Contacts of the helix formed by residues 317 - 331 (chain A) in PDB entry 1SHZ
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 THR 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A ILE* 4.5 2.5 - - - -
315A SER* 3.0 20.3 + - - -
316A ASN* 1.3 76.9 - - - +
318A TYR* 1.3 64.5 + - + +
319A GLU* 3.6 17.5 - - + +
320A GLU* 4.0 17.6 + - + +
321A ALA* 2.9 32.3 + - - +
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Residues in contact with TYR 318 (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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249A LEU* 5.4 0.4 - - + -
293A LYS* 3.6 38.9 + - + +
296A PHE* 3.5 35.2 - + - -
297A GLU* 3.4 48.9 - - + -
300A ILE* 4.1 13.7 - - + +
317A THR* 1.3 75.3 - - + +
319A GLU* 1.3 82.9 + - + +
322A ALA* 3.0 40.4 + - + +
345A PHE* 4.0 12.8 - + - +
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Residues in contact with GLU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A THR* 3.6 10.8 - - + +
318A TYR* 1.3 99.4 - - + +
320A GLU* 1.3 60.4 + - - +
322A ALA* 4.2 1.6 - - - +
323A ALA* 3.2 28.6 + - - +
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Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A TYR* 3.7 8.8 + - + +
314A GLY* 3.3 11.8 - - - -
315A SER* 2.7 38.9 + - - +
317A THR* 3.6 17.6 + - + +
318A TYR 3.4 0.2 - - - -
319A GLU* 1.3 76.2 - - - +
321A ALA* 1.3 65.1 + - - +
323A ALA* 3.7 4.9 + - - +
324A TYR* 3.3 19.6 + - - +
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Residues in contact with ALA 321 (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 PHE* 3.8 16.6 - - + -
300A ILE* 4.0 8.1 - - + -
305A LEU* 3.5 25.5 - - + +
312A TYR* 3.5 11.6 + - - +
315A SER 4.3 2.9 - - - +
317A THR 2.9 23.2 + - - +
320A GLU* 1.3 70.4 - - - +
322A ALA* 1.3 66.0 + - - +
324A TYR* 2.9 15.2 + - - +
325A ILE* 3.0 17.2 + - - +
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 5.3 2.7 - - + -
290A LEU* 4.7 0.5 - - - +
296A PHE* 4.0 16.7 - - + -
318A TYR* 3.0 31.3 + - + +
319A GLU* 4.2 2.7 - - - +
321A ALA* 1.3 77.2 - - - +
323A ALA* 1.3 61.1 + - - +
325A ILE* 3.4 8.6 + - - +
326A GLN 3.2 18.2 + - - -
345A PHE* 3.6 36.1 - - + -
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Residues in contact with ALA 323 (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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319A GLU* 3.2 20.6 + - - +
320A GLU* 3.9 6.3 - - - +
321A ALA 3.2 0.4 - - - -
322A ALA* 1.3 79.3 - - - +
324A TYR* 1.3 61.9 + - - +
326A GLN* 3.8 9.2 + - - +
327A CYS* 3.6 18.7 + - - +
345A PHE* 4.8 3.1 - - - -
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Residues in contact with TYR 324 (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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305A LEU* 4.6 2.9 - - + -
309A TYR* 3.6 34.3 - + + -
311A GLU* 3.6 28.9 + - - +
312A TYR* 3.5 45.0 - + + -
320A GLU 3.3 12.3 + - - +
321A ALA 2.9 11.6 + - - +
323A ALA* 1.3 76.9 - - - +
325A ILE* 1.3 65.8 + - - +
327A CYS* 3.1 7.7 + - + +
328A GLN* 3.1 52.2 + - + +
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Residues in contact with ILE 325 (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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249A LEU* 4.1 20.2 - - + -
252A TYR* 5.3 0.2 - - + -
265A MET* 3.7 29.2 - - + -
290A LEU* 4.9 2.0 - - + -
296A PHE* 4.0 27.6 - - + -
305A LEU* 4.5 11.7 - - + -
309A TYR* 4.0 19.7 - - + +
321A ALA 3.0 14.3 + - - +
322A ALA* 3.4 7.4 + - - +
324A TYR* 1.3 78.0 - - + +
326A GLN* 1.3 57.5 + - - +
328A GLN* 2.9 29.0 + - - +
329A PHE* 3.2 31.5 + - + -
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Residues in contact with GLN 326 (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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288A LEU* 5.3 1.3 - - + +
290A LEU* 3.9 13.0 - - + +
322A ALA 3.2 14.2 + - - +
323A ALA* 4.0 8.4 - - - +
324A TYR 3.3 0.2 - - - -
325A ILE* 1.3 79.2 - - - +
327A CYS* 1.3 57.5 + - - +
329A PHE* 3.6 5.5 + - - +
330A GLU* 2.7 49.3 + - - +
343A THR* 3.6 29.5 - - + +
345A PHE* 3.1 25.8 - - - -
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Residues in contact with CYS 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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323A ALA 3.6 9.7 + - - +
324A TYR* 3.1 11.3 + - + +
325A ILE 3.1 0.4 - - - -
326A GLN* 1.3 75.4 - - - +
328A GLN* 1.3 71.4 + - - +
329A PHE 3.0 2.9 + - - -
330A GLU* 4.5 8.1 - - - +
331A ASP* 3.1 29.9 + - - +
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Residues in contact with GLN 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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269A MET* 3.6 33.6 - - + +
309A TYR* 3.8 29.9 - - + +
311A GLU* 5.3 0.7 - - - +
324A TYR* 3.1 58.3 + - + +
325A ILE* 2.9 17.7 + - - +
327A CYS* 1.3 81.6 - - - +
329A PHE* 1.3 57.4 + - + +
331A ASP* 3.9 7.8 - - - +
332A LEU* 3.6 9.5 - - - +
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Residues in contact with PHE 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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247A VAL* 3.7 32.5 - - + -
265A MET* 4.0 11.9 - - - -
268A SER* 3.8 6.7 - - - -
269A MET* 3.4 46.4 - - + -
272A PHE* 3.5 36.4 - + + -
288A LEU* 4.3 13.9 - - + -
290A LEU* 4.3 12.8 - - + -
309A TYR* 5.0 1.1 - - - -
325A ILE* 3.2 40.5 + - + -
326A GLN* 3.9 6.1 - - - +
327A CYS 3.0 0.4 - - - -
328A GLN* 1.3 79.1 - - + +
330A GLU* 1.3 58.9 + - - +
331A ASP 2.9 4.5 - - - -
332A LEU* 2.7 34.0 + - + +
333A ASN 4.0 0.3 + - - -
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Residues in contact with GLU 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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272A PHE* 4.7 0.2 - - - -
288A LEU* 5.5 0.4 - - + -
326A GLN* 2.7 46.9 + - - +
327A CYS* 4.5 8.5 - - - +
329A PHE* 1.3 76.0 - - + +
331A ASP* 1.3 56.6 + - - +
332A LEU 3.2 0.2 - - - -
333A ASN* 3.1 24.4 + - - +
336A LYS* 4.3 10.3 - - - -
341A ILE* 4.2 35.2 + - + +
343A THR* 3.8 18.3 - - - +
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Residues in contact with ASP 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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327A CYS* 3.1 23.7 + - - +
328A GLN* 3.9 8.1 - - - +
329A PHE 2.8 0.6 + - - -
330A GLU* 1.3 74.0 - - - +
332A LEU* 1.3 59.0 + - + +
333A ASN 2.9 16.7 + - - +
336A LYS* 4.6 15.9 - - - +
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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