Contacts of the strand formed by residues 163 - 171 (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 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A PHE* 4.1 23.8 - + - -
153A ILE* 4.0 12.8 - - + -
154A ARG 3.2 19.7 - - - +
155A GLU* 3.6 33.7 - - + -
156A SER 3.9 1.8 - - - +
161A GLY 4.5 5.2 - - - -
162A SER* 1.3 84.4 - - - +
164A SER* 1.3 65.2 + - - +
182A LYS* 3.8 3.5 - - - +
183A ILE* 2.8 42.6 + - + +
185A ASN* 4.5 8.1 - - - -
191A PHE* 3.9 33.9 - + - -
202A LEU* 4.4 13.0 - - + -
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Residues in contact with SER 164 (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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152A LEU 4.0 0.2 - - - +
153A ILE* 3.5 3.3 - - - +
154A ARG* 2.9 65.8 + - - +
156A SER* 3.7 8.1 + - - +
163A PHE* 1.3 75.5 + - - +
165A LEU* 1.3 60.7 + - - +
180A HIS* 5.5 0.2 - - - -
181A TYR 3.2 8.7 - - - -
182A LYS* 4.1 0.7 - - - +
183A ILE* 4.6 2.7 - - - -
204B PTR 2.9 33.7 + - - -
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Residues in contact with LEU 165 (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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151A PHE* 4.0 23.3 - - + -
152A LEU 3.5 14.1 - - - +
153A ILE* 4.0 16.4 - - + -
164A SER* 1.3 72.7 - - - +
166A SER* 1.3 64.3 + - - +
167A VAL* 4.9 3.1 - - + -
179A LYS 3.6 1.0 - - - +
180A HIS* 3.2 5.5 - - - +
181A TYR* 2.8 58.8 + - + +
183A ILE* 4.1 17.7 - - + +
193A ILE* 3.9 22.2 - - + -
205A LEU* 5.5 3.6 - - + -
209A TYR* 6.1 0.2 - - + -
216A LEU* 4.2 17.9 - - + -
220A LEU* 4.2 16.4 - - + -
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Residues in contact with SER 166 (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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137A ALA* 3.7 3.0 - - - +
141A LEU* 3.7 19.9 - - - +
151A PHE* 3.2 5.9 - - - +
152A LEU* 2.9 45.9 + - - -
154A ARG* 3.2 20.1 + - - -
164A SER 4.0 0.6 + - - -
165A LEU* 1.3 71.6 - - - +
167A VAL* 1.3 60.0 + - - +
179A LYS 3.4 5.2 - - - -
180A HIS* 2.8 31.2 + - - -
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Residues in contact with VAL 167 (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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141A LEU* 4.0 1.0 - - - +
149A GLY 4.1 5.8 - - - +
150A SER 3.5 10.5 - - - +
151A PHE* 4.3 3.1 - - + -
165A LEU* 4.9 5.2 - - + -
166A SER* 1.3 75.7 - - - +
168A ARG* 1.3 65.2 + - - +
169A ASP* 3.9 0.4 + - + -
177A VAL 3.8 0.3 - - - +
178A VAL* 3.3 7.2 - - - +
179A LYS* 2.8 43.4 + - + +
181A TYR* 4.3 11.0 - - + -
216A LEU* 5.9 0.7 - - + -
217A CYS* 3.6 29.2 - - - -
218A THR* 3.7 24.5 - - + -
220A LEU* 3.8 23.6 - - + -
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Residues in contact with ARG 168 (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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141A LEU* 2.9 39.4 + - + +
142A LEU* 3.6 31.4 + - - +
143A ALA 3.6 9.5 + - - -
144A PRO* 5.6 0.2 - - - +
146A ASN* 2.9 28.0 + - - +
147A THR* 3.3 25.4 - - - +
148A HIS 4.5 0.4 - - - +
149A GLY* 2.9 28.5 + - - -
150A SER* 2.8 19.3 + - - +
167A VAL* 1.3 74.3 - - - +
169A ASP* 1.3 63.6 + - - +
176A GLU* 2.9 45.5 + - - +
177A VAL 3.5 5.4 - - - +
178A VAL* 4.5 2.7 - - + +
218A THR* 4.1 1.2 - - - +
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Residues in contact with ASP 169 (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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148A HIS* 4.5 9.5 - - - +
167A VAL 4.7 0.7 - - - +
168A ARG* 1.3 76.3 - - - +
170A PHE* 1.3 86.0 + - - +
176A GLU* 3.6 8.5 - - - +
177A VAL* 2.7 44.1 + - + +
179A LYS* 3.2 30.3 + - + -
217A CYS* 3.7 26.8 - - - +
218A THR* 3.5 24.7 - - + -
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Residues in contact with PHE 170 (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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148A HIS* 3.7 38.4 - + + +
169A ASP* 1.3 92.3 + - - +
171A ASP* 1.3 76.8 + - - +
172A GLN* 4.0 19.0 + - + -
175A GLY* 3.7 13.7 - - - -
176A GLU* 4.1 7.9 - - - -
177A VAL* 4.8 0.4 - - - -
179A LYS* 5.6 0.2 + - - -
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Residues in contact with ASP 171 (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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169A ASP* 4.1 1.0 - - - -
170A PHE* 1.3 80.0 - - - +
172A GLN* 1.3 69.2 + - - +
173A ASN* 2.7 31.4 + - - +
174A GLN* 3.2 30.7 + - + +
175A GLY* 3.0 32.6 + - - +
177A VAL* 4.1 14.4 - - + +
179A LYS* 5.5 7.9 + - - +
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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