Contacts of the strand formed by residues 190 - 197 (chain C) in PDB entry 1FZB
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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153C CYS* 3.4 23.3 - - - +
154C GLN* 2.6 40.5 + - - +
157C ALA* 3.8 6.1 - - - -
183C GLU 3.6 5.2 - - - -
184C ILE* 4.7 2.7 - - - -
188C GLY 3.6 0.6 + - - -
189C ASN* 1.3 70.3 - - - +
191C TRP* 1.3 64.5 + - - -
192C THR* 3.5 3.5 + - - +
387C ILE* 3.8 7.5 - - - +
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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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153C CYS* 3.4 4.3 - - - +
182C CYS* 3.5 1.2 - - - -
183C GLU* 2.8 68.4 + - + +
185C ASP* 4.4 8.8 + - + -
189C ASN* 4.3 17.6 - - + +
190C GLY* 1.3 70.8 - - - +
192C THR* 1.3 61.0 + - - +
193C VAL* 3.7 1.7 + - + -
245C ALA* 4.5 1.1 - - + -
246C LEU 5.2 0.2 - - - -
247C ARG* 3.5 64.3 - - + +
261C ASP* 5.0 0.4 - - - -
385C LYS* 3.2 48.5 - - + +
386C ILE* 3.8 4.3 - - - -
387C ILE* 3.8 38.1 - - + -
392C LEU* 4.4 16.8 - - + -
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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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152C ASP* 4.1 16.6 - - + +
153C CYS* 3.1 43.0 - - + +
169C ILE* 4.7 4.4 - - - +
180C VAL* 4.9 5.8 - - - +
181C TYR 4.0 0.2 - - - -
190C GLY 4.0 4.0 - - - +
191C TRP* 1.3 72.3 - - - +
193C VAL* 1.3 62.1 + - - +
194C PHE* 3.8 1.9 + - - +
236C ILE* 4.2 19.4 - - + +
244C TYR* 5.0 1.8 - - + -
385C LYS* 3.8 0.2 - - - -
386C ILE* 3.0 54.4 + - + +
387C ILE* 5.1 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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180C VAL* 5.2 1.0 - - - +
181C TYR* 3.2 44.2 + - + +
183C GLU* 4.3 17.7 - - + +
191C TRP 4.3 6.1 - - - +
192C THR* 1.3 73.6 + - - +
194C PHE* 1.3 62.5 + - - +
195C GLN 3.7 19.1 - - - +
196C LYS* 4.8 8.5 - - + +
226C PHE* 3.7 22.4 - - + -
228C LEU* 4.3 8.5 - - - +
383C THR* 4.4 8.7 - - - +
384C MET 3.7 14.8 - - - +
385C LYS* 3.9 13.9 - - + -
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Residues in contact with PHE 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 4.6 2.7 - - - +
193C VAL* 1.3 73.9 - - - +
195C GLN* 1.3 64.6 + - + +
226C PHE* 3.9 6.3 - - - -
227C TRP* 3.9 16.7 - + - -
228C LEU* 3.1 43.4 + - + -
233C ILE* 3.5 31.6 - - + -
246C LEU* 3.6 17.0 - - + -
265C PHE* 4.1 17.5 - + - -
335C TRP* 5.5 5.2 - + - -
384C MET* 3.0 55.1 + - + -
385C LYS* 4.5 1.1 - - - -
386C ILE* 3.5 36.1 - - + -
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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* 3.7 8.0 - - - +
194C PHE* 1.3 82.3 - - + +
196C LYS* 1.3 65.9 + - - +
197C ARG* 3.2 6.2 - - - +
204C PHE* 3.6 14.5 - - - -
226C PHE* 3.6 9.8 - - - -
227C TRP* 3.2 22.6 - - + -
344C LEU 3.1 9.5 + - - +
345C ASN* 2.8 25.4 + - - -
382C THR* 2.7 30.1 - - + +
383C THR* 3.3 1.9 - - - -
384C MET* 3.0 52.6 + - + +
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Residues in contact with LYS 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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181C TYR* 5.4 6.9 - - - -
183C GLU* 5.8 2.0 + - - -
193C VAL* 4.8 7.6 - - + +
195C GLN* 1.3 77.2 - - - +
197C ARG* 1.3 84.7 + - - +
198C LEU* 3.9 21.7 - - + +
222C GLY* 3.5 23.5 + - - +
224C THR 4.0 10.1 - - - +
225C GLU* 2.9 19.2 - - - +
226C PHE* 3.2 30.9 + - + +
381C LYS* 5.6 2.5 - - + -
382C THR 3.1 11.2 - - - +
383C THR* 3.3 30.5 - - + -
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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* 3.2 21.1 - - - +
196C LYS* 1.3 82.1 - - - +
198C LEU* 1.3 68.3 + - - +
202C VAL 4.5 4.2 + - - -
204C PHE* 3.5 46.1 - - - +
225C GLU* 3.7 15.9 + - - +
344C LEU 2.9 20.9 + - - +
345C ASN* 3.2 10.9 - - - +
346C GLY 3.0 29.9 + - - +
347C VAL* 4.9 0.2 - - - +
348C TYR* 3.9 26.2 - - + +
367C ILE* 3.6 19.2 - - + +
381C LYS* 3.6 2.4 - - - +
382C THR* 2.7 42.0 + - - +
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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