Contacts of the helix formed by residues 233 - 244 (chain C) in PDB entry 4D2W
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 SER 233 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106C GLU* 2.9 24.0 + - - -
231C TRP 3.5 4.4 + - - -
232C LEU* 1.3 73.4 - - - +
234C PRO* 1.4 73.7 - - - +
235C SER* 2.8 25.6 + - - -
236C SER* 3.1 11.7 + - - -
237C ILE* 3.1 19.7 + - - +
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Residues in contact with PRO 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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232C LEU 4.6 1.6 - - - +
233C SER* 1.4 83.6 - - - +
235C SER* 1.4 56.6 + - - +
237C ILE* 3.2 14.9 + - + +
238C LEU* 3.0 30.4 + - - +
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Residues in contact with SER 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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106C GLU* 3.6 3.5 + - - -
233C SER* 2.8 22.3 + - - -
234C PRO* 1.4 76.5 - - - +
236C SER* 1.3 60.0 + - - +
238C LEU* 3.4 9.0 + - - +
239C LEU* 3.1 23.2 + - - +
260C HIS* 4.9 2.5 - - - -
261C PRO* 6.0 0.9 - - - -
262C TRP* 3.7 13.5 - - - +
265C GLN* 3.0 30.7 + - - -
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Residues in contact with SER 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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106C GLU* 3.7 5.0 + - - -
199C LEU* 4.9 0.9 - - - +
203C MET* 3.3 29.9 - - - -
232C LEU* 4.3 8.1 - - - -
233C SER* 3.1 28.0 + - - -
235C SER* 1.3 72.9 + - - +
237C ILE* 1.4 60.1 + - - +
239C LEU* 3.5 2.4 + - - +
240C LEU* 2.9 36.2 + - - +
262C TRP* 2.9 27.5 + - - +
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Residues in contact with ILE 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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226C TYR* 4.9 0.2 + - - -
228C VAL* 3.6 41.5 - - + -
229C PRO 5.4 0.2 - - - +
232C LEU* 3.7 22.0 - - + +
233C SER 3.1 19.7 + - - +
234C PRO* 3.2 14.1 + - + +
236C SER* 1.4 73.7 - - - +
238C LEU* 1.3 58.2 + - - +
240C LEU* 3.3 9.0 + - - +
241C GLN* 3.0 46.1 + - + +
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Residues in contact with LEU 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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234C PRO 3.0 15.9 + - - +
235C SER* 3.7 8.5 - - - +
236C SER 3.3 0.2 - - - -
237C ILE* 1.3 74.0 - - - +
239C LEU* 1.4 64.6 + - - +
241C GLN* 3.2 22.6 + - - +
242C GLN* 3.2 43.9 + - + +
260C HIS* 5.1 6.5 - - + +
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Residues in contact with LEU 239 (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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113C PHE* 4.6 6.1 - - + -
199C LEU* 3.7 22.9 - - + -
235C SER 3.1 16.8 + - - +
236C SER 4.0 3.4 - - - +
238C LEU* 1.4 75.2 - - - +
240C LEU* 1.4 61.6 + - - +
242C GLN* 3.2 8.9 + - + +
243C MET* 3.1 39.1 + - + +
252C ILE* 4.5 4.5 - - + -
257C LEU* 3.8 24.0 - - + -
260C HIS* 3.8 30.4 - - + +
262C TRP* 3.6 40.6 - - + -
263C ILE* 4.6 5.2 - - + -
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Residues in contact with LEU 240 (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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196C GLY* 3.4 26.2 - - - +
199C LEU* 3.8 15.7 - - + -
200C TYR* 3.7 32.3 - - + +
203C MET* 4.4 10.8 - - + -
226C TYR* 3.7 15.9 - - + +
228C VAL* 6.2 1.1 - - + -
232C LEU* 3.9 27.8 - - + -
236C SER 2.9 23.8 + - - +
237C ILE* 3.6 6.7 - - - +
238C LEU 3.3 0.2 - - - -
239C LEU* 1.4 75.7 - - - +
241C GLN* 1.4 56.1 + - - +
243C MET* 3.8 2.2 - - - -
244C LEU* 2.9 43.9 + - + +
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Residues in contact with GLN 241 (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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226C TYR* 3.8 13.5 - - - +
237C ILE* 3.0 35.3 + - + +
238C LEU* 3.2 25.0 + - - +
240C LEU* 1.4 75.4 - - - +
242C GLN* 1.3 62.4 - - + +
243C MET 3.6 0.2 + - - -
244C LEU* 3.7 6.0 + - - +
245C GLN* 2.8 32.1 + - - +
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Residues in contact with GLN 242 (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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238C LEU* 3.2 31.8 + - + +
239C LEU* 3.2 6.7 + - - +
241C GLN* 1.3 78.2 - - + +
243C MET* 1.3 59.9 + - - +
245C GLN* 3.8 6.4 - - - +
250C LYS 4.5 0.6 - - - +
251C ARG* 3.6 7.4 - - - -
252C ILE* 2.9 54.6 + - + +
256C ASN* 6.1 0.2 - - - +
260C HIS* 2.8 29.7 + - - -
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Residues in contact with MET 243 (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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113C PHE* 3.9 16.4 - - + -
192C VAL* 3.5 28.7 - - + +
193C TRP* 3.8 13.0 + - - -
195C MET* 3.6 21.5 - - + -
196C GLY* 3.7 24.2 - - - +
199C LEU* 4.1 5.6 - - - -
239C LEU* 3.1 35.9 + - + +
240C LEU* 4.0 2.7 - - - +
242C GLN* 1.3 74.9 - - - +
244C LEU* 1.3 59.1 + - - +
245C GLN 3.3 7.3 + - - -
251C ARG* 3.3 17.3 - - - +
252C ILE* 3.8 16.6 - - + -
257C LEU* 3.8 25.4 - - + -
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Residues in contact with LEU 244 (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 TRP* 3.6 46.1 - - + +
196C GLY* 3.8 18.2 - - - +
197C ILE* 3.7 24.0 - - + +
200C TYR* 4.9 0.4 - - + -
208C PRO* 4.4 16.8 - - + -
209C PHE* 4.7 1.6 - - + -
224C GLY 5.0 4.3 - - - +
226C TYR* 3.8 42.9 + - + +
240C LEU* 2.9 26.7 + - + +
241C GLN* 3.8 7.2 - - - +
242C GLN 3.5 0.2 - - - -
243C MET* 1.3 76.1 - - - +
245C GLN* 1.3 59.4 + - - +
246C VAL* 3.8 2.4 + - - +
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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