Contacts of the helix formed by residues 228 - 243 (chain C) in PDB entry 1AV1
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 228 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226C LYS* 2.6 15.8 + - - +
227C VAL* 1.3 81.8 + - - +
229C PHE* 1.3 73.0 + - - +
230C LEU 3.1 0.2 - - - -
231C SER* 2.6 40.1 + - - +
232C ALA* 3.3 2.3 + - - +
242D THR* 5.4 4.8 + - - -
243D GLN* 5.9 4.9 - - - -
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Residues in contact with PHE 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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115A TYR* 4.4 3.8 - + - -
119A VAL* 3.6 31.0 - - + -
122A LEU* 6.4 1.3 - - + -
123A ARG* 6.5 0.7 - - - -
126A LEU* 5.1 16.4 - - + -
137B LEU* 6.0 6.7 - - + -
141B LEU* 4.9 7.0 - - + -
227C VAL* 3.0 49.1 - - + -
228C SER* 1.3 87.0 + - - +
230C LEU* 1.3 67.6 + - + +
232C ALA* 2.7 37.8 + - - +
233C LEU* 3.5 8.7 - - + +
239D LYS 5.3 6.7 - - - +
240D LEU* 5.4 14.1 - - + +
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Residues in contact with LEU 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 5.1 18.8 - - + +
137B LEU* 5.6 7.2 - - + -
138B GLN* 5.4 14.6 - - + +
141B LEU* 4.6 13.0 - - + -
227C VAL* 3.0 27.6 - - + +
228C SER 3.0 0.6 + - - -
229C PHE* 1.3 89.5 - - + +
231C SER* 1.3 56.4 + - - +
233C LEU* 2.6 41.7 + - + +
234C GLU* 3.1 20.0 + - + +
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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
----------------------------------------------------------
226C LYS* 5.0 18.0 - - - +
227C VAL* 4.4 0.8 - - - +
228C SER* 2.6 27.0 + - - -
230C LEU* 1.3 76.6 - - - +
232C ALA* 1.3 58.8 + - - -
234C GLU* 3.0 29.5 - - - +
235C GLU* 3.3 8.3 + - - +
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Residues in contact with ALA 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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228C SER 3.3 1.8 + - - -
229C PHE* 2.7 23.1 + - - +
231C SER* 1.3 77.5 - - - +
233C LEU* 1.3 58.5 + - + +
235C GLU* 3.3 6.1 + - - +
236C TYR* 2.8 29.1 + - - +
236D TYR* 3.8 23.5 - - + +
239D LYS* 4.9 24.5 - - + +
240D LEU* 5.8 2.2 - - + +
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Residues in contact with LEU 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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126A LEU* 6.5 0.9 - - + -
130B ALA* 5.8 5.4 - - + +
134B LEU* 5.5 15.3 - - + -
137B LEU* 5.9 9.0 - - + -
229C PHE* 3.5 16.8 - - + +
230C LEU* 2.6 28.9 + - + +
232C ALA* 1.3 69.6 - - - +
234C GLU* 1.3 63.9 + - - +
236C TYR* 3.5 27.8 - - + -
237C THR* 3.0 36.5 + - + +
236D TYR* 3.3 30.5 - - + +
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Residues in contact with GLU 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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230C LEU* 3.1 20.6 + - + +
231C SER* 3.0 30.1 - - - +
233C LEU* 1.3 78.5 - - - +
235C GLU* 1.3 59.3 + - - +
237C THR* 4.3 2.8 + - - -
238C LYS* 3.7 15.4 + - - +
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Residues in contact with GLU 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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231C SER 3.3 5.7 + - - +
232C ALA* 3.3 7.2 + - - +
233C LEU 3.1 0.2 - - - -
234C GLU* 1.3 76.5 - - - +
236C TYR* 1.3 70.0 + - - +
238C LYS* 2.9 29.0 + - + +
239C LYS* 3.5 24.3 + - + +
235D GLU* 4.9 7.5 - - - +
239D LYS* 4.0 23.2 + - - +
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Residues in contact with TYR 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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126B LEU* 3.6 22.7 - - - +
130B ALA* 4.1 17.0 - - + +
232C ALA 2.8 19.8 + - - +
233C LEU* 3.1 23.1 + - + +
235C GLU* 1.3 79.4 - - - +
237C THR* 1.3 89.9 + - + +
238C LYS 3.0 0.3 + - - -
239C LYS* 3.3 12.7 + - - +
240C LEU* 3.6 27.6 + - + +
229D PHE 5.8 0.2 - - - -
232D ALA* 4.8 9.5 - - + +
233D LEU* 3.4 38.5 - - + +
236D TYR* 3.6 33.2 - + + -
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Residues in contact with THR 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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127B GLN* 5.9 0.9 - - + +
130B ALA* 4.5 12.6 - - + -
131B ARG* 5.3 6.3 - - + +
134B LEU* 5.8 8.3 - - + +
233C LEU* 3.0 21.0 + - + +
234C GLU* 4.3 3.1 + - - -
236C TYR* 1.3 95.7 - - + +
238C LYS* 1.3 62.1 + - - +
240C LEU* 3.1 36.5 - - + +
241C ASN* 3.7 11.6 + - - -
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Residues in contact with LYS 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 GLU 3.7 14.1 + - - +
235C GLU* 2.9 23.0 + - + +
237C THR* 1.3 77.6 + - - +
239C LYS* 1.3 67.6 + - + +
241C ASN* 3.1 14.4 + - - +
242C THR* 3.2 28.5 + - + +
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Residues in contact with LYS 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 GLU* 3.5 22.5 + - + +
236C TYR* 3.3 9.6 + - - +
238C LYS* 1.3 75.6 - - + +
240C LEU* 1.3 55.6 + - + +
241C ASN 2.7 16.8 + - - -
242C THR* 3.0 23.0 + - - +
243C GLN* 3.2 17.7 + - + +
228D SER* 4.2 21.9 + - - +
229D PHE* 5.8 3.2 - - - -
231D SER* 5.6 3.8 + - - -
232D ALA* 4.7 20.2 - - + +
235D GLU* 3.7 24.9 + - - +
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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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123B ARG* 4.2 23.7 + - - +
126B LEU* 4.9 12.1 - - + -
127B GLN* 3.5 52.0 - - + +
130B ALA* 5.1 0.4 - - + -
236C TYR* 3.6 32.3 - - + +
237C THR* 3.1 45.3 - - + +
238C LYS 3.1 0.2 - - - -
239C LYS* 1.3 77.9 - - + +
241C ASN* 1.3 60.2 + - - +
243C GLN 4.7 1.5 - - - +
229D PHE* 6.0 10.3 - - + -
232D ALA* 5.7 5.8 - - + -
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Residues in contact with ASN 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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127B GLN* 3.1 28.4 + - - +
237C THR 3.7 12.3 + - - -
238C LYS* 3.1 5.9 + - - +
239C LYS 2.7 3.6 + - - -
240C LEU* 1.3 78.7 - - - +
242C THR* 1.3 57.9 + - + +
243C GLN 3.0 17.9 + - - +
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Residues in contact with THR 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 LYS* 3.2 30.7 + - + +
239C LYS* 3.1 27.4 + - - +
241C ASN* 1.3 75.3 - - + +
243C GLN* 1.3 62.3 + - - +
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Residues in contact with GLN 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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116B ARG* 5.2 17.9 + - - +
123B ARG* 3.7 32.4 + - - +
239C LYS* 3.2 13.1 + - + +
240C LEU 4.7 2.0 - - - +
241C ASN 3.0 11.5 - - - +
242C THR* 1.3 82.1 - - - +
228D SER* 4.3 19.4 + - - +
229D PHE* 4.0 28.0 - - + -
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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