER* 3.2 28.4 + - - -
155B PRO 2.8 20.4 + - - -
156B ILE* 3.8 0.7 - - - -
158B GLN* 1.3 74.8 - - - +
160B PHE* 1.3 56.8 + - - +
162B THR* 2.7 30.8 + - - +
196B PHE* 4.0 8.0 - - - -
201B PHE* 4.5 0.7 - - - -
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Residues in contact with PHE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B VAL* 3.6 44.2 - - + -
104B ARG* 4.7 2.9 - - + -
105B ILE* 3.8 30.5 - - + -
120B ILE* 3.8 7.6 - - + -
121B VAL* 5.0 0.7 - - - -
124B MET* 3.8 14.1 - - + -
139B ILE* 3.3 28.4 - - + +
143B PHE* 3.5 35.7 - + - -
156B ILE* 2.9 35.8 + - + +
157B LEU 4.0 0.9 - - - +
159B GLY* 1.3 72.2 - - - +
161B ARG* 1.3 62.2 + - - +
162B THR 2.9 5.8 - - - -
163B PHE* 3.0 34.3 + + - +
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Residues in contact with ARG 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B VAL* 4.4 24.9 - - + +
139B ILE* 4.1 9.4 - - - -
157B LEU* 2.8 39.8 + - - +
158B GLN* 3.2 36.0 + - - +
160B PHE* 1.3 77.4 - - - +
162B THR* 1.3 56.8 + - + +
163B PHE 3.0 5.2 + - - -
164B ALA* 3.2 17.8 + - + +
165B LYS* 6.0 0.2 - - - +
554B PRO* 3.4 37.2 - - - +
555B ALA* 5.3 0.2 - - - +
556B ASN* 3.2 34.6 - - - +
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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