Contacts of the helix formed by residues 290 - 300 (chain A) in PDB entry 1HS6
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 SER 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A GLU* 4.9 8.0 - - - +
234A PHE* 5.6 3.8 - - - -
236A GLU* 3.2 21.9 + - - -
240A MET* 3.6 18.5 - - - +
287A LYS 3.2 18.0 + - - -
288A SER 3.3 1.9 - - - -
289A LEU* 1.3 72.7 - - - +
291A ASN* 1.3 67.7 + - - +
292A VAL 2.9 2.7 - - - -
293A ILE* 2.7 27.6 + - - +
294A ALA 3.0 9.9 + - - -
329A CYS* 5.7 0.3 - - - -
333A PHE* 4.8 9.0 - - - -
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Residues in contact with ASN 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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288A SER 4.6 4.2 + - - +
289A LEU* 3.1 17.7 - - - +
290A SER* 1.3 79.0 + - - +
292A VAL* 1.3 68.2 + - - +
294A ALA* 3.2 3.0 + - - +
295A HIS* 2.9 29.1 + - - +
325A GLU* 2.9 29.6 + - - +
329A CYS* 4.1 25.8 - - - -
337A PHE* 6.4 0.7 - - + -
341A ASN* 5.7 4.5 - - - +
901A BES 4.1 11.1 - - - +
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Residues in contact with VAL 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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268A GLY 3.7 29.6 - - - +
269A GLY* 4.1 8.7 - - - +
278A VAL* 4.8 2.5 - - + -
282A LEU* 3.7 26.7 - - + -
289A LEU* 3.6 15.7 - - + +
290A SER 2.9 0.8 - - - -
291A ASN* 1.3 88.8 - - - +
293A ILE* 1.3 64.3 + - - +
295A HIS* 3.3 1.7 + - - +
296A GLU* 3.0 29.8 + - + +
533A GLU* 6.0 0.2 - - - +
563A ARG* 4.3 13.0 - - - +
901A BES 3.9 18.6 - - + -
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Residues in contact with ILE 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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234A PHE* 3.6 39.7 - - + -
237A THR* 3.7 23.3 - - + +
240A MET* 4.2 8.3 - - - -
256A TYR* 4.0 9.2 + - - +
258A LEU* 3.9 15.7 - - + -
276A THR* 5.3 0.2 - - + -
278A VAL* 3.8 26.7 - - + -
282A LEU* 4.2 3.8 - - + -
290A SER* 2.7 19.6 + - - +
292A VAL* 1.3 75.1 - - - +
294A ALA* 1.3 65.7 + - - +
295A HIS 3.1 0.3 + - - -
296A GLU* 3.2 2.9 + - - -
297A ILE* 2.9 37.6 + - + +
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Residues in contact with ALA 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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240A MET* 3.7 20.7 - - + -
290A SER 3.0 5.8 + - - +
291A ASN 3.2 10.3 + - - +
293A ILE* 1.3 75.5 - - - +
295A HIS* 1.3 62.6 + - - +
297A ILE* 3.5 5.8 - - - +
298A SER* 3.0 28.8 + - - -
325A GLU* 4.1 9.2 - - + +
328A ILE* 3.6 30.4 - - + +
329A CYS* 4.1 12.6 - - - -
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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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291A ASN 2.9 9.3 + - - +
292A VAL 3.4 4.3 - - - +
293A ILE 3.0 0.4 - - - -
294A ALA* 1.3 77.7 - - - +
296A GLU* 1.3 83.2 + - - +
298A SER 3.0 8.1 + - - -
299A HIS* 3.1 3.5 + + - -
318A GLU* 3.3 7.9 - - - -
321A THR* 3.0 37.6 - - + +
322A VAL* 3.9 19.0 + - + +
325A GLU* 2.9 30.1 + - - +
383A TYR* 4.0 0.2 - + - -
701A ZN 2.0 36.8 - - - -
901A BES 3.1 38.2 + - + +
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Residues in contact with GLU 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 TYR* 3.8 4.8 - - - +
269A GLY* 3.2 22.1 - - - -
270A MET 3.7 5.8 - - - +
271A GLU* 3.2 20.2 + - - +
276A THR* 3.6 38.5 + - + +
278A VAL* 5.3 0.4 - - + -
292A VAL* 3.0 15.9 + - + +
293A ILE* 4.2 0.9 - - - +
295A HIS* 1.3 78.4 - - - +
297A ILE* 1.3 66.1 + - - +
299A HIS* 3.2 21.2 + - - +
300A SER* 3.8 3.8 + - - -
304A ASN* 5.6 0.2 + - - -
901A BES 2.4 51.8 + - - +
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Residues in contact with ILE 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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237A THR* 3.9 10.5 - - + +
240A MET* 3.4 31.2 - - + -
241A LEU* 4.0 16.2 - - + +
244A ALA* 3.7 27.8 - - + -
256A TYR* 3.4 31.1 + - + -
293A ILE* 2.9 32.8 + - + +
294A ALA* 3.5 6.1 - - - +
296A GLU* 1.3 75.5 - - - +
298A SER* 1.3 59.9 + - - +
300A SER* 2.7 34.4 + - - -
301A TRP* 3.3 7.3 - - + -
328A ILE* 4.5 2.7 - - + -
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Residues in contact with SER 298 (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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244A ALA* 5.1 1.4 - - - +
294A ALA 3.0 11.9 + - - -
295A HIS 3.0 11.7 + - - -
297A ILE* 1.3 82.6 - - - +
299A HIS* 1.3 60.9 + - - +
301A TRP* 3.1 14.7 + - - +
302A THR* 3.1 21.4 + - - -
321A THR* 3.6 11.9 - - - -
324A LEU* 3.3 30.8 - - - +
325A GLU 3.6 3.1 + - - -
328A ILE* 3.3 17.7 - - - +
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Residues in contact with HIS 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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271A GLU* 3.2 40.0 + - + -
295A HIS* 3.1 10.8 + + - -
296A GLU* 3.2 14.5 + - - +
298A SER* 1.3 73.1 - - - +
300A SER* 1.3 52.9 + - - +
301A TRP 2.7 17.3 + - - -
302A THR 2.8 22.6 + - - -
303A GLY* 4.1 3.6 - - - -
304A ASN* 2.8 31.1 + - - +
317A ASN* 3.5 15.3 - - + -
318A GLU* 3.4 15.1 + - - -
321A THR* 3.0 17.2 + - + -
701A ZN 2.0 35.8 - - - -
901A BES 2.9 10.9 + - - -
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Residues in contact with SER 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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251A TYR* 3.4 35.3 + - - -
253A TRP* 2.9 30.7 + - - +
256A TYR* 4.5 6.4 - - - -
296A GLU 3.8 2.3 + - - -
297A ILE* 2.7 26.0 + - - -
299A HIS* 1.3 76.4 - - - +
301A TRP* 1.3 66.9 + - - +
304A ASN* 4.1 13.9 + - - +
305A LEU* 3.8 11.1 - - - +
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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