Contacts of the strand formed by residues 178 - 184 (chain C) in PDB entry 1FZC
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 178 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207B SER* 6.5 2.2 - - - -
168C PHE* 3.6 8.1 - - - -
169C ILE* 3.0 37.8 + - + +
171C PRO* 3.7 36.8 - - + -
174C ALA* 4.6 0.4 - - + -
176C GLN* 3.9 13.5 - - - +
177C GLN* 1.4 74.4 - - - +
179C LEU* 1.3 62.4 + - - +
180C VAL* 3.7 26.1 + - + -
228C LEU* 4.6 0.2 - - + -
232C LYS* 3.6 60.6 - - + +
235C LEU* 4.5 13.5 - - + -
236C ILE* 4.0 11.2 - - + -
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Residues in contact with LEU 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE* 4.1 39.0 - - + -
204B PRO 5.5 1.3 - - - +
205B VAL* 5.3 5.7 + - - +
226B LEU* 4.4 8.7 - - + -
145C ILE* 3.8 22.2 - - + -
166C LEU* 4.2 11.9 - - + -
167C TYR 3.5 28.3 - - - +
168C PHE* 3.7 20.5 - - + -
178C PHE* 1.3 75.9 - - - +
180C VAL* 1.3 70.4 + - - +
218C LEU* 3.6 27.0 - - + +
228C LEU* 3.8 10.0 - - - +
232C LYS* 5.1 2.6 + - - +
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Residues in contact with VAL 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C CYS* 3.8 26.7 - - - -
165C GLY 3.7 0.3 - - - +
166C LEU* 3.4 8.0 - - - +
167C TYR 3.1 37.5 + - - +
169C ILE* 3.8 22.7 - - + -
178C PHE* 3.7 27.1 - - + -
179C LEU* 1.3 80.3 - - - +
181C TYR* 1.3 61.9 + - - +
182C CYS* 4.0 4.9 - - - -
192C THR* 4.6 5.4 - - - +
193C VAL 5.3 2.2 - - - +
218C LEU* 4.2 9.9 - - - -
228C LEU* 4.0 22.0 - - + -
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Residues in contact with TYR 181 (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* 4.2 1.0 - - - -
164C SER* 3.9 14.7 + - - -
165C GLY* 3.4 17.7 - - - -
166C LEU* 4.1 3.4 - - + -
180C VAL* 1.3 76.0 - - - +
182C CYS* 1.3 74.5 + - - +
183C GLU* 4.2 12.8 - - + +
192C THR* 4.1 2.1 - - - -
193C VAL* 3.3 47.1 + - + -
218C LEU* 4.3 19.1 - - + +
219C SER 3.1 30.3 - - - +
220C PRO 3.6 10.6 + - - -
221C THR 4.2 3.1 + - - -
222C GLY* 3.5 27.8 + - - -
226C PHE* 4.6 13.5 - + + -
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Residues in contact with CYS 182 (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* 2.1 55.2 - - + -
156C ILE* 4.0 12.8 - - - -
164C SER* 3.3 6.8 + - - -
165C GLY 2.8 31.6 + - - -
167C TYR* 3.7 30.3 - - + -
180C VAL* 4.0 7.6 - - - -
181C TYR* 1.3 77.6 - - - +
183C GLU* 1.3 60.2 + - - +
184C ILE* 4.4 9.9 - - + -
191C TRP 3.5 0.4 - - - -
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Residues in contact with GLU 183 (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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164C SER* 3.6 8.5 - - - +
181C TYR* 4.0 10.5 + - + +
182C CYS* 1.3 72.2 - - - +
184C ILE* 1.3 62.7 + - - +
185C ASP* 6.3 0.4 - - + -
189C ASN 3.7 2.6 - - - +
190C GLY* 3.8 0.5 - - - -
191C TRP* 2.7 51.9 + - + +
193C VAL* 4.1 14.1 - - + +
196C LYS* 5.9 0.7 + - - -
249C GLU* 4.6 2.5 - - - +
383C THR* 5.2 1.9 + - - -
385C LYS* 2.9 41.4 + - - +
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Residues in contact with ILE 184 (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 5.2 1.1 - - - +
156C ILE* 4.9 3.1 - - + -
157C ALA* 4.5 15.7 - - + +
161C ALA* 3.8 30.3 - - + +
162C LYS* 3.8 20.7 - - - +
163C GLN 3.4 22.9 - - - +
164C SER* 3.0 18.8 + - - +
167C TYR* 4.0 15.0 - - + +
182C CYS* 4.4 12.8 - - + -
183C GLU* 1.3 81.8 - - - +
185C ASP* 1.3 73.7 + - - +
188C GLY* 5.2 2.9 - - - -
189C ASN 3.7 7.2 - - - +
190C GLY* 4.5 8.3 - - - -
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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