Contacts of the helix formed by residues 1231 - 1235 (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 ALA1231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A PHE 6.0 1.3 - - - +
144A GLN* 5.7 3.6 - - - +
146A ASN 5.4 1.6 - - - +
147A LEU* 4.6 7.6 - - + -
153A TYR* 3.4 20.1 - - - -
426A ARG* 3.7 30.3 - - - +
428A GLU* 3.9 18.8 - - + +
1229A ILE 3.3 1.0 + - - -
1230A PRO* 1.3 70.8 - - - +
1232A PHE* 1.3 69.2 + - - +
1233A GLY 3.2 1.1 - - - +
1234A SER* 2.9 24.0 + - - +
1235A ILE* 4.0 1.4 + - - +
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Residues in contact with PHE1232 (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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120A ILE* 3.9 26.9 - - + -
140A GLU* 4.5 19.2 - - + +
143A PHE* 3.4 46.2 + + + +
144A GLN* 6.1 0.2 - - - -
146A ASN* 3.5 18.2 - - + -
153A TYR* 3.3 45.5 - + + -
156A ILE* 3.8 30.1 - - + -
157A LEU* 3.8 29.8 - - + +
1231A ALA* 1.3 75.9 - - - +
1233A GLY* 1.3 57.8 + - - +
1234A SER 3.2 2.8 + - - -
1235A ILE* 3.6 22.7 - - - +
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Residues in contact with GLY1233 (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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140A GLU* 3.8 21.6 + - - +
427A ARG* 3.6 20.1 + - - -
428A GLU* 4.1 22.8 + - - +
1231A ALA* 3.2 3.8 - - - +
1232A PHE* 1.3 78.0 - - - +
1234A SER* 1.3 59.2 + - - +
1235A ILE 3.5 5.2 - - - +
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Residues in contact with SER1234 (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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426A ARG* 4.1 3.8 - - - +
427A ARG* 5.4 1.3 - - - +
428A GLU* 4.0 5.2 + - - -
1173A ASN* 2.6 34.3 + - - +
1203A LEU* 3.8 6.5 - - - +
1208A LEU* 4.0 15.3 - - - +
1230A PRO* 3.8 15.2 - - - +
1231A ALA* 2.9 37.0 + - - +
1233A GLY* 1.3 77.0 - - - +
1235A ILE* 1.3 61.2 + - - +
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Residues in contact with ILE1235 (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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152A GLY 3.1 29.2 - - - +
153A TYR* 3.8 22.2 - - + -
154A ARG* 3.8 25.1 - - + +
157A LEU* 4.6 10.8 - - + -
556A ASN* 5.6 1.6 - - - +
1173A ASN* 4.0 3.5 - - - +
1200A VAL* 4.2 15.7 - - + -
1203A LEU* 4.6 1.8 - - - -
1231A ALA 4.2 0.9 - - - +
1232A PHE 3.6 14.6 - - - +
1233A GLY 4.4 4.5 - - - +
1234A SER* 1.3 81.9 - - - +
1236A PRO* 1.3 84.8 - - + +
1237A THR* 3.3 5.5 + - - -
1239A PHE* 4.7 6.5 - - + -
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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