Contacts of the helix formed by residues 287 - 305 (chain A) in PDB entry 3A3K
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 ASN 287 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A PRO* 3.8 11.3 - - - +
286A ASP* 1.3 86.4 + - - +
288A PRO* 1.3 73.0 - - + +
289A GLU* 2.8 33.2 + - - +
290A TYR* 3.3 13.7 + - - +
291A LEU* 3.9 6.5 + - - +
359A GLY 4.1 2.0 + - - -
360A VAL 3.2 27.1 + - - +
361A THR 3.7 3.3 - - - -
362A GLY* 3.5 25.5 + - - +
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Residues in contact with PRO 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ASP 3.8 3.1 - - - +
287A ASN* 1.3 84.9 - - + +
289A GLU* 1.3 77.4 + - - +
290A TYR 3.2 0.2 - - - -
291A LEU* 3.5 16.3 + - + +
292A GLU* 3.3 20.3 + - - +
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Residues in contact with GLU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 6.3 0.9 - - - +
287A ASN* 2.8 31.4 + - - +
288A PRO* 1.3 86.8 - - - +
290A TYR* 1.3 57.5 + - - +
292A GLU* 3.3 8.2 + - - +
293A PHE* 2.8 28.7 + - - +
359A GLY 4.8 3.8 - - - +
360A VAL* 4.2 19.6 - - + +
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Residues in contact with TYR 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU* 3.3 23.2 + - - -
285A PRO* 3.7 37.9 - - + +
287A ASN* 3.3 18.0 + - - +
288A PRO 3.2 0.2 - - - -
289A GLU* 1.3 76.2 - - - +
291A LEU* 1.3 65.7 + - + +
293A PHE* 3.0 9.8 + + - +
294A LEU* 2.8 58.2 + - + +
312A GLY 4.6 2.4 + - - -
313A LEU* 5.7 0.2 - - - -
315A ASN* 3.5 11.6 - - - +
316A ILE* 3.5 28.7 + - - +
319A ALA* 3.8 26.5 - - + -
360A VAL 3.1 27.5 + - - +
361A THR* 4.4 2.2 - - + -
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU* 5.9 1.6 - - - +
285A PRO 5.6 3.1 - - - +
286A ASP 5.4 6.1 - - - +
287A ASN 3.9 7.6 + - - +
288A PRO* 3.5 15.8 + - + +
289A GLU 3.5 0.4 - - - -
290A TYR* 1.3 82.0 - - + +
292A GLU* 1.3 59.3 + - - +
294A LEU* 3.5 18.3 + - + +
295A LYS* 3.1 32.0 + - + +
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Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A PRO 3.3 11.2 + - - +
289A GLU* 3.3 11.1 + - - +
290A TYR 3.1 0.4 - - - -
291A LEU* 1.3 78.6 - - - +
293A PHE* 1.3 64.9 + - - +
295A LYS* 3.2 21.0 + - - +
296A GLN* 2.9 59.3 + - + +
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Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 3.7 23.1 - - + -
29A LEU* 4.2 15.7 - - + -
289A GLU 2.8 14.7 + - - +
290A TYR* 3.0 11.4 + + - +
292A GLU* 1.3 75.5 - - - +
294A LEU* 1.3 65.5 + - + +
296A GLN* 3.1 5.3 + - - +
297A LEU* 2.7 59.0 + - + +
315A ASN 4.7 2.0 - - - -
318A PRO 4.2 0.2 - - - -
319A ALA* 3.5 40.2 - - + -
322A HIS* 3.6 29.6 - + + -
360A VAL* 3.8 29.8 - - + -
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU* 4.8 3.8 - - - +
290A TYR* 2.8 52.7 + - + +
291A LEU* 3.8 16.2 - - + +
293A PHE* 1.3 84.6 - - + +
295A LYS* 1.3 62.6 + - + +
297A LEU* 3.9 8.5 - - + +
298A LYS* 3.0 42.7 + - - +
309A VAL* 6.0 0.7 - - + -
311A ASP* 4.4 14.8 - - - +
312A GLY 6.0 0.4 - - - +
315A ASN* 3.8 35.7 - - + +
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Residues in contact with LYS 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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291A LEU* 3.1 23.6 + - + +
292A GLU* 3.2 29.1 + - - +
294A LEU* 1.3 77.2 - - - +
296A GLN* 1.3 69.1 + - - +
298A LYS* 3.5 7.3 + - - +
299A LEU* 3.3 29.9 + - + +
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Residues in contact with GLN 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.9 25.7 - - + +
292A GLU* 2.9 44.9 + - + +
293A PHE* 3.8 4.5 - - - +
295A LYS* 1.3 81.0 - - - +
297A LEU* 1.3 67.3 + - - +
299A LEU* 3.5 20.7 + - - +
300A LEU* 3.1 24.6 + - - +
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG* 3.3 25.4 - - + +
25A PRO* 3.6 12.1 - - + -
26A ALA* 3.5 27.8 - - + +
29A LEU* 3.7 7.7 - - + +
293A PHE* 2.7 41.1 + - + +
294A LEU* 3.9 11.9 - - + +
296A GLN* 1.3 73.6 - - - +
298A LYS* 1.3 55.0 + - - +
300A LEU* 3.3 2.5 + - - +
301A ALA* 2.9 29.8 + - - +
309A VAL* 4.0 30.1 - - + -
315A ASN* 4.5 3.8 - - - +
318A PRO* 4.4 17.0 - - + -
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Residues in contact with LYS 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LEU* 3.0 32.7 + - - +
295A LYS* 3.8 7.0 - - - +
297A LEU* 1.3 75.3 - - - +
299A LEU* 1.3 63.7 + - + +
301A ALA* 3.6 1.8 + - - +
302A ASP* 3.2 24.9 + - - +
307A PHE 4.7 1.4 - - - +
309A VAL* 3.7 46.0 + - + +
310A GLU 4.9 0.9 - - - -
311A ASP* 2.8 41.8 + - - +
315A ASN* 5.6 1.6 - - - +
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LYS* 3.3 21.4 + - + +
296A GLN* 3.9 24.2 - - - +
297A LEU 3.3 0.2 - - - -
298A LYS* 1.3 79.6 - - + +
300A LEU* 1.3 59.0 + - - +
302A ASP* 3.8 4.5 - - + +
303A LYS* 3.0 29.9 + - - +
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Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PRO* 3.3 35.2 - - + +
28A GLU* 3.8 32.8 - - + +
29A LEU* 3.9 19.3 - - + -
296A GLN 3.1 14.0 + - - +
297A LEU* 3.8 2.9 - - - +
299A LEU* 1.3 76.6 - - - +
301A ALA* 1.3 59.5 + - - +
303A LYS* 4.5 8.7 - - + -
304A LYS* 2.9 50.4 + - + +
305A PHE* 3.8 2.8 - - + -
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Residues in contact with ALA 301 (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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21A ALA 3.8 15.7 - - - +
25A PRO* 3.8 14.3 - - + +
297A LEU 2.9 18.1 + - - +
298A LYS 4.0 1.8 - - - +
299A LEU 3.4 0.2 - - - -
300A LEU* 1.3 76.2 - - - +
302A ASP* 1.3 56.6 + - - +
305A PHE* 3.1 9.8 + - - -
306A ASN 3.1 24.4 + - - -
307A PHE* 3.1 19.3 + - + +
309A VAL* 3.7 21.8 - - + -
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Residues in contact with ASP 302 (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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298A LYS 3.2 16.9 + - - +
299A LEU* 3.8 4.7 - - - +
301A ALA* 1.3 80.0 - - - +
303A LYS* 1.3 63.7 + - - +
306A ASN* 3.9 13.5 + - - -
307A PHE 3.3 17.6 + - - +
308A THR* 4.7 9.4 + - - -
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Residues in contact with LYS 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU 3.0 18.9 + - - +
300A LEU* 3.8 10.3 - - + +
302A ASP* 1.3 82.1 + - - +
304A LYS* 1.3 79.7 + - + +
306A ASN* 4.7 1.4 + - - -
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Residues in contact with LYS 304 (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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28A GLU* 3.4 35.1 + - - +
300A LEU* 2.9 21.2 + - + +
303A LYS* 1.3 95.9 - - + +
305A PHE* 1.3 80.2 + - + +
306A ASN 3.6 1.1 - - - -
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Residues in contact with PHE 305 (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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14A THR* 5.6 1.6 - - - +
20A TRP* 3.4 44.0 - + - -
21A ALA* 4.0 22.7 - - + +
24A GLY* 3.6 11.2 - - - -
25A PRO* 3.4 40.2 - - + -
28A GLU* 3.6 24.9 - - - -
300A LEU* 3.8 7.2 - - + -
301A ALA* 3.1 10.3 + - + +
304A LYS* 1.3 93.6 - - + +
306A ASN* 1.3 74.9 + - - +
307A PHE* 3.3 5.8 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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