Contacts of the helix formed by residues 128 - 136 (chain A) in PDB entry 1ECX
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 LYS 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A VAL* 3.5 7.8 - - - +
120A PRO* 2.9 42.4 + - + +
121A VAL 3.8 23.6 + - - +
122A ASP* 3.9 17.9 - - + +
127A VAL* 1.3 73.0 - - - +
129A LEU* 1.3 66.2 + - - +
130A GLU* 3.4 2.2 - - + +
131A GLU* 3.3 21.2 + - + +
132A LEU* 3.2 15.4 + - - +
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Residues in contact with LEU 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* 6.3 0.2 - - + -
127A VAL* 3.4 17.7 + - + +
128A LYS* 1.3 68.4 - - - +
130A GLU* 1.3 68.9 + - + +
132A LEU* 2.9 20.6 + - + +
133A GLU* 3.0 11.4 + - - +
157A PRO* 4.1 8.1 - - + -
160A ASP* 3.8 26.2 - - + +
161A VAL* 3.8 29.8 - - + +
163A ARG* 5.0 1.8 - - - +
164A ILE* 3.7 32.9 - - + +
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Residues in contact with GLU 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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128A LYS* 3.4 1.3 - - + -
129A LEU* 1.3 76.2 - - + +
131A GLU* 1.3 66.4 + - + +
133A GLU* 2.9 20.3 + - - +
134A LYS* 3.4 9.7 + - - +
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Residues in contact with GLU 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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119A VAL* 4.3 2.0 - - - -
120A PRO* 4.0 36.6 - - + +
128A LYS* 3.3 23.1 + - + +
129A LEU 3.3 0.8 - - - -
130A GLU* 1.3 80.8 - - + +
132A LEU* 1.3 61.5 + - - +
134A LYS* 3.6 17.0 + - - +
135A LEU* 3.3 28.7 + - + +
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Residues in contact with LEU 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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93A ILE* 4.1 13.9 - - + -
119A VAL* 3.4 30.5 - - + +
127A VAL* 5.3 4.5 - - + -
128A LYS 3.2 11.3 + - - +
129A LEU* 2.9 19.5 + - + +
131A GLU* 1.3 75.0 - - - +
133A GLU* 1.3 65.1 + - - +
134A LYS 3.3 0.2 + - - -
135A LEU* 3.3 0.7 + - + +
136A VAL* 3.2 35.3 + - + +
143A VAL* 4.8 5.8 - - + -
161A VAL* 3.8 38.8 - - + +
164A ILE* 4.4 11.4 - - + -
165A VAL* 4.2 12.8 - - + -
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Residues in contact with GLU 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 LEU 3.0 8.0 + - - +
130A GLU* 2.9 13.0 + - - +
132A LEU* 1.3 78.0 - - - +
134A LYS* 1.3 60.1 + - - +
136A VAL* 3.7 3.8 - - - +
164A ILE* 4.1 23.5 - - + +
167A LYS* 6.5 1.3 - - + -
168A LYS* 2.5 62.7 + - + +
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Residues in contact with LYS 134 (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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130A GLU 3.4 7.1 + - - +
131A GLU* 3.9 20.0 - - - +
132A LEU 3.2 0.6 - - - -
133A GLU* 1.3 86.7 + - - +
135A LEU* 1.3 69.7 + - + +
136A VAL 3.7 0.9 - - - +
137A ASP* 5.3 1.6 - - - +
168A LYS* 3.7 9.5 + - - +
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Residues in contact with LEU 135 (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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93A ILE* 3.9 15.9 - - + +
117A LYS* 4.1 37.4 - - + +
118A TYR 4.1 6.3 - - - +
119A VAL* 3.2 45.8 - - + +
120A PRO* 5.0 3.1 - - + -
131A GLU* 3.3 16.9 + - + +
132A LEU 3.3 4.0 + - - +
134A LYS* 1.3 79.7 - - + +
136A VAL* 1.3 65.6 - - - +
137A ASP* 3.1 15.4 + - - +
140A THR* 4.2 0.2 + - - -
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Residues in contact with VAL 136 (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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93A ILE* 3.4 23.3 - - + -
132A LEU* 3.2 21.6 + - + +
133A GLU* 4.9 0.7 - - - -
134A LYS 3.4 0.7 - - - +
135A LEU* 1.3 75.0 - - - +
137A ASP* 1.3 62.9 + - - +
140A THR* 4.5 2.9 - - + -
143A VAL* 4.5 3.1 - - + -
164A ILE* 6.1 0.7 - - + -
165A VAL* 3.9 32.5 - - + +
168A LYS* 2.7 60.1 + - + +
169A ASN* 4.2 17.0 - - + -
172A THR* 4.4 7.9 - - - +
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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