Contacts of the helix formed by residues 326 - 336 (chain A) in PDB entry 1YDY
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 ASP 326 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A LEU* 3.7 7.0 - - - -
324A THR* 3.8 4.7 - - - +
325A PRO* 1.3 81.2 - - - +
327A VAL* 1.3 64.9 + - - +
328A ASN* 3.1 23.0 + - - +
329A GLN* 2.8 48.4 + - - +
330A LEU 3.6 3.3 + - - -
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Residues in contact with VAL 327 (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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315A VAL* 3.4 31.0 - - + -
317A SER* 3.8 31.0 - - - +
320A LEU* 3.6 14.6 - - + +
326A ASP* 1.3 73.4 - - - +
328A ASN* 1.3 74.9 + - - +
330A LEU* 2.9 12.0 + - - +
331A TYR* 2.9 33.5 + - + +
347A PHE* 6.2 0.2 - - + -
350A LYS* 4.3 20.4 - - + +
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Residues in contact with ASN 328 (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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326A ASP* 3.1 11.6 + - - +
327A VAL* 1.3 85.3 - - - +
329A GLN* 1.3 57.6 + - - +
331A TYR* 3.7 18.6 - - - -
332A ASP* 2.9 30.2 + - - +
350A LYS* 4.4 3.5 - - - +
354A PHE* 3.6 29.1 - - + +
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Residues in contact with GLN 329 (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 PRO* 4.5 2.0 - - - +
292A GLY* 4.2 15.0 - - - +
294A ILE* 5.6 0.7 - - - +
323A TYR 4.1 4.6 + - - -
324A THR* 3.7 12.9 - - + +
325A PRO* 3.1 35.0 - - - +
326A ASP* 2.8 35.3 + - - +
328A ASN* 1.3 77.2 - - + +
330A LEU* 1.3 57.3 + - - +
332A ASP* 3.6 7.1 - - - +
333A ALA* 2.9 27.4 + - - +
337A LYS* 5.1 2.4 - - - -
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Residues in contact with LEU 330 (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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281A TYR* 3.8 43.1 - - + +
285A ILE* 5.9 1.6 - - + -
315A VAL* 3.8 30.1 - - + -
316A ARG 5.1 0.4 - - - +
320A LEU* 3.9 11.0 - - + -
321A PRO* 3.9 11.9 - - + -
323A TYR* 4.6 7.4 - - + -
324A THR* 3.6 23.6 - - + +
326A ASP 3.6 1.0 + - - -
327A VAL 2.9 11.7 + - - +
329A GLN* 1.3 78.0 - - - +
331A TYR* 1.3 65.7 + - - +
333A ALA* 3.2 5.9 + - + +
334A LEU* 3.1 37.2 + - + +
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Residues in contact with TYR 331 (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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315A VAL* 3.5 30.8 - - + +
327A VAL* 2.9 36.1 + - + +
328A ASN* 3.7 17.3 - - - +
330A LEU* 1.3 76.5 - - - +
332A ASP* 1.3 57.5 + - - +
335A TYR* 2.8 44.9 + + + +
343A LEU* 3.9 19.1 - - + -
345A THR* 2.8 21.1 + - - -
347A PHE* 3.4 17.8 + - - +
350A LYS* 3.7 13.8 - - + +
351A ALA* 3.5 28.4 + - + -
354A PHE* 3.7 31.0 - + + -
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Residues in contact with ASP 332 (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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328A ASN 2.9 18.0 + - - +
329A GLN* 3.6 8.5 - - - +
331A TYR* 1.3 75.1 - - - +
333A ALA* 1.3 65.9 + - - +
336A ASN* 2.8 52.9 + - - +
337A LYS* 3.1 34.2 + - - +
354A PHE* 3.5 14.8 - - + -
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Residues in contact with ALA 333 (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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285A ILE* 4.8 8.4 - - + +
294A ILE* 4.1 24.2 - - + -
323A TYR* 6.0 0.2 - - + -
324A THR* 4.7 0.9 - - + -
329A GLN 2.9 19.7 + - - +
330A LEU* 3.2 15.0 + - + +
332A ASP* 1.3 76.2 - - - +
334A LEU* 1.3 61.7 + - + +
337A LYS* 3.2 24.3 - - + +
338A ALA* 2.9 28.9 + - - +
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Residues in contact with LEU 334 (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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281A TYR* 3.9 31.9 - - + -
284A LEU* 4.2 19.5 - - + -
285A ILE* 4.7 15.3 - - + -
312A PRO* 4.2 8.3 - - + -
315A VAL* 3.8 29.2 - - + -
330A LEU* 3.1 25.3 + - + +
333A ALA* 1.3 80.1 - - - +
335A TYR* 1.3 64.0 + - - +
336A ASN 3.4 0.2 - - - -
338A ALA* 3.6 7.4 - - + +
339A GLY 3.1 6.8 + - - -
340A VAL* 2.9 31.1 + - + +
343A LEU* 3.8 17.7 - - + -
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Residues in contact with TYR 335 (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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31A LYS* 2.7 46.4 + - + -
32A ILE 2.7 29.5 + - - -
33A VAL* 3.5 17.2 - - - +
331A TYR* 2.8 38.3 + + + +
334A LEU* 1.3 75.6 - - - +
336A ASN* 1.3 66.2 + - - +
339A GLY* 3.3 7.6 - - - -
340A VAL* 3.8 16.2 - - + -
342A GLY* 3.9 10.1 - - - -
343A LEU* 3.4 36.9 - - + +
351A ALA* 4.3 3.9 - - + +
354A PHE* 3.9 14.6 - + + -
355A LEU* 3.7 28.5 - - + -
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Residues in contact with ASN 336 (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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31A LYS* 4.8 6.5 - - - +
332A ASP* 2.8 34.7 + - - +
335A TYR* 1.3 90.1 + - - +
337A LYS* 1.3 67.2 + - + +
338A ALA 3.5 0.2 - - - -
339A GLY* 3.5 8.2 + - - -
354A PHE* 3.7 16.2 - - - -
355A LEU* 6.2 0.2 - - - +
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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