Contacts of the strand formed by residues 232 - 238 (chain C) in PDB entry 4I7C
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 ARG 232 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A TRP* 4.3 10.3 - - + -
237A GLU 3.3 7.0 - - - -
238A ALA* 4.9 1.8 - - + -
241A ARG* 4.7 4.4 - - - +
255A ASP* 2.7 43.7 + - - +
228C ASN* 3.8 3.6 - - - +
229C GLY* 3.1 27.4 + - - +
230C HIS* 2.8 37.1 + - - +
231C ARG* 1.3 79.4 + - - +
233C ARG* 1.3 65.7 - - - +
266C LEU* 3.9 33.3 - - - +
267C PHE* 4.0 15.5 - - + -
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Residues in contact with ARG 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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235A THR 3.7 0.9 - - - +
236A TRP* 3.4 12.0 - - - -
237A GLU* 2.9 72.3 + - + +
226C GLU* 4.1 22.6 + - + -
227C LEU 3.3 12.6 - - - +
228C ASN* 3.2 31.1 + - - +
232C ARG* 1.3 76.9 - - - +
234C LEU* 1.3 62.0 + - - +
235C THR* 3.6 14.2 + - - +
267C PHE* 4.3 1.3 - - - -
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Residues in contact with LEU 234 (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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234A LEU* 4.4 10.1 - - + -
235A THR 3.4 15.0 - - - +
236A TRP* 4.0 17.9 - - + -
256A CYS 5.6 0.4 - - - +
257A LEU* 4.3 18.4 - - + -
258A VAL 5.7 3.1 - - - +
225C LEU 3.9 0.2 - - - +
226C GLU* 3.2 5.4 - - - +
227C LEU* 2.9 45.5 + - + +
233C ARG* 1.3 71.2 - - - +
235C THR* 1.3 63.1 + - - +
257C LEU* 4.2 23.5 - - + +
258C VAL 5.1 2.9 - - - +
259C PHE* 4.7 7.9 - - + -
263C ILE* 4.1 29.2 - - + -
267C PHE* 4.1 13.9 - - + -
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Residues in contact with THR 235 (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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233A ARG 3.8 0.8 - - - +
234A LEU* 3.4 8.9 - - - +
235A THR* 2.7 50.5 + - - +
237A GLU* 4.0 9.2 + - - -
224C ARG* 3.4 37.7 - - + -
225C LEU 3.4 5.4 - - - +
226C GLU* 4.0 7.5 + - + +
233C ARG* 3.6 18.2 + - - +
234C LEU* 1.3 76.5 + - - +
236C TRP* 1.3 64.9 + - - +
237C GLU* 4.2 9.4 - - + +
257C LEU* 4.9 2.0 - - - -
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Residues in contact with TRP 236 (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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232A ARG* 4.2 17.0 - - + -
233A ARG 3.5 16.6 - - - -
234A LEU* 3.9 16.2 - - + -
263A ILE* 5.8 2.0 - - + -
266A LEU* 4.7 2.7 - - + -
267A PHE* 3.9 25.8 - + - -
223C TYR* 3.1 37.8 + + - -
224C ARG* 3.3 3.6 - - - +
225C LEU* 2.8 38.8 + - + +
235C THR* 1.3 73.8 - - - +
237C GLU* 1.3 64.6 + - - +
238C ALA* 3.4 19.4 - - + +
254C SER 5.2 1.1 - - - -
255C ASP* 3.6 22.0 - - - -
256C CYS* 3.4 41.5 - - - +
257C LEU* 3.7 35.6 - - + +
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Residues in contact with GLU 237 (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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231A ARG 5.4 0.2 - - - -
232A ARG* 3.5 3.3 + - - -
233A ARG* 2.9 82.0 + - + +
235A THR* 4.3 6.8 + - - -
223C TYR 3.2 6.1 - - - +
224C ARG* 3.6 37.2 + - + +
235C THR* 4.2 6.1 - - + -
236C TRP* 1.3 82.3 - - - +
238C ALA* 1.3 63.7 + - - +
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Residues in contact with ALA 238 (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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231A ARG 3.7 13.0 - - - +
232A ARG* 5.0 2.9 - - + -
222C ALA* 3.5 6.4 - - - +
223C TYR* 2.9 46.4 + - + +
236C TRP* 3.4 31.8 - - + +
237C GLU* 1.3 76.9 - - - +
239C THR* 1.3 64.6 + - - +
255C ASP* 5.4 1.3 - - - +
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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