Contacts of the helix formed by residues 123 - 131 (chain A) in PDB entry 1EBF
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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119A ALA 5.0 0.2 - - - +
122A SER* 1.3 88.1 + - - +
124A LEU* 1.3 63.4 + - - +
125A ALA* 4.0 6.9 + - + +
126A THR* 2.9 29.3 + - - +
127A TRP* 3.4 14.4 + - - +
229A ARG* 3.6 6.4 + - - -
236A GLU 5.0 1.3 - - - -
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Residues in contact with LEU 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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122A SER 3.5 0.8 + - - -
123A ASP* 1.3 73.2 + - - +
125A ALA* 1.3 64.6 + - - +
127A TRP* 3.5 10.2 - - + +
128A LYS* 3.2 20.3 + - - +
229A ARG* 3.6 37.4 - - + +
234A GLU* 3.7 52.3 - - + +
235A VAL 3.9 4.0 - - - +
236A GLU* 4.0 22.2 + - - +
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Residues in contact with ALA 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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123A ASP* 3.3 7.3 - - + +
124A LEU* 1.3 78.5 - - - +
126A THR* 1.3 65.7 + - - +
128A LYS* 3.3 7.5 + - - +
129A ALA* 3.0 23.9 + - - +
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Residues in contact with THR 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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99A ALA 5.4 4.0 - - - +
102A TYR* 5.8 1.3 - - + -
103A THR* 4.4 13.7 - - - +
119A ALA* 3.8 23.1 - - + +
122A SER* 4.1 9.5 + - - +
123A ASP* 2.9 30.8 + - - +
125A ALA* 1.3 79.5 - - - +
127A TRP* 1.3 62.4 + - - +
129A ALA* 3.1 8.4 + - - +
130A LEU* 3.0 34.1 + - + +
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Residues in contact with TRP 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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119A ALA 4.6 2.6 + - - +
120A PHE* 3.3 44.2 - + + -
123A ASP 3.4 10.5 + - - +
124A LEU* 3.5 19.1 - - + +
126A THR* 1.3 79.3 - - - +
128A LYS* 1.3 68.5 + - + +
130A LEU* 3.2 15.3 + - - +
131A PHE* 3.2 57.3 - + + +
142A HIS* 4.3 0.7 - - - -
157A ARG* 4.0 11.0 - - - -
226A ILE* 3.6 31.2 - - + -
229A ARG* 3.7 45.1 + - + +
230A ILE* 3.8 11.9 - - + -
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Residues in contact with LYS 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 LEU 3.2 10.8 + - - +
125A ALA* 3.8 9.9 - - - +
126A THR 3.3 0.2 - - - -
127A TRP* 1.3 87.5 - - + +
129A ALA* 1.3 62.5 + - - +
131A PHE* 3.4 4.2 + - - +
132A SER* 3.2 24.3 + - - -
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Residues in contact with ALA 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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103A THR* 4.0 26.9 - - + +
106A VAL* 4.6 10.8 - - - +
125A ALA 3.0 14.3 + - - +
126A THR* 3.1 9.8 + - - +
128A LYS* 1.3 77.7 - - - +
130A LEU* 1.3 63.5 + - - +
131A PHE 3.4 0.3 + - - -
132A SER* 3.5 16.9 + - - -
133A ASN 5.0 0.3 + - - -
134A LYS* 5.9 1.7 - - - +
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Residues in contact with LEU 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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102A TYR* 3.6 31.9 - - + -
103A THR* 4.1 15.0 - - - +
106A VAL* 4.3 10.4 - - + +
119A ALA* 3.7 33.9 - - + +
120A PHE* 3.9 25.1 - - + -
126A THR* 3.0 21.7 + - + +
127A TRP* 3.2 9.4 + - - +
129A ALA* 1.3 78.2 - - - +
131A PHE* 1.3 69.6 + - + +
132A SER 3.5 0.9 + - - -
133A ASN* 4.8 6.1 + - - -
138A GLY 4.9 1.0 - - - +
140A VAL* 3.6 33.7 + - + +
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Residues in contact with PHE 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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120A PHE* 3.7 17.0 - + - -
127A TRP* 3.2 67.6 + + - +
128A LYS* 3.4 5.1 + - - +
129A ALA 3.3 0.4 - - - -
130A LEU* 1.3 83.3 - - + +
132A SER* 1.3 63.2 + - - +
133A ASN* 3.3 11.6 - - - +
140A VAL* 3.7 29.6 - - + -
142A HIS* 3.4 15.5 - + - -
157A ARG* 3.1 37.5 - - - +
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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