Contacts of the strand formed by residues 179 - 185 (chain I) in PDB entry 1LWU
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 179 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169I TYR* 3.1 10.7 - - - -
170I ILE* 2.9 40.3 + - + +
172I PRO* 3.4 39.5 - - + -
175I ALA* 4.5 6.1 - - + -
177I GLN 3.9 11.7 - - - +
178I PRO* 1.3 74.5 - - + +
180I LEU* 1.3 64.6 + - - +
181I VAL* 3.2 37.4 + - + -
228I LEU* 4.2 5.8 - - + -
232I LYS* 3.6 62.8 - - + +
235I LEU* 5.3 2.0 - - + -
236I LEU* 5.1 2.9 - - + -
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Residues in contact with LEU 180 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224H VAL* 3.6 41.3 - - + -
247H TYR* 6.0 1.6 - - + -
146I ILE* 3.6 40.6 - - + -
167I LEU* 3.8 15.9 - - + -
168I TYR 3.4 13.2 - - - +
169I TYR* 3.6 26.7 - - + +
179I PHE* 1.3 78.6 - - - +
181I VAL* 1.3 66.4 + - - +
218I LEU* 3.4 24.2 - - + +
228I LEU* 3.9 6.2 - - - +
232I LYS* 4.6 2.9 + - - -
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Residues in contact with VAL 181 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154I CYS* 4.0 15.0 - - - -
167I LEU* 3.4 7.6 - - - -
168I TYR 2.9 36.5 + - - +
170I ILE* 3.4 33.0 - - + -
179I PHE* 3.2 33.2 - - + -
180I LEU* 1.3 82.2 - - - +
182I PHE* 1.3 61.3 + - - +
183I CYS* 3.6 1.5 + - - -
192I THR* 5.1 2.2 - - - +
193I VAL 5.0 4.3 - - - +
218I LEU* 4.2 6.1 - - - -
228I LEU* 3.8 17.7 - - + -
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Residues in contact with PHE 182 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154I CYS* 4.3 0.4 - - - -
165I SER* 4.1 14.1 - - - -
166I GLY* 3.4 11.9 - - - -
167I LEU* 4.2 6.3 - - + -
181I VAL* 1.3 74.1 - - - +
183I CYS* 1.3 80.2 + - - +
184I GLU* 4.0 10.8 - - + -
192I THR* 4.1 0.3 - - - -
193I VAL* 3.2 45.8 + - + +
218I LEU* 4.3 14.7 - - + +
219I ALA 3.3 19.1 - - - +
220I PRO 3.7 8.5 - - - -
221I THR* 3.4 15.3 - - - -
222I LEU* 3.2 54.3 - - + -
226I PHE* 4.8 1.1 - - + -
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Residues in contact with CYS 183 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154I CYS* 2.0 57.2 - - + +
157I VAL* 4.5 5.4 - - - -
165I SER* 3.3 5.9 - - - -
166I GLY 2.7 30.6 + - - -
168I TYR* 3.7 40.8 - - + -
181I VAL* 4.2 4.3 - - - -
182I PHE* 1.3 77.1 - - - +
184I GLU* 1.3 59.2 + - - +
185I ILE* 3.9 10.8 - - + -
191I TRP 3.4 0.2 - - - -
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Residues in contact with GLU 184 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I SER* 3.4 8.3 - - - +
182I PHE* 3.8 12.2 + - + -
183I CYS* 1.3 72.3 - - - +
185I ILE* 1.3 65.8 + - - +
186I GLU* 4.0 18.5 - - + +
189I ASN 3.1 1.4 - - - +
190I GLY 3.7 0.3 - - - -
191I TRP* 2.7 54.1 + - + +
193I VAL* 4.6 7.0 - - + +
222I LEU* 4.5 14.2 - - - +
247I ASP* 4.9 0.9 - - - +
381I THR* 5.2 1.6 + - - +
383I LYS* 3.1 35.0 + - - -
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Residues in contact with ILE 185 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157I VAL* 5.2 1.6 - - + -
158I VAL* 3.7 33.0 - - + -
162I GLY* 3.9 17.7 - - - +
163I LYS* 3.5 24.0 - - - +
164I ASP 3.4 23.6 - - - +
165I SER* 2.7 20.0 + - - +
168I TYR* 3.9 10.8 - - + +
183I CYS* 4.5 10.8 - - + +
184I GLU* 1.3 78.4 - - - +
186I GLU* 1.3 72.4 + - - +
188I GLY* 4.8 2.0 - - - +
189I ASN 3.1 9.9 - - - +
190I GLY* 4.7 0.9 - - - -
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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