Contacts of the strand formed by residues 190 - 197 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C CYS* 3.2 38.3 - - - +
155C GLN* 2.7 25.6 + - - +
158C VAL* 3.6 6.4 - - - +
184C GLU 3.8 2.5 - - - -
185C ILE* 4.7 1.3 - - - -
189C ASN* 1.3 70.0 - - - +
191C TRP* 1.3 64.1 + - - -
192C THR* 3.2 6.9 + - - +
384C LEU 3.8 2.8 - - - +
385C LEU* 4.5 6.2 - - - +
386C PRO* 4.5 0.9 - - - +
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Residues in contact with TRP 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C CYS* 3.8 0.2 - - - -
183C CYS* 3.4 3.5 - - - -
184C GLU* 2.6 61.8 + - + +
186C GLU* 2.8 33.7 + - + -
189C ASN* 4.3 6.2 - - + +
190C GLY* 1.3 71.3 - - - +
192C THR* 1.3 59.6 + - - +
193C VAL 3.5 3.0 + - - -
243C ARG* 3.7 24.0 - - - -
245C ARG* 3.6 46.7 - - + -
383C LYS* 3.2 51.4 - - + +
384C LEU 3.5 8.1 - - - -
385C LEU* 3.2 48.3 - - + +
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Residues in contact with THR 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ASP* 3.9 13.9 - - + -
154C CYS* 3.1 44.0 - - + +
170C ILE* 4.3 6.7 - - - +
181C VAL* 5.1 3.6 - - - +
190C GLY 3.6 4.3 - - - +
191C TRP* 1.3 70.8 - - - +
193C VAL* 1.3 65.1 + - - +
194C ILE* 3.5 3.1 + - - +
228C LEU* 5.2 1.0 - - - +
236C LEU* 3.3 26.0 - - + +
242C TYR* 4.7 3.4 - - + -
383C LYS* 4.4 0.2 - - - -
384C LEU* 2.9 42.2 + - + +
385C LEU* 5.3 0.2 - - - -
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Residues in contact with VAL 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C VAL* 5.0 2.0 - - - +
182C PHE* 3.2 43.4 + - + +
184C GLU* 4.6 8.3 - - + +
191C TRP 4.3 5.6 - - - +
192C THR* 1.3 70.2 + - - +
194C ILE* 1.3 64.2 + - - +
195C GLN 3.4 22.0 - - - +
222C LEU* 4.1 17.3 - - + -
226C PHE* 3.5 29.7 - - + -
228C LEU* 3.9 15.6 - - - +
381C THR* 4.4 7.2 - - - +
382C MET 4.0 4.7 - - - +
383C LYS* 4.1 11.9 - - + +
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Residues in contact with ILE 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C THR 3.5 2.9 + - - +
193C VAL* 1.3 75.7 - - - +
195C GLN* 1.3 63.7 + - + +
226C PHE* 3.8 3.2 - - - -
227C TRP* 3.9 8.1 - - + -
228C LEU* 3.0 47.0 + - + +
233C ILE* 3.1 51.8 - - + -
236C LEU* 4.4 7.6 - - + -
263C PHE* 5.6 2.9 - - + -
382C MET* 2.7 31.7 + - + +
384C LEU* 3.7 36.3 - - + -
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Residues in contact with GLN 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C VAL* 3.4 9.4 - - - +
194C ILE* 1.3 79.1 - - - +
196C HIS* 1.3 87.0 + - - +
197C ARG* 4.4 5.1 - - - +
204C PHE* 4.5 1.8 - - + -
226C PHE* 3.3 20.0 - - - +
227C TRP* 3.3 30.5 - - + -
342C LEU* 3.0 29.5 + - - +
343C ASN* 2.9 23.1 + - - +
380C THR* 3.0 24.5 - - - +
381C THR* 3.1 4.5 + - - -
382C MET* 2.9 34.1 + - + -
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Residues in contact with HIS 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C GLN* 1.3 86.1 + - - +
197C ARG* 1.3 79.8 + - - +
198C HIS* 2.9 36.4 + - + -
222C LEU* 3.7 37.6 + - + +
224C THR 3.3 13.5 + - - -
225C GLU* 3.2 23.2 - - - +
226C PHE* 3.2 28.0 + - + +
379C MET* 4.9 6.3 - - - +
380C THR 2.8 20.8 + - - -
381C THR* 3.5 18.6 - - + +
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Residues in contact with ARG 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C GLN* 3.8 2.2 + - - +
196C HIS* 1.3 86.7 - - - +
198C HIS* 1.3 61.5 + - - +
200C GLY* 5.1 1.4 - - - -
202C VAL 4.2 5.1 + - - -
204C PHE* 3.1 55.8 - - - +
225C GLU* 3.9 8.3 + - - -
342C LEU 3.2 20.7 + - - +
343C ASN* 3.4 5.1 - - - +
344C GLY 2.6 30.7 + - - -
345C LYS* 4.5 1.2 - - - +
346C TYR* 3.9 25.2 - - + +
365C ILE* 3.0 33.3 - - + +
379C MET* 3.5 5.8 - - - -
380C THR* 2.8 44.0 + - + +
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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