Contacts of the helix formed by residues 296 - 308 (chain A) in PDB entry 1A4Y
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 GLY 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A GLU 3.5 1.8 - - - -
295A LEU* 1.3 79.9 - - - +
297A ASP* 1.3 60.4 + - - -
298A GLU* 3.1 3.6 - - - -
299A GLY 3.1 0.2 + - - -
300A ALA 3.1 18.5 + - - -
322A CYS 2.9 9.7 + - - -
323A SER* 3.4 19.7 - - - -
324A PHE* 3.1 14.3 - - - -
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Residues in contact with ASP 297 (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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296A GLY* 1.3 70.1 - - - -
298A GLU* 1.3 60.8 + - - +
299A GLY 3.2 0.2 - - - -
300A ALA* 3.7 7.3 - - - +
301A ARG* 2.9 30.0 + - - +
323A SER 4.0 1.4 + - - +
324A PHE* 3.4 4.5 - - - -
325A THR* 2.6 49.8 + - - +
327A ALA* 3.9 9.7 - - + +
328A CYS* 3.3 28.6 - - + +
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ALA* 3.8 21.8 - - + -
295A LEU 4.5 2.0 - - - +
296A GLY* 3.1 0.6 - - - -
297A ASP* 1.3 80.7 - - - +
299A GLY* 1.3 61.1 + - - +
301A ARG* 3.2 47.6 + - - +
302A LEU* 3.2 37.7 + - + +
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Residues in contact with GLY 299 (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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269A ALA* 4.2 8.7 - - - -
272A CYS* 3.8 8.2 - - - -
295A LEU* 3.0 33.8 + - - -
296A GLY 3.1 1.1 + - - -
298A GLU* 1.3 75.8 - - - +
300A ALA* 1.3 63.3 + - - +
301A ARG 3.3 0.2 + - - -
302A LEU* 3.3 9.4 + - - +
303A LEU* 3.1 29.8 + - - +
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Residues in contact with ALA 300 (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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296A GLY 3.1 6.9 + - - +
297A ASP 3.7 3.6 - - - +
299A GLY* 1.3 71.9 - - - +
301A ARG* 1.3 57.0 + - - +
303A LEU* 3.3 6.6 + - - +
304A CYS* 2.8 41.2 + - - -
324A PHE* 3.6 26.5 - - + -
328A CYS* 3.6 30.7 - - + -
331A HIS* 5.6 0.7 - - - -
332A PHE* 3.7 14.4 - - + -
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Residues in contact with ARG 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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297A ASP 2.9 18.2 + - - +
298A GLU* 3.2 41.8 + - - +
300A ALA* 1.3 77.5 - - - +
302A LEU* 1.3 74.6 + - - +
304A CYS* 3.2 5.6 + - - +
305A GLU* 3.0 48.1 + - - +
328A CYS* 5.5 0.2 - - - +
331A HIS* 4.2 31.0 - - + +
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Residues in contact with LEU 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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269A ALA* 3.5 27.1 - - + +
272A CYS* 4.4 2.0 - - + -
273A GLY* 4.2 13.9 - - - +
276A CYS* 3.8 15.4 - - + -
298A GLU* 3.2 34.5 + - - +
299A GLY* 3.3 11.2 + - - +
301A ARG* 1.3 90.3 - - + +
303A LEU* 1.3 61.4 + - - +
305A GLU* 3.4 16.3 + - - +
306A THR* 2.9 28.1 + - - -
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Residues in contact with LEU 303 (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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272A CYS* 4.0 9.9 - - - -
275A LEU* 5.6 1.6 - - + -
276A CYS* 4.1 11.2 - - - -
279A LEU* 4.2 25.3 - - + +
288A LEU* 4.9 2.2 - - + -
290A LEU* 4.4 19.5 - - + -
295A LEU* 4.5 10.3 - - + -
299A GLY 3.1 16.8 + - - +
300A ALA* 3.5 14.1 - - - +
302A LEU* 1.3 74.5 - - - +
304A CYS* 1.3 60.3 + - - +
306A THR* 3.1 5.6 + - - -
307A LEU* 2.8 38.8 + - + +
314A LEU* 6.2 0.2 - - + -
317A LEU* 4.6 13.9 - - + -
319A VAL* 4.3 24.7 - - + -
324A PHE* 4.7 3.1 - - + -
332A PHE* 5.2 3.6 - - + -
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Residues in contact with CYS 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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300A ALA 2.8 26.7 + - - +
301A ARG 3.7 3.6 - - - +
303A LEU* 1.3 71.2 - - - +
305A GLU* 1.3 65.7 + - - +
307A LEU* 3.3 4.3 + - - +
308A LEU* 3.2 30.5 + - + +
331A HIS* 3.7 38.6 - - + +
332A PHE* 3.7 39.9 - - - -
335A VAL* 3.8 14.3 - - + +
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Residues in contact with GLU 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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301A ARG* 3.0 48.1 + - + +
302A LEU* 3.6 18.7 - - - +
303A LEU 3.3 0.2 - - - -
304A CYS* 1.3 75.8 - - - +
306A THR* 1.3 64.1 + - - +
308A LEU* 3.2 15.4 + - - +
309A GLU* 3.2 25.3 + - - +
331A HIS* 5.6 5.1 - - + -
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Residues in contact with THR 306 (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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276A CYS* 3.5 22.4 - - + +
279A LEU* 3.8 32.3 - - + -
280A ARG* 3.9 31.1 + - + +
302A LEU 2.9 12.6 + - - -
303A LEU* 3.1 9.5 + - - -
305A GLU* 1.3 80.9 - - - +
307A LEU* 1.3 60.3 + - + +
309A GLU* 3.0 24.1 + - - +
312A CYS* 3.6 14.9 - - - +
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 6.0 2.5 - - + -
303A LEU* 2.8 27.5 + - + +
304A CYS* 3.8 8.5 - - - +
305A GLU 3.3 0.4 - - - -
306A THR* 1.3 76.0 - - + +
308A LEU* 1.3 59.0 + - - +
309A GLU 3.4 4.2 + - - +
312A CYS* 4.1 21.6 - - - +
314A LEU* 4.4 20.2 - - + +
317A LEU* 4.0 25.4 - - + -
332A PHE* 5.1 5.6 - - + -
335A VAL* 3.8 25.8 - - + -
339A ASN* 2.7 45.4 + - - +
342A LEU* 4.5 15.9 - - + -
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Residues in contact with LEU 308 (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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304A CYS* 3.2 19.5 + - + +
305A GLU* 3.2 9.8 + - - +
306A THR 3.0 1.4 - - - -
307A LEU* 1.3 80.7 - - - +
309A GLU* 1.3 61.7 + - - +
310A PRO* 4.7 1.2 - - - +
331A HIS* 5.0 1.8 - - + +
334A SER* 3.8 30.1 - - - +
335A VAL* 3.9 14.4 - - + -
338A GLN* 3.7 45.4 + - + +
339A ASN 4.4 2.7 - - - +
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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