Contacts of the strand formed by residues 137 - 144 (chain D) in PDB entry 1EN6
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 137 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D ASP* 3.8 17.0 - - - +
133D LEU* 3.6 5.0 - - - -
134D LYS* 2.9 58.2 + - + +
135D GLY 3.7 0.2 - - - -
136D ASP* 1.3 85.3 - - - +
138D LEU* 1.3 65.2 + - - +
139D ALA* 5.4 5.8 - - + -
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 4.4 7.9 - - + -
101D ALA* 3.8 22.7 - - + -
102D ILE* 3.7 33.7 - - + +
104D ARG* 5.3 0.7 - - - +
105D ASP* 3.1 23.6 + - - +
106D PHE* 3.7 22.1 - - + -
131D LEU* 4.1 9.0 - - + -
132D VAL 3.4 3.4 - - - +
133D LEU* 3.7 18.2 - - + -
137D LYS* 1.3 78.9 - - - +
139D ALA* 1.3 63.5 + - - +
163D ILE* 3.1 33.9 - - + -
201D PHE* 4.0 6.3 - - + -
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Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D PHE* 3.8 7.6 - - - -
131D LEU* 3.5 4.6 - - - +
132D VAL* 2.8 46.5 + - + +
134D LYS* 4.4 22.4 - - + +
137D LYS* 4.9 7.2 - - - +
138D LEU* 1.3 77.1 - - - +
140D VAL* 1.3 67.0 + - - +
141D VAL* 4.8 1.1 - - + -
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Residues in contact with VAL 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D PHE* 3.9 17.2 - - + -
112D PHE* 3.9 29.6 - - + -
115D GLU* 3.9 16.4 - - + +
116D PHE* 3.9 19.7 - - + +
119D ALA* 3.5 30.1 - - + -
130D TRP 3.2 11.0 - - - +
131D LEU* 4.8 0.2 - - + -
139D ALA* 1.3 76.6 - - - +
141D VAL* 1.3 72.3 + - - +
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ALA* 4.9 2.2 - - - -
129D ALA* 3.6 1.7 - - - +
130D TRP* 2.6 45.9 + - + -
132D VAL* 3.9 30.7 - - + -
134D LYS* 4.1 29.2 - - - +
139D ALA* 4.8 1.1 - - + -
140D VAL* 1.3 85.7 - - - +
142D SER* 1.3 59.7 + - - +
149D PRO* 4.3 1.8 - - + -
158D ALA* 4.1 25.8 - - + -
159D SER 4.9 0.7 - - - +
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Residues in contact with SER 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ALA* 4.2 20.1 + - - -
122D SER* 5.7 0.2 + - - -
123D ARG* 2.9 32.6 + - - +
128D TRP 3.1 15.3 - - - -
129D ALA* 4.2 5.6 - - - +
130D TRP* 4.2 1.1 - - - -
141D VAL* 1.3 77.3 - - - +
143D THR* 1.3 68.3 + - - +
156D SER 4.9 1.7 - - - +
157D GLY 5.5 0.5 - - - +
158D ALA* 4.3 7.8 - - - +
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Residues in contact with THR 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ARG* 3.5 11.1 + - - +
127D GLY* 3.1 4.0 - - - -
128D TRP* 2.9 33.0 + - - +
130D TRP* 2.9 27.8 + - + +
142D SER* 1.3 78.9 - - - +
144D ALA* 1.3 60.9 + - - +
147D ASP* 3.1 24.7 + - - +
149D PRO* 4.2 10.1 - - + -
156D SER* 4.1 21.5 - - - +
158D ALA* 4.0 20.9 - - + -
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Residues in contact with ALA 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ARG* 3.6 18.9 - - - +
126D SER 3.7 6.7 - - - +
143D THR* 1.3 75.1 - - - +
145D ASN* 1.3 81.7 + - - +
146D LEU 3.1 0.3 + - - -
147D ASP* 3.0 31.0 + - - +
156D SER 5.1 2.6 + - - -
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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