Contacts of the strand formed by residues 158 - 168 (chain A) in PDB entry 1LCG
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 LEU 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A HIS* 2.9 43.5 - - + +
153A VAL 3.6 0.5 - - - +
154A SER* 3.3 6.1 + - - -
155A VAL* 2.9 36.9 + - + +
156A GLU* 2.9 26.2 - - + +
157A GLY* 1.3 81.7 - - - +
159A THR* 1.3 64.4 + - - +
160A VAL* 3.6 8.2 + - + -
204A MET* 5.2 3.1 - - + -
209A LEU* 3.3 40.8 - - + +
210A VAL* 4.2 9.6 - - + -
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Residues in contact with THR 159 (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 GLN* 2.9 33.7 - - - +
153A VAL 3.8 3.4 - - - -
154A SER* 4.7 6.7 - - - +
157A GLY 4.0 5.8 + - - +
158A LEU* 1.3 76.0 - - - +
160A VAL* 1.3 59.8 + - - +
161A VAL* 3.3 12.6 + - - +
209A LEU* 3.2 15.3 - - - +
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Residues in contact with VAL 160 (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 ASP 3.9 1.2 - - - +
152A GLN* 3.4 2.8 - - - -
153A VAL* 2.7 51.1 + - + +
155A VAL* 3.7 17.5 - - + -
158A LEU* 4.5 3.8 - - + +
159A THR* 1.3 71.5 - - - +
161A VAL* 1.3 58.9 + - - +
163A GLN* 3.6 20.3 - - + +
203A ASN* 3.8 6.7 - - + +
204A MET* 3.1 44.6 - - + -
207A GLN* 3.3 17.3 - - - +
209A LEU* 3.7 7.0 - - + -
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Residues in contact with VAL 161 (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 THR* 5.9 2.0 - - - +
151A ASP 5.9 0.2 - - - -
152A GLN* 3.2 36.3 - - + +
159A THR* 3.3 12.9 + - - +
160A VAL* 1.3 71.5 - - - +
162A GLY* 1.4 78.9 + - - +
163A GLN 3.2 0.4 - - - -
203A ASN* 3.1 10.9 + - - -
207A GLN* 2.8 29.6 + - - +
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Residues in contact with GLY 162 (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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150A ALA* 4.8 12.2 - - - +
151A ASP 3.6 8.2 + - - -
161A VAL* 1.4 84.8 - - - +
163A GLN* 1.3 61.7 + - - +
164A GLN 3.6 2.4 + - - -
203A ASN* 3.2 10.6 + - - -
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Residues in contact with GLN 163 (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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102A LEU* 4.6 4.2 - - + +
150A ALA* 3.3 2.7 - - - -
151A ASP 2.9 33.0 + - - +
153A VAL* 3.8 33.7 - - + -
160A VAL* 3.6 9.1 - - + +
161A VAL 3.2 0.2 - - - -
162A GLY* 1.3 77.7 - - - +
164A GLN* 1.3 82.7 + - - +
165A PHE* 3.5 5.5 - - + -
198A THR* 2.9 29.9 + - - -
199A PRO 3.8 6.5 + - - -
200A VAL* 3.3 26.4 - - + +
203A ASN* 3.2 29.6 + - - +
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Residues in contact with GLN 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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102A LEU* 4.9 3.1 + - - +
133A GLN* 5.6 1.8 + - - +
148A ILE* 2.9 45.6 - - + +
149A GLY 3.4 6.1 - - - -
150A ALA* 4.4 4.0 - - + +
162A GLY 3.6 4.4 + - - +
163A GLN* 1.3 95.2 + - - +
165A PHE* 1.4 60.4 + - - +
195A GLY 5.1 1.6 + - - -
196A GLY 4.9 0.7 - - - +
197A VAL* 2.9 48.3 - - + +
198A THR* 3.7 14.6 + - - +
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Residues in contact with PHE 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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84A ILE* 4.0 24.9 - - + -
102A LEU* 3.7 35.0 - - + +
104A VAL* 4.6 15.5 - - + -
120A PHE* 4.2 2.9 - + - -
128A TYR* 4.0 17.3 - + - -
135A PHE* 6.1 0.2 - - - -
148A ILE* 3.4 7.5 - - - +
149A GLY 2.9 44.5 + - - +
150A ALA 4.0 2.0 - - - -
151A ASP* 3.6 26.5 - - + -
153A VAL* 5.2 2.7 - - + -
163A GLN* 3.5 11.9 - - + -
164A GLN* 1.4 76.0 - - - +
166A GLY* 1.4 71.2 + - - +
167A GLU* 2.8 33.2 - - + -
197A VAL* 4.9 5.2 - - - -
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Residues in contact with GLY 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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102A LEU 2.9 15.1 + - - -
103A TRP* 3.1 9.5 - - - -
104A VAL 3.0 25.8 + - - -
135A PHE* 5.0 15.7 - - - -
137A ILE* 6.0 0.9 - - - -
147A ILE 3.4 7.9 - - - -
148A ILE* 4.5 1.3 - - - -
165A PHE* 1.4 83.0 - - - +
167A GLU* 1.4 61.7 + - - -
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Residues in contact with GLU 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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104A VAL* 3.2 14.0 - - - +
105A PRO 3.4 14.6 - - - +
106A SER* 3.4 19.6 + - - +
120A PHE* 2.7 41.0 - - + +
122A PRO* 5.1 3.1 - - + -
128A TYR* 4.6 10.5 - - + +
135A PHE* 5.8 0.2 - - - +
146A GLY* 3.1 3.7 - - - -
147A ILE* 2.7 51.7 + - + +
149A GLY 5.7 0.4 - - - +
165A PHE* 2.8 28.2 - - + +
166A GLY* 1.4 73.5 - - - -
168A SER* 1.3 61.7 + - - +
169A VAL* 3.5 2.1 + - + +
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Residues in contact with SER 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TRP* 4.2 22.4 - - - -
104A VAL 3.0 15.2 + - - -
105A PRO* 3.9 4.0 - - - +
106A SER* 3.2 20.5 + - - +
109A CYS* 3.8 9.0 - - - +
114A CYS* 5.4 0.3 - - - -
137A ILE* 5.3 5.6 - - - -
144A LEU* 3.8 23.9 - - - +
145A SER 3.6 11.2 + - - -
146A GLY* 4.1 1.3 - - - -
166A GLY 4.1 0.8 - - - -
167A GLU* 1.3 71.3 - - - +
169A VAL* 1.4 61.4 + - - +
170A THR 4.0 10.3 + - - -
172A PRO* 5.4 1.7 - - - +
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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