Contacts of the strand formed by residues 125 - 132 (chain B) in PDB entry 1LJ1
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 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123B PRO* 3.7 4.7 - - - +
124B HIS* 1.3 107.5 + - - +
126B THR* 1.3 63.2 + - - +
127B VAL* 4.2 4.3 - - + -
153B ILE* 3.7 19.9 - - + +
271B ASP* 4.9 0.3 - - - +
273B ARG* 2.9 37.9 + - - -
303B TRP 4.1 2.0 + - - -
304B VAL* 3.6 11.1 - - + +
305B LYS 2.9 26.0 + - - -
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Residues in contact with THR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PRO* 4.0 17.3 - - - +
125B ASP* 1.3 75.2 + - - +
127B VAL* 1.3 69.4 + - - +
151B LYS* 5.2 1.2 - - - +
305B LYS* 3.5 29.0 - - + +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ASP* 4.4 2.2 - - + -
126B THR* 1.3 85.9 - - - +
128B ASP* 1.3 69.5 + - - +
129B VAL 3.7 22.0 - - - +
130B VAL* 4.0 7.4 - - + -
151B LYS* 3.7 31.6 - - + +
153B ILE* 3.6 29.4 - - + +
304B VAL* 4.0 19.7 - - + -
305B LYS 3.0 7.9 + - - +
306B ALA* 3.3 18.5 - - + -
307B ASP* 4.0 2.3 + - - +
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Residues in contact with ASP 128 (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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127B VAL* 1.3 79.5 - - - +
129B VAL* 1.3 62.8 + - + +
149B GLY 4.4 2.8 - - - +
150B ALA* 3.6 15.6 - - + -
151B LYS* 2.8 36.3 + - - +
306B ALA* 4.0 2.0 - - - -
307B ASP* 3.2 30.2 + - - +
308B ALA 3.3 6.6 + - - -
568B SER 3.4 23.0 - - - +
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 3.7 3.7 - - - +
128B ASP* 1.3 84.7 - - + +
130B VAL* 1.3 76.6 + - - +
131B VAL* 4.3 6.3 - - + -
145B ALA* 4.5 5.6 - - + -
150B ALA* 4.2 21.3 - - + -
151B LYS 3.1 3.5 + - - +
152B VAL* 3.2 15.0 - - + +
153B ILE 3.2 21.0 + - - -
306B ALA* 4.4 0.2 - - - -
308B ALA* 3.3 12.3 - - + +
310B ILE* 4.0 27.6 - - + -
564B ALA* 4.0 28.7 - - + +
565B ALA* 4.4 0.9 - - - +
568B SER 4.8 0.2 - - - -
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 4.0 6.5 - - + -
129B VAL* 1.3 78.0 - - - +
131B VAL* 1.3 72.1 + - - +
132B VAL* 4.2 7.9 - - + -
153B ILE* 3.4 18.8 - - + +
155B ILE* 4.7 13.2 - - + -
292B ILE* 4.1 24.9 - - + -
294B VAL* 5.8 0.4 - - + -
304B VAL* 3.5 35.4 - - + -
306B ALA* 4.2 7.2 - - + -
308B ALA 3.0 9.3 + - - +
309B VAL* 3.4 7.5 - - + +
310B ILE 3.1 23.9 + - - -
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Residues in contact with VAL 131 (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 VAL* 4.3 3.6 - - + -
130B VAL* 1.3 76.2 - - - +
132B VAL* 1.3 63.0 + - - +
133B GLY 4.3 1.3 - - - +
138B GLY* 3.4 36.8 - - - +
141B ALA* 4.2 5.6 - - + +
142B ALA* 4.1 14.4 - - - +
152B VAL* 4.1 18.6 - - + -
153B ILE 2.9 11.9 + - - +
154B LEU* 3.4 16.7 - - + +
155B ILE* 3.0 27.2 + - - +
310B ILE* 3.6 31.2 - - + +
312B ALA* 4.5 1.8 - - + -
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Residues in contact with VAL 132 (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 VAL* 4.7 3.4 - - + -
131B VAL* 1.3 75.0 - - - +
133B GLY* 1.3 57.5 + - - +
155B ILE* 3.8 14.1 - - + -
278B GLY* 4.3 4.9 - - - -
292B ILE* 3.7 28.3 - - + -
309B VAL* 4.2 6.1 - - + -
310B ILE 2.8 17.2 + - - +
311B LEU* 4.0 16.4 - - + -
312B ALA* 3.0 28.9 + - - -
313B THR* 3.4 15.7 - - + +
1800B FAD 3.3 35.4 - - + +
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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