Contacts of the helix formed by residues 285 - 296 (chain A) in PDB entry 1AII
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 LEU 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ARG 3.4 2.4 + - - -
11A GLY* 4.4 0.2 - - - -
12A THR* 3.5 29.6 - - + +
259A LEU* 4.7 2.0 - - + -
276A ILE 4.9 0.9 - - - +
277A MET* 3.9 53.6 - - + +
280A ARG* 3.1 20.1 + - + +
281A SER* 4.0 4.5 - - - +
284A ASP* 1.3 76.2 + - - +
286A LEU* 1.3 56.9 + - - +
288A ILE* 3.2 29.7 + - + +
289A ARG* 2.8 33.6 + - + +
300A LEU* 4.2 6.3 - - + -
319A ILE* 3.8 12.8 - - + +
320A CYS* 4.3 2.0 - - - -
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A HIS 5.3 0.4 - - - +
10A ARG* 2.9 56.6 + - + +
11A GLY 3.6 19.5 - - - +
12A THR* 3.8 10.8 - - + +
285A LEU* 1.3 77.8 - - - +
287A ASP* 1.3 57.4 + - - +
289A ARG* 3.4 36.1 + - - +
290A THR* 3.1 27.6 + - - -
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Residues in contact with ASP 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 3.0 49.8 + - - +
252A PRO* 3.8 22.1 - - + +
284A ASP* 3.0 14.0 + - + +
286A LEU* 1.3 74.7 - - - +
288A ILE* 1.3 64.5 + - - +
290A THR* 3.2 8.9 + - - -
291A GLU* 3.0 28.4 + - + +
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Residues in contact with ILE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A PRO* 3.7 27.4 - - + +
255A LEU* 3.8 17.7 - - + -
256A ALA* 3.8 15.4 - - + +
259A LEU* 3.6 28.7 - - + -
276A ILE* 4.3 3.8 - - + -
280A ARG* 3.8 21.1 - - + -
284A ASP* 3.0 32.7 + - - +
285A LEU* 3.5 18.8 - - + +
287A ASP* 1.3 71.4 - - - +
289A ARG* 1.3 66.4 + - - +
291A GLU* 3.3 2.1 + - - +
292A PHE* 2.9 24.0 + - + +
300A LEU* 4.5 3.4 - - + -
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Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A THR* 3.8 7.8 - - - +
285A LEU* 2.8 18.3 + - + +
286A LEU* 3.5 32.6 + - - +
288A ILE* 1.3 79.3 - - - +
290A THR* 1.3 61.1 + - - +
292A PHE* 3.4 7.2 + - - +
293A LYS* 3.1 23.4 + - - +
300A LEU* 4.0 27.6 + - + -
320A CYS* 2.8 36.5 + - - +
321A GLY 3.8 4.8 + - - -
322A GLY* 3.6 22.8 + - - +
323A ASP 3.6 16.2 + - - -
324A ASP* 3.0 39.9 + - - +
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Residues in contact with THR 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 5.0 6.8 + - - -
286A LEU 3.1 15.3 + - - -
287A ASP* 3.2 12.7 + - - -
289A ARG* 1.3 77.9 - - - +
291A GLU* 1.3 62.5 + - - +
293A LYS* 3.4 6.1 + - - +
294A LYS* 3.0 29.9 + - + +
324A ASP* 5.0 7.6 + - - -
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ASN* 3.3 29.2 + - - +
252A PRO* 4.0 5.2 - - + +
253A ALA* 3.8 32.3 - - + +
256A ALA* 4.2 2.0 - - + -
287A ASP* 3.0 21.5 + - + +
288A ILE 3.8 2.9 - - - +
290A THR* 1.3 77.7 - - - +
292A PHE* 1.3 68.0 + - - +
294A LYS* 3.1 18.7 + - - +
295A HIS* 2.9 51.3 + - - +
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Residues in contact with PHE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ALA* 3.6 26.6 - - + +
259A LEU* 4.4 2.9 - - + -
260A HIS* 3.9 34.3 - + + -
263A LEU* 4.8 1.8 - - + -
288A ILE* 2.9 18.6 + - + +
289A ARG* 3.6 8.3 - - - +
291A GLU* 1.3 76.7 - - - +
293A LYS* 1.3 56.4 + - - +
296A TYR* 2.9 48.1 + + + +
298A TYR* 3.4 37.0 - + - -
299A SER 3.7 12.8 - - - -
300A LEU* 3.6 32.3 - - + -
303A ALA* 3.7 18.8 - - + -
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Residues in contact with LYS 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ARG 3.1 14.5 + - - +
290A THR* 3.9 3.8 - - - +
292A PHE* 1.3 79.9 - - - +
294A LYS* 1.3 58.8 + - - +
297A GLY* 2.9 32.6 + - - -
298A TYR* 3.5 26.4 - - - +
299A SER* 4.2 9.1 - - - +
324A ASP* 3.0 46.2 + - + +
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Residues in contact with LYS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A THR* 3.0 22.0 + - + +
291A GLU* 3.1 25.8 + - - +
293A LYS* 1.3 77.4 - - - +
295A HIS* 1.3 69.0 + - + +
297A GLY* 4.6 1.2 + - - -
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Residues in contact with HIS 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ASN* 5.3 0.9 - - - -
253A ALA* 3.7 24.9 - - + +
256A ALA* 5.9 0.9 - - + -
257A GLU* 5.8 4.3 - - + -
291A GLU* 2.9 45.2 + - - +
294A LYS* 1.3 88.5 - - + +
296A TYR* 1.3 91.6 + + + +
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Residues in contact with TYR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ALA* 4.0 13.5 - - + -
257A GLU* 3.3 36.4 + - - +
260A HIS* 3.4 52.2 + + + +
292A PHE* 2.9 43.9 + + + +
295A HIS* 1.3 96.7 - + + +
297A GLY* 1.3 61.5 + - - +
298A TYR* 3.4 32.1 - + + +
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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