Contacts of the strand formed by residues 190 - 197 (chain F) 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 GLY 190 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154F CYS* 3.2 38.1 - - - +
155F GLN* 2.7 26.8 + - - +
158F VAL* 3.6 6.7 - - - +
184F GLU 3.9 2.2 - - - -
185F ILE* 4.7 1.6 - - - -
189F ASN* 1.3 70.0 - - - +
191F TRP* 1.3 63.5 + - - -
192F THR* 3.2 6.2 + - - +
384F LEU 3.8 2.9 - - - +
385F LEU* 4.8 2.7 - - - +
386F PRO* 4.5 4.3 - - - +
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Residues in contact with TRP 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F CYS* 3.8 0.2 - - - -
183F CYS* 3.4 2.9 - - - -
184F GLU* 2.7 59.8 + - + +
186F GLU* 2.8 36.1 + - + -
189F ASN* 3.4 6.4 + - + +
190F GLY* 1.3 71.3 - - - +
192F THR* 1.3 61.4 + - - +
193F VAL 3.5 2.0 + - - -
243F ARG* 3.7 23.3 - - - -
245F ARG* 3.6 56.3 - - + -
383F LYS* 3.2 44.7 - - + +
384F LEU 3.5 8.3 - - - -
385F LEU* 3.2 48.0 - - + +
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Residues in contact with THR 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F ASP* 3.9 13.7 - - + -
154F CYS* 3.1 44.9 - - + +
170F ILE* 4.3 6.8 - - - +
181F VAL* 5.1 3.5 - - - +
190F GLY 3.6 4.0 - - - +
191F TRP* 1.3 70.7 - - - +
193F VAL* 1.3 64.6 + - - +
194F ILE* 3.5 3.5 + - - +
228F LEU* 5.3 0.7 - - - +
236F LEU* 3.3 26.0 - - + +
242F TYR* 4.7 3.1 - - + -
383F LYS* 4.4 0.2 - - - -
384F LEU* 2.9 43.2 + - + +
385F LEU* 5.3 0.2 - - - -
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Residues in contact with VAL 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F VAL* 5.0 1.8 - - - +
182F PHE* 3.2 45.3 + - + +
184F GLU* 4.6 7.6 - - + +
191F TRP 4.3 5.8 - - - +
192F THR* 1.3 71.8 + - - +
194F ILE* 1.3 63.2 + - - +
195F GLN 3.4 22.0 - - - +
222F LEU* 4.1 17.5 - - + -
226F PHE* 3.5 29.5 - - + -
228F LEU* 3.9 15.4 - - - +
381F THR* 4.4 7.4 - - - +
382F MET 4.0 4.5 - - - +
383F LYS* 4.1 11.2 - - + +
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Residues in contact with ILE 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F THR 4.1 3.1 - - - +
193F VAL* 1.3 76.3 - - - +
195F GLN* 1.3 62.9 + - + +
226F PHE* 3.8 3.3 - - - -
227F TRP* 3.9 8.6 - - + -
228F LEU* 3.0 46.6 + - + +
233F ILE* 3.1 54.3 - - + -
236F LEU* 4.4 7.6 - - + -
263F PHE* 5.5 2.7 - - + -
382F MET* 2.7 31.5 + - + +
384F LEU* 3.7 37.0 - - + -
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Residues in contact with GLN 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F VAL* 3.4 9.4 - - - +
194F ILE* 1.3 78.4 - - - +
196F HIS* 1.3 86.2 + - - +
197F ARG* 4.3 5.0 - - - +
204F PHE* 4.5 2.5 - - + -
226F PHE* 3.3 19.1 - - - +
227F TRP* 3.3 30.4 - - + -
342F LEU* 2.9 30.8 + - - +
343F ASN* 2.9 22.8 + - - +
380F THR* 3.0 25.2 - - - +
381F THR* 3.1 4.9 + - - -
382F MET* 2.9 34.5 + - + +
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Residues in contact with HIS 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F GLN* 1.3 86.7 + - - +
197F ARG* 1.3 79.0 + - - +
198F HIS* 2.9 36.4 + - + +
222F LEU* 3.7 38.0 + - + +
224F THR 3.3 13.3 + - - -
225F GLU* 3.2 22.9 - - - +
226F PHE* 3.2 28.5 + - + +
379F MET* 4.8 6.5 - - - +
380F THR 2.8 22.1 + - - -
381F THR* 3.5 18.4 - - + +
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Residues in contact with ARG 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F GLN* 3.8 2.4 + - - +
196F HIS* 1.3 87.5 - - - +
198F HIS* 1.3 60.0 + - - +
200F GLY* 5.1 1.4 - - - -
202F VAL 4.2 5.3 + - - -
204F PHE* 3.1 56.9 - - - +
225F GLU* 3.9 7.7 + - - -
342F LEU 3.2 20.6 + - - +
343F ASN* 3.5 5.1 - - - +
344F GLY 2.6 30.1 + - - -
345F LYS* 4.5 1.2 - - - +
346F TYR* 3.9 25.0 - - + +
365F ILE* 3.0 33.4 - - + +
379F MET* 3.5 6.1 - - - -
380F THR* 2.7 43.5 + - + +
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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