Contacts of the helix formed by residues 128 - 136 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B VAL* 3.6 7.8 - - - +
120B PRO* 3.0 38.8 + - + +
121B VAL 3.7 17.6 + - - -
122B ASP* 3.9 24.0 - - + +
127B VAL* 1.3 72.8 - - - +
129B LEU* 1.3 65.8 + - - +
130B GLU* 3.2 4.0 + - + +
131B GLU* 3.2 33.2 + - + +
132B LEU 3.3 8.1 + - - -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B VAL* 6.1 0.7 - - + -
127B VAL* 3.4 11.3 + - + +
128B LYS* 1.3 72.3 - - - +
130B GLU* 1.3 63.9 + - + +
132B LEU* 3.1 17.5 + - + +
133B GLU* 3.2 14.0 + - - +
157B PRO* 4.0 15.0 - - + -
160B ASP* 3.8 28.5 - - + +
161B VAL* 3.9 28.9 - - + +
163B ARG* 5.5 1.1 - - - +
164B ILE* 3.6 29.0 - - + +
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LYS* 3.2 2.3 + - + -
129B LEU* 1.3 79.9 - - + +
131B GLU* 1.3 71.5 + - + +
132B LEU 3.2 0.5 + - - -
133B GLU* 3.4 14.4 + - - +
134B LYS* 3.5 10.7 + - - +
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL* 4.1 1.6 - - + -
120B PRO* 4.0 30.9 - - + +
128B LYS* 3.2 37.5 + - + +
130B GLU* 1.3 81.4 - - + +
132B LEU* 1.3 56.6 + - - +
134B LYS* 3.4 11.4 + - - +
135B LEU* 2.9 38.5 + - + +
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 4.4 8.5 - - + -
119B VAL* 3.9 29.8 - - + +
127B VAL* 5.2 4.3 - - + -
128B LYS 3.3 9.8 + - - +
129B LEU* 3.1 18.8 + - + +
130B GLU 3.1 0.4 - - - -
131B GLU* 1.3 77.1 - - - +
133B GLU* 1.3 69.5 + - - +
134B LYS 3.1 0.7 + - - -
135B LEU* 3.2 1.4 + - - -
136B VAL* 3.1 41.9 + - + +
143B VAL* 4.9 3.6 - - + -
161B VAL* 3.8 49.4 - - + +
164B ILE* 4.3 12.6 - - + -
165B VAL* 4.4 7.9 - - + -
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Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LEU 3.2 6.5 + - - +
130B GLU* 3.7 11.0 - - - +
132B LEU* 1.3 79.7 - - - +
134B LYS* 1.3 81.5 + - - +
136B VAL* 3.6 5.2 + - - -
164B ILE* 3.8 24.6 - - + +
168B LYS* 2.7 61.2 + - + +
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Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU 3.5 6.6 + - - +
131B GLU* 3.4 14.1 + - - +
132B LEU 3.1 0.8 - - - -
133B GLU* 1.3 92.8 + - - +
135B LEU* 1.3 70.0 + - + +
136B VAL 3.0 3.8 + - - +
137B ASP* 5.3 1.0 - - - +
168B LYS* 3.4 11.2 + - - +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ILE* 3.4 20.0 - - + +
117B LYS* 3.7 41.0 - - + +
118B TYR 4.1 9.2 - - - +
119B VAL* 3.8 36.6 - - + +
120B PRO* 4.7 5.2 - - + -
131B GLU* 2.9 27.6 + - + +
132B LEU* 3.2 4.4 + - - +
134B LYS* 1.3 77.1 - - + +
136B VAL* 1.3 59.2 + - - +
137B ASP* 3.3 5.4 + - - +
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Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 3.6 20.0 - - + -
132B LEU* 3.1 31.6 + - + +
133B GLU* 5.0 0.7 - - - -
134B LYS 3.0 4.0 + - - +
135B LEU* 1.3 74.6 - - - +
137B ASP* 1.3 66.8 + - - +
140B THR* 4.3 11.4 - - + -
143B VAL* 4.6 3.8 - - + -
164B ILE* 6.1 0.4 - - + -
165B VAL* 4.5 22.0 - - + +
168B LYS* 2.9 59.7 + - + +
169B ASN* 4.2 12.1 - - + -
172B THR* 4.5 2.2 - - - +
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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