Contacts of the strand formed by residues 220 - 226 (chain C) in PDB entry 4F9P
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 220 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173C ARG* 6.0 0.4 - - - -
174C GLN 3.6 11.4 - - - -
175C LYS* 4.2 4.0 - - - -
176C SER 4.9 2.7 - - - -
218C ASP 4.0 0.8 + - - -
219C PHE* 1.3 76.6 - - - +
221C ILE* 1.3 60.2 + - - -
222C TYR* 4.1 6.0 - - - -
238C THR 3.7 0.7 - - - +
239C LYS* 4.0 1.4 - - - -
240C LEU* 3.2 35.0 + - - +
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Residues in contact with ILE 221 (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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174C GLN* 2.8 45.7 + - + +
220C GLY* 1.3 73.7 - - - -
222C TYR* 1.3 59.2 + - - +
223C PHE* 4.1 22.8 - - + -
237C GLY* 5.5 1.3 - - - -
238C THR 3.4 13.5 - - - +
239C LYS* 5.1 4.5 - - + -
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Residues in contact with TYR 222 (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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142C GLN* 2.2 36.5 + - - +
171C TRP* 5.1 13.7 - + + -
172C TYR 2.8 20.9 - - - +
173C ARG* 3.6 22.4 - - + +
198C PHE* 4.2 21.1 - + - -
209C LEU* 6.2 3.6 - - + -
218C ASP* 2.4 39.5 + - - +
219C PHE 4.7 0.4 - - - -
220C GLY 4.1 13.9 - - - -
221C ILE* 1.3 74.6 - - - +
223C PHE* 1.3 55.5 + - - +
237C GLY* 3.7 0.7 - - - -
238C THR* 3.2 21.9 + - - +
240C LEU* 4.0 19.8 - - + +
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Residues in contact with PHE 223 (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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44C GLY* 5.6 6.5 - - - -
45C LEU* 4.2 37.5 - - + -
142C GLN* 3.9 0.4 - - - +
170C HIS 3.5 1.4 - - - +
171C TRP* 3.4 4.4 - - - -
172C TYR* 2.9 49.4 + - + -
174C GLN* 3.9 24.0 - - + -
180C PRO* 5.8 1.6 - - + -
221C ILE* 4.1 28.0 - - + -
222C TYR* 1.3 72.4 - - - +
224C CYS* 1.3 59.7 + - - +
234C PHE* 4.6 8.3 - - + -
235C GLY 3.2 28.3 - - - -
236C THR* 3.5 21.8 - - - -
237C GLY* 3.8 5.2 - - - -
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Residues in contact with CYS 224 (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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140C LEU* 3.3 6.9 - - - +
142C GLN* 3.5 26.7 + - - +
159C CYS* 2.2 49.8 - - + -
169C LEU* 4.4 2.5 - - + -
170C HIS 3.2 5.4 - - - +
171C TRP* 3.4 27.6 - - + -
223C PHE* 1.3 73.2 - - - +
225C GLN* 1.3 57.5 + - - +
234C PHE* 3.6 3.6 - - - -
235C GLY* 3.2 26.7 + - - +
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Residues in contact with GLN 225 (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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47C TRP* 5.5 1.8 - - - +
100C ASP* 4.7 3.8 - - - +
140C LEU* 4.3 0.9 - - - -
169C LEU* 2.9 16.1 - - - +
170C HIS* 2.8 60.5 + - + +
172C TYR* 3.9 17.6 + - + -
224C CYS* 1.3 71.9 - - - +
226C GLN* 1.3 69.0 + - - +
227C SER* 5.2 0.2 - - - -
232C HIS* 3.0 43.3 + - - +
233C THR 3.0 18.5 + - - +
234C PHE* 3.1 30.5 - - + -
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Residues in contact with GLN 226 (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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138C ILE* 3.1 22.1 - - + +
140C LEU* 4.0 8.0 - - + +
165C ILE* 4.0 24.2 - - + -
168C ASN 3.7 7.0 - - - +
225C GLN* 1.3 89.1 + - - +
227C SER* 1.3 58.8 + - - +
228C ASN* 3.4 17.0 - - + +
229C SER 2.8 14.3 + - - +
231C PRO 2.6 30.3 + - - -
232C HIS* 3.2 7.2 - - - +
233C THR* 2.5 41.4 + - - +
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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