Contacts of the helix formed by residues 123 - 133 (chain A) in PDB entry 1FXT
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 ASP 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A HIS 5.2 2.4 + - - +
78A PRO 4.0 5.3 + - - +
81A SER* 2.5 25.4 + - - -
82A SER* 2.7 41.3 + - - +
83A VAL* 3.0 16.7 + - - +
84A THR* 4.4 2.3 + - - +
122A GLN* 1.3 89.9 + - - +
124A ALA* 1.3 64.3 + - - +
125A GLU 3.6 2.0 - - - -
126A VAL* 3.1 24.9 + - + +
127A ALA* 3.2 12.0 + - - +
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Residues in contact with ALA 124 (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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121A PRO* 6.0 4.7 - - + -
122A GLN 3.3 8.8 + - - +
123A ASP* 1.3 70.1 - - - +
125A GLU* 1.3 58.1 + - + +
127A ALA* 3.4 9.7 + - - +
128A GLN* 3.0 26.6 + - - +
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Residues in contact with GLU 125 (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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76A TYR* 5.2 1.1 + - - -
123A ASP 3.6 0.2 - - - -
124A ALA* 1.3 74.8 - - + +
126A VAL* 1.3 60.3 + - + +
128A GLN* 3.0 40.7 + - - +
129A HIS* 2.9 28.9 + - - +
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Residues in contact with VAL 126 (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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76A TYR* 3.9 36.3 - - + +
77A HIS* 3.6 38.8 - - - +
78A PRO* 3.9 1.6 - - - -
82A SER* 3.3 28.7 - - - +
123A ASP* 3.1 18.7 + - + +
125A GLU* 1.3 73.5 - - + +
127A ALA* 1.3 59.3 + - - +
129A HIS* 3.6 6.0 + - - +
130A TYR* 3.0 29.6 + - - +
137A PHE* 4.3 3.8 - - + -
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Residues in contact with ALA 127 (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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78A PRO* 4.2 28.2 - - + +
118A PRO* 4.3 11.6 - - + +
121A PRO* 5.2 12.3 - - + -
123A ASP 3.2 11.3 + - - +
124A ALA* 3.6 11.4 - - - +
126A VAL* 1.3 71.5 - - - +
128A GLN* 1.4 59.2 + - - +
130A TYR* 3.5 2.6 + - - +
131A LEU* 3.1 37.4 + - + +
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Residues in contact with GLN 128 (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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124A ALA 3.0 18.7 + - - +
125A GLU* 3.0 42.4 + - - +
127A ALA* 1.4 70.6 - - - +
129A HIS* 1.3 65.7 + - - +
131A LEU* 3.5 11.8 + - - +
132A ARG* 3.0 42.3 + - - +
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Residues in contact with HIS 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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76A TYR* 3.0 29.5 + + - +
125A GLU 2.9 22.4 + - - +
126A VAL* 3.6 6.1 - - - +
127A ALA 3.5 0.2 - - - -
128A GLN* 1.3 77.4 + - - +
130A TYR* 1.3 58.5 + - - +
132A ARG* 3.2 25.5 + - - +
133A ASP* 2.9 44.4 + - + +
136A SER* 3.6 16.3 - - - -
137A PHE* 3.2 41.9 + + - -
140A THR* 5.1 1.8 - - - -
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Residues in contact with TYR 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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78A PRO* 3.7 20.0 - - + -
116A PRO* 2.7 47.4 + - + +
118A PRO* 3.9 24.9 - - + -
126A VAL 3.0 20.1 + - - +
127A ALA 3.5 2.2 + - - +
129A HIS* 1.3 73.0 - - - +
131A LEU* 1.3 60.4 + - - +
133A ASP* 3.5 5.8 - - - +
134A ARG* 2.9 68.6 + - - -
137A PHE* 3.7 43.3 - + + -
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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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118A PRO* 3.7 29.2 - - + +
127A ALA* 3.1 27.2 + - + +
128A GLN* 3.7 8.7 - - - +
130A TYR* 1.3 75.4 - - - +
132A ARG* 1.3 60.4 + - - +
134A ARG* 5.3 1.2 + - - -
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Residues in contact with ARG 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 GLN* 3.0 36.5 + - - +
129A HIS* 3.2 32.5 + - - +
131A LEU* 1.3 72.5 - - - +
133A ASP* 1.3 98.3 + - - +
135A GLU* 5.5 1.6 + - - +
136A SER* 4.8 2.2 - - - -
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Residues in contact with ASP 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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129A HIS* 2.9 27.3 + - + +
130A TYR* 3.5 4.9 - - - +
131A LEU 3.6 1.6 - - - -
132A ARG* 1.3 107.9 + - - +
134A ARG* 1.3 87.6 + - - +
135A GLU* 2.8 24.6 + - - +
136A SER* 3.4 17.0 + - - -
137A PHE* 2.8 32.2 + - + +
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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