Contacts of the strand formed by residues 137 - 144 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B ARG* 5.1 0.7 - - - +
105B ASP* 3.8 18.4 - - - +
133B LEU* 3.6 3.6 - - - +
134B LYS* 3.0 34.9 + - + +
136B ASP* 1.3 99.3 - - - +
138B LEU* 1.3 66.8 + - - +
139B ALA* 4.9 0.4 - - + +
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Residues in contact with LEU 138 (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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98B LEU* 4.3 8.3 - - + -
101B ALA* 3.7 29.4 - - + -
102B ILE* 3.4 33.0 - - + +
104B ARG* 5.1 0.9 - - - +
105B ASP* 3.0 22.9 + - - +
106B PHE* 3.9 21.1 - - + -
131B LEU* 4.2 7.9 - - + -
132B VAL 3.4 13.2 - - - +
133B LEU* 4.0 21.3 - - + -
137B LYS* 1.3 76.8 - - - +
139B ALA* 1.3 63.2 + - - +
163B ILE* 4.2 13.9 - - + -
201B PHE* 4.2 12.1 - - + -
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Residues in contact with ALA 139 (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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106B PHE* 3.9 7.4 - - - -
131B LEU* 3.5 4.2 - - - +
132B VAL* 2.8 46.0 + - + +
134B LYS* 4.5 20.6 - - + +
137B LYS* 4.9 0.7 - - + +
138B LEU* 1.3 77.7 - - - +
140B VAL* 1.3 67.2 + - - +
141B VAL* 4.9 1.3 - - + -
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Residues in contact with VAL 140 (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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106B PHE* 3.8 24.2 - - + -
112B PHE* 3.9 22.0 - - + -
115B GLU* 3.9 19.7 - - + +
116B PHE* 4.0 20.6 - - + +
119B ALA* 3.5 29.8 - - + -
130B TRP 3.2 11.4 - - - +
131B LEU* 4.5 1.3 - - + -
139B ALA* 1.3 75.8 - - - +
141B VAL* 1.3 73.1 + - - +
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Residues in contact with VAL 141 (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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119B ALA* 4.8 2.6 - - - +
129B ALA* 3.6 1.2 - - - +
130B TRP* 2.6 47.1 + - + +
132B VAL* 3.9 30.7 - - + -
134B LYS* 4.3 26.5 - - - +
139B ALA* 4.9 2.0 - - + -
140B VAL* 1.3 85.9 - - - +
142B SER* 1.3 60.8 + - - +
149B PRO* 4.3 2.5 - - + -
158B ALA* 4.0 26.7 - - + -
159B SER 4.9 0.4 - - - +
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Residues in contact with SER 142 (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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119B ALA* 4.3 20.4 + - - -
123B ARG* 3.0 34.6 + - - +
128B TRP 3.1 15.3 - - - -
129B ALA* 4.2 5.4 - - - -
130B TRP* 4.2 1.3 - - - -
141B VAL* 1.3 76.4 - - - +
143B THR* 1.3 68.0 + - - +
156B SER 4.9 2.1 - - - +
157B GLY 5.6 0.5 - - - +
158B ALA* 4.4 7.6 - - - +
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Residues in contact with THR 143 (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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123B ARG* 3.5 12.3 + - - +
127B GLY* 3.1 3.8 - - - -
128B TRP* 2.9 32.3 + - - +
130B TRP* 3.0 27.3 + - + +
142B SER* 1.3 80.3 - - - +
144B ALA* 1.3 59.5 + - - +
147B ASP* 3.1 24.0 + - - -
148B SER 4.3 0.9 - - - -
149B PRO 4.2 11.0 - - - -
156B SER* 4.1 27.4 - - - +
158B ALA* 4.1 15.0 - - + -
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Residues in contact with ALA 144 (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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123B ARG* 3.6 20.0 - - - +
126B SER 3.7 6.5 - - - +
143B THR* 1.3 75.3 - - - +
145B ASN* 1.3 79.7 + - - +
146B LEU 3.1 0.2 + - - -
147B ASP* 3.0 31.8 + - - +
156B SER 5.1 3.0 + - - +
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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