Contacts of the helix formed by residues 228 - 243 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239C LYS* 4.2 25.3 + - - +
243C GLN* 4.3 23.4 + - - +
227D VAL* 1.3 70.8 - - - +
229D PHE* 1.3 63.0 + - - +
231D SER* 2.9 11.9 + - - -
232D ALA* 2.4 39.0 + - - +
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Residues in contact with PHE 229 (chain D).
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* 5.6 7.2 - - + -
119B VAL* 4.6 15.3 - - + -
120B GLU 5.9 0.2 - - - -
123B ARG* 3.1 58.6 - - + -
126B LEU* 5.9 5.1 - - + +
239C LYS* 5.8 4.0 - - + -
240C LEU* 6.0 11.2 - - + -
243C GLN* 4.0 33.7 - - + -
227D VAL* 3.3 34.5 - - + -
228D SER* 1.3 82.3 - - - +
230D LEU* 1.3 60.8 + - - +
232D ALA* 3.1 20.3 - - - +
233D LEU* 3.1 14.9 + - - +
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Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU* 5.6 3.8 - - + +
137A LEU* 3.5 32.8 - - + -
138A GLN* 5.1 16.2 - - + +
141A LEU* 4.2 18.6 - - + -
226D LYS* 4.3 22.4 - - + -
227D VAL* 3.0 24.8 + - + +
229D PHE* 1.3 74.7 - - - +
231D SER* 1.3 69.0 + - - +
232D ALA 2.9 1.1 - - - -
233D LEU* 2.8 26.8 + - + +
234D GLU* 3.0 21.4 + - + +
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Residues in contact with SER 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C LYS* 5.6 3.1 + - - -
226D LYS* 4.9 11.1 - - - +
227D VAL 2.7 16.0 + - - +
228D SER* 3.1 16.7 + - - -
230D LEU* 1.3 73.0 - - - +
232D ALA* 1.3 55.0 + - - +
234D GLU* 3.3 13.6 + - - +
235D GLU* 3.0 35.8 + - - +
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Residues in contact with ALA 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C TYR* 4.8 15.2 - - + +
239C LYS* 4.7 22.0 - - + +
240C LEU* 5.7 3.8 - - + -
228D SER 2.4 21.6 + - - +
229D PHE* 3.1 17.5 - - - +
230D LEU 2.9 0.2 - - - -
231D SER* 1.3 72.5 - - - +
233D LEU* 1.3 55.7 + - - +
235D GLU* 3.5 12.3 + - - +
236D TYR* 2.7 37.7 + - - +
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Residues in contact with LEU 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ALA* 6.1 0.7 - - + -
134A LEU* 3.3 44.6 - - + -
137A LEU* 4.3 11.2 - - + -
126B LEU* 4.1 19.5 - - + -
236C TYR* 3.4 34.8 - - + +
229D PHE 3.1 10.5 + - - +
230D LEU* 2.8 30.5 + - + +
232D ALA* 1.3 72.2 - - - +
234D GLU* 1.3 62.1 + - - +
236D TYR* 2.9 9.3 + - + +
237D THR* 2.6 35.2 + - - -
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Residues in contact with GLU 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU* 5.6 0.4 - - - -
138A GLN* 5.4 4.9 + - - +
226D LYS* 3.1 31.9 + - - +
230D LEU* 3.0 22.7 + - + +
231D SER* 3.4 12.7 - - - +
233D LEU* 1.3 79.6 - - + +
235D GLU* 1.3 63.1 + - - +
236D TYR 3.0 0.2 + - - -
237D THR* 3.2 5.3 + - - -
238D LYS* 3.0 21.2 + - - +
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Residues in contact with GLU 235 (chain D).
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* 4.9 6.9 - - - +
239C LYS* 3.7 25.3 + - - +
231D SER* 3.0 15.1 + - - +
232D ALA* 3.7 11.2 - - - +
234D GLU* 1.3 78.1 - - - +
236D TYR* 1.3 64.3 + - - +
238D LYS* 3.0 31.7 - - + +
239D LYS* 3.3 41.2 + - - +
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Residues in contact with TYR 236 (chain D).
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* 5.3 5.0 + - - +
130A ALA* 4.3 12.6 - - + -
232C ALA* 3.8 28.3 - - + -
233C LEU* 3.3 38.5 - - + +
236C TYR* 3.6 32.5 - + + -
232D ALA 2.7 23.6 + - - +
233D LEU* 2.9 18.5 + - + +
235D GLU* 1.3 69.6 - - - +
237D THR* 1.3 84.6 + - + +
238D LYS 2.8 4.0 - - - -
239D LYS* 2.7 36.4 + - - +
240D LEU* 3.4 21.2 + - + +
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Residues in contact with THR 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLN 4.7 0.9 - - - +
130A ALA* 3.5 24.0 - - + -
131A ARG* 4.1 13.0 - - + +
134A LEU* 3.3 29.3 - - + +
233D LEU 2.6 16.2 + - - -
234D GLU* 3.2 6.9 + - - -
236D TYR* 1.3 84.5 - - + +
238D LYS* 1.3 50.7 + - - +
240D LEU* 3.0 25.1 + - + +
241D ASN* 2.5 28.4 - - - +
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Residues in contact with LYS 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D GLU 3.0 14.2 + - - +
235D GLU* 3.0 28.6 - - + +
237D THR* 1.3 76.6 - - - +
239D LYS* 1.3 69.3 + - + +
241D ASN* 3.1 20.4 + - - +
242D THR* 4.6 5.0 - - - +
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Residues in contact with LYS 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C PHE* 5.3 7.2 - - - +
232C ALA* 4.9 16.4 - - + -
235C GLU* 4.0 24.0 + - - +
235D GLU* 3.3 44.0 + - - +
236D TYR* 2.7 16.6 + - - +
238D LYS* 1.3 82.7 - - + +
240D LEU* 1.3 58.4 + - - -
241D ASN 3.4 1.6 - - - -
242D THR* 3.6 25.7 + - + +
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Residues in contact with LEU 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ARG* 3.7 19.2 + - + +
126A LEU* 3.0 42.0 - - + +
127A GLN* 3.5 33.9 - - + +
130A ALA* 4.6 1.8 - - + -
131A ARG* 5.2 3.1 - - - +
229C PHE* 5.4 13.7 - - + +
236D TYR* 3.4 28.3 + - + +
237D THR* 3.0 28.6 + - + +
239D LYS* 1.3 78.1 - - - +
241D ASN* 1.3 62.5 + - + +
242D THR* 3.7 2.6 + - - -
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Residues in contact with ASN 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ARG* 3.1 26.7 + - - +
127A GLN* 4.6 7.4 - - + +
131A ARG* 4.5 16.7 - - - +
237D THR 2.5 29.8 - - - +
238D LYS* 3.1 11.5 + - - +
239D LYS 3.4 0.8 - - - -
240D LEU* 1.3 85.9 - - + +
242D THR* 1.3 59.6 + - - +
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Residues in contact with THR 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ARG* 4.0 1.4 - - - +
228C SER* 5.4 5.0 + - - -
238D LYS 4.6 2.7 - - - +
239D LYS* 3.6 31.0 + - + +
240D LEU 3.7 1.7 + - - -
241D ASN* 1.3 78.1 - - - +
243D GLN* 1.3 82.9 + - - +
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Residues in contact with GLN 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ARG* 4.0 34.8 + - - +
120A GLU* 4.7 6.6 - - - +
123A ARG* 3.5 26.1 + - - -
228C SER* 5.9 4.9 - - - -
242D THR* 1.3 95.0 + - - +
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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