Contacts of the helix formed by residues 231 - 241 (chain C) in PDB entry 1XV9
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 PRO 231 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227C ASN 4.1 8.7 - - - +
228C GLU 4.2 6.7 - - - +
229C ASP 3.2 13.5 - - - +
230C MET* 1.3 81.4 - - - +
232C VAL* 1.3 54.4 + - - +
233C GLU* 3.0 14.8 - - - +
234C ARG* 2.8 61.5 + - + +
235C ILE* 2.9 14.8 + - - +
287C PRO* 3.4 21.1 - - + -
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Residues in contact with VAL 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C ASN* 4.8 4.4 + - - +
230C MET 3.1 1.9 + - - +
231C PRO* 1.3 70.8 - - - +
233C GLU* 1.3 69.0 + - - +
235C ILE* 3.8 9.4 - - + +
236C LEU* 3.0 28.1 + - - +
365C THR* 3.3 31.4 - - + -
369C CYS* 4.8 9.6 - - - -
399C SER* 3.4 43.3 - - - +
402C ALA* 5.8 0.9 - - + -
403C TYR* 4.0 17.5 - - + +
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Residues in contact with GLU 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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227C ASN 5.3 1.9 - - - +
231C PRO* 3.0 9.4 - - - +
232C VAL* 1.3 94.6 + - - +
234C ARG* 1.3 56.1 + - + +
236C LEU* 4.4 4.9 - - - +
237C GLU* 2.7 37.9 + - - +
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Residues in contact with ARG 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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231C PRO* 2.8 37.3 + - + +
233C GLU* 1.3 77.8 - - + +
235C ILE* 1.3 60.7 + - - +
237C GLU* 3.5 22.3 + - - +
238C ALA* 3.1 24.3 + - - +
285C ARG* 3.7 9.2 + - - +
286C ILE 5.7 1.2 - - - -
287C PRO* 4.5 20.9 - - + +
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Residues in contact with ILE 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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230C MET* 3.8 27.6 - - + +
231C PRO 2.9 16.0 + - - +
232C VAL* 3.9 10.3 - - + +
234C ARG* 1.3 74.3 - - - +
236C LEU* 1.3 59.7 + - - +
238C ALA* 2.7 28.7 + - - +
239C GLU* 3.1 10.8 + - + +
282C TRP* 5.1 0.8 + - + -
286C ILE* 4.6 10.3 - - + -
287C PRO* 3.6 21.5 - - + -
365C THR 4.8 2.2 - - - +
368C GLY* 3.8 32.1 - - - +
369C CYS* 4.1 25.1 - - - +
372C ALA* 4.9 4.3 - - + -
396C VAL* 4.7 8.5 - - + -
399C SER* 5.2 2.0 - - - -
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Residues in contact with LEU 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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232C VAL* 3.0 17.3 + - + +
233C GLU* 4.4 4.5 - - - +
235C ILE* 1.3 80.4 - - - +
237C GLU* 1.3 57.2 + - - +
239C GLU* 2.8 23.9 + - + +
240C LEU* 2.9 43.3 + - + +
364C LYS* 3.0 46.4 - - + +
365C THR* 3.0 24.5 - - + +
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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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233C GLU* 2.7 30.5 + - - +
234C ARG* 3.5 22.9 + - - +
235C ILE 3.0 0.2 - - - -
236C LEU* 1.3 76.1 - - - +
238C ALA* 1.3 56.7 + - - +
239C GLU 3.4 0.2 - - - -
240C LEU* 4.5 7.5 - - - +
241C ALA* 3.2 30.7 + - + +
285C ARG* 5.4 0.5 - - - -
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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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234C ARG 3.1 6.4 + - - +
235C ILE* 2.7 15.0 + - - +
237C GLU* 1.3 77.6 - - - +
239C GLU* 1.3 56.6 + - - -
241C ALA* 4.0 4.4 + - - +
242C VAL* 2.8 30.0 - - - +
282C TRP* 3.5 17.0 - - + +
285C ARG* 2.9 45.4 - - + +
286C ILE* 4.6 3.1 - - + -
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Residues in contact with GLU 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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235C ILE* 3.1 13.7 + - + +
236C LEU* 2.8 12.5 + - + +
238C ALA* 1.3 75.1 - - - +
240C LEU* 1.3 68.5 + - + +
242C VAL* 3.1 20.3 + - - +
243C GLU* 3.7 8.1 + - - +
282C TRP* 2.9 27.8 + - - +
364C LYS* 3.5 22.0 - - + +
367C LEU* 3.3 21.6 - - - +
368C GLY* 2.8 37.7 + - - -
371C ARG* 4.1 9.6 + - - +
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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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236C LEU* 2.9 42.8 + - + +
237C GLU* 4.5 5.2 - - - +
239C GLU* 1.3 72.4 - - + +
241C ALA* 1.3 56.9 + - - +
242C VAL 3.0 10.7 + - - -
243C GLU* 3.0 39.7 + - - +
364C LYS* 3.8 22.4 - - + -
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Residues in contact with ALA 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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237C GLU* 3.2 21.6 + - + +
238C ALA 4.5 2.2 - - - +
239C GLU 3.3 1.6 - - - -
240C LEU* 1.3 75.9 - - - +
242C VAL* 1.3 62.3 + - - +
243C GLU 5.3 0.4 - - - -
285C ARG* 4.5 21.3 + - - +
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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