Contacts of the strand formed by residues 228 - 233 (chain C) in PDB entry 5I2C
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 228 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LEU 3.8 0.7 - - - +
45C THR* 3.3 1.8 - - - -
46C GLU* 2.7 52.2 + - - +
201C LEU* 3.4 33.2 - - + -
204C VAL* 4.0 21.5 - - + -
205C LEU* 3.6 28.0 - - + -
227C PHE* 1.3 77.9 - - - +
229C ALA* 1.3 63.8 + - - +
230C PHE* 4.1 15.3 - - + -
239C ILE* 4.0 13.5 - - + -
240C VAL 3.4 9.4 - - - -
241C MET* 3.5 38.6 - - + -
245C THR* 4.5 4.3 - - + -
249C PHE* 4.6 3.6 - + - -
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Residues in contact with ALA 229 (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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43C SER* 6.0 0.2 - - - +
44C LEU 3.3 4.3 - - - -
45C THR* 3.9 15.5 - - + +
227C PHE* 4.2 11.9 - - + -
228C PHE* 1.3 76.1 - - - +
230C PHE* 1.3 59.1 + - - +
239C ILE* 3.2 9.4 - - - +
240C VAL* 2.8 43.7 + - + +
298C ILE* 4.6 0.9 - - + -
402C ACT 3.7 28.0 - - + +
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Residues in contact with PHE 230 (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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31C LEU* 3.5 40.4 - - + -
42C PHE* 4.2 6.3 - + - +
43C SER* 3.6 0.7 + - - -
44C LEU* 2.8 37.8 + - + +
194C LEU* 4.2 18.8 - - + -
201C LEU* 3.7 29.8 - - + -
205C LEU* 5.1 2.9 - - + -
228C PHE* 4.1 13.2 - - + -
229C ALA* 1.3 74.8 - - - +
231C SER* 1.3 74.9 + - - +
232C LEU* 4.1 11.9 - - + -
237C ILE* 3.9 28.9 - - + -
238C SER 3.4 3.8 - - - -
239C ILE* 3.6 21.8 - - + -
402C ACT 4.3 1.3 - - - -
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Residues in contact with SER 231 (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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42C PHE 3.2 12.1 - - - -
43C SER* 4.1 10.3 - - - -
115C LEU* 5.2 0.4 - - - -
117C THR* 3.6 10.4 - - - +
230C PHE* 1.3 83.4 - - - +
232C LEU* 1.3 61.3 + - - +
233C ILE* 3.9 17.0 - - - +
236C TYR 3.6 1.3 + - - +
237C ILE* 3.3 4.9 - - - -
238C SER* 2.8 43.2 + - - +
402C ACT 3.3 21.4 - - - +
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Residues in contact with LEU 232 (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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30C LEU 4.2 10.8 - - - +
31C LEU 4.1 19.5 - - - +
34C PRO* 5.6 12.1 - - + -
40C LYS 4.2 2.4 - - - +
41C PHE* 3.9 2.6 + - - -
42C PHE* 2.8 38.1 + - + +
191C PRO* 5.8 1.1 - - + -
194C LEU* 5.3 4.7 - - + -
230C PHE* 4.1 14.5 - - + -
231C SER* 1.3 72.9 - - - +
233C ILE* 1.3 59.2 + - - +
234C GLU 4.2 0.2 - - - -
235C GLY* 3.6 37.2 - - - +
236C TYR 3.4 1.1 - - - +
237C ILE* 3.7 21.1 - - + -
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Residues in contact with ILE 233 (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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8C HIS* 4.6 2.2 - - - +
40C LYS 3.7 3.4 - - - +
41C PHE* 3.8 43.7 - - + -
42C PHE 4.0 9.9 - - - +
115C LEU* 3.9 13.9 - - + -
117C THR* 4.3 2.5 - - + -
122C PHE* 3.8 40.2 - - + -
231C SER* 3.9 17.9 - - - +
232C LEU* 1.3 79.4 - - - +
234C GLU* 1.3 84.5 + - + +
235C GLY 3.2 0.2 - - - -
236C TYR* 3.0 28.5 + - + +
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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