Contacts of the helix formed by residues 128 - 133 (chain A) in PDB entry 1FX8
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 SER 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A GLU* 5.3 0.4 - - - -
121A ILE* 4.0 13.9 - - - -
122A VAL 3.4 21.3 - - - -
123A ARG* 3.8 7.2 - - - -
124A GLY* 2.9 20.2 + - - -
125A SER* 2.7 20.6 + - - -
127A GLU* 1.3 75.8 - - - +
129A VAL* 1.3 63.7 + - - +
130A ASP 3.1 2.9 - - - -
131A LEU* 3.1 7.7 + - - +
132A ALA 3.0 17.3 + - - -
219A TRP* 3.3 19.3 + - - -
222A VAL* 4.2 1.6 - - - +
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Residues in contact with VAL 129 (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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126A VAL* 3.1 23.3 - - + +
127A GLU 3.2 0.8 - - - -
128A SER* 1.3 79.2 + - - +
130A ASP* 1.3 62.2 + - - +
132A ALA* 3.2 9.9 + - + +
133A GLY* 2.9 19.2 + - - -
138A TYR* 3.9 36.3 - - + -
219A TRP* 5.2 0.2 - - - -
222A VAL* 3.9 29.6 - - + +
226A GLY* 3.9 24.2 - - - +
227A GLY* 4.4 0.7 - - - +
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Residues in contact with ASP 130 (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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33A LYS* 3.2 38.4 + - - +
115A PHE* 6.0 1.2 - - - -
127A GLU 3.8 13.4 + - - +
128A SER 3.1 0.2 - - - -
129A VAL* 1.3 78.5 - - - +
131A LEU* 1.3 64.1 + - + +
133A GLY* 3.0 15.3 + - - -
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Residues in contact with LEU 131 (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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33A LYS* 4.0 17.9 - - + -
34A VAL* 3.6 26.9 - - + -
112A PHE* 4.3 18.7 - - + +
115A PHE* 4.0 26.9 - - + -
116A GLU* 3.6 37.5 - - + +
121A ILE* 4.8 10.3 - - + -
128A SER* 3.1 11.3 + - - +
130A ASP* 1.3 78.6 + - + +
132A ALA* 1.3 57.5 + - - +
133A GLY 2.9 5.2 - - - -
134A THR* 2.8 33.0 + - - +
135A PHE* 4.5 0.7 - - - -
219A TRP* 4.2 11.7 - - + +
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Residues in contact with ALA 132 (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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128A SER 3.0 7.3 + - - +
129A VAL* 3.2 15.0 + - - +
131A LEU* 1.3 70.6 - - - +
133A GLY* 1.3 56.6 + - - +
134A THR 2.9 11.5 + - - -
135A PHE* 2.9 22.7 + - - +
136A SER* 3.5 8.3 + - - -
138A TYR* 3.8 21.2 + - + +
214A ALA* 5.0 5.5 - - + +
219A TRP* 3.6 35.1 - - + +
222A VAL* 5.9 0.9 - - + -
223A ALA* 5.1 3.1 - - - -
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Residues in contact with GLY 133 (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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29A VAL* 3.8 8.5 - - - +
33A LYS* 4.0 9.9 - - - -
129A VAL 2.9 12.7 + - - -
130A ASP* 3.0 8.9 + - - -
131A LEU 2.9 2.4 - - - -
132A ALA* 1.3 76.6 - - - +
134A THR* 1.3 63.1 + - - +
135A PHE 3.2 0.6 - - - -
136A SER 3.1 22.2 + - - +
138A TYR* 3.9 8.3 - - - -
206A ARG* 5.5 1.7 + - - -
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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