Contacts of the strand formed by residues 151 - 155 (chain A) in PDB entry 1LCJ
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 PHE 151 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TRP* 3.4 36.8 - + + +
141A LEU* 3.8 4.6 - - - +
149A GLY 3.4 14.6 - - - +
150A SER* 1.3 75.2 - - - +
152A LEU* 1.3 70.3 + - - +
153A ILE 4.8 0.2 - - - -
165A LEU* 4.0 15.0 - - + -
166A SER 3.2 13.7 - - - +
167A VAL* 4.3 2.2 - - + -
206A VAL* 3.6 35.2 - - + -
210A THR* 4.8 2.0 - - - -
220A LEU* 3.9 33.0 - - + -
221A SER 4.3 3.4 - - - -
222A ARG* 3.2 27.7 + - - -
223A PRO* 3.5 9.1 - - + +
224A CYS 2.9 23.5 + - - +
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Residues in contact with LEU 152 (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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127A TRP 3.4 11.7 - - - +
129A PHE* 3.8 15.0 - - + -
132A LEU* 3.9 24.9 - - + -
137A ALA* 3.9 13.5 - - + +
140A GLN* 4.6 0.9 - - + -
141A LEU* 3.8 24.9 - - + -
151A PHE* 1.3 80.3 - - - +
153A ILE* 1.3 64.0 + - - +
154A ARG* 3.8 36.1 - - + -
165A LEU* 3.5 5.5 - - - +
166A SER* 2.9 40.6 + - - +
224A CYS* 4.0 15.5 - - + -
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Residues in contact with ILE 153 (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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127A TRP* 2.9 29.2 + - + +
128A PHE* 3.7 9.3 - - + -
129A PHE* 2.9 28.2 + - - +
151A PHE* 5.0 1.3 - - + -
152A LEU* 1.3 78.2 - - - +
154A ARG* 1.3 71.3 + - - +
163A PHE* 4.0 18.2 - - + -
164A SER 3.5 5.2 - - - +
165A LEU* 4.0 14.6 - - + -
183A ILE* 4.0 21.1 - - + -
202A LEU* 4.2 23.1 - - + -
205A LEU* 4.6 3.4 - - + -
206A VAL* 3.5 32.3 - - + -
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Residues in contact with ARG 154 (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 PHE* 5.3 0.2 - - - -
129A PHE 3.4 21.5 - - - +
130A LYS* 4.2 1.8 - - - +
132A LEU* 3.3 19.5 + - - +
133A SER 4.1 0.2 - - - -
134A ARG* 3.6 20.5 - - - +
137A ALA* 3.6 14.1 - - - +
152A LEU* 3.8 17.9 - - + -
153A ILE* 1.3 74.5 - - - +
155A GLU* 1.3 67.0 + - - +
157A GLU* 3.8 10.3 - - - +
163A PHE* 3.2 13.8 - - - +
164A SER* 2.9 47.0 + - - +
166A SER* 3.2 11.1 + - - +
180A HIS* 3.1 27.1 + - - -
204B PTR 3.0 39.2 + - - -
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Residues in contact with GLU 155 (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 PHE* 5.2 0.5 - - - -
130A LYS* 3.1 49.1 + - + +
131A ASN* 4.5 5.4 - - - +
132A LEU 4.4 4.2 - - - +
154A ARG* 1.3 91.2 + - - +
156A SER* 1.3 69.7 + - - +
157A GLU* 3.6 3.3 + - - +
162A SER 3.8 6.5 - - - +
163A PHE* 3.6 28.4 - - + -
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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