Contacts of the helix formed by residues 293 - 301 (chain O) in PDB entry 3H1I
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 293 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80N GLU* 4.3 0.2 + - - -
279O LEU 3.1 9.0 + - - -
280O GLY* 3.2 20.9 - - - -
290O SER* 3.5 19.0 - - - -
291O VAL 2.9 3.8 - - - -
292O THR* 1.3 76.7 - - - +
294O LYS* 1.3 68.8 + - - +
296O TYR* 2.7 39.3 + - - +
297O GLN* 2.9 24.9 + - - +
309O ALA 4.9 1.6 + - - -
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Residues in contact with LYS 294 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278O VAL* 3.0 30.6 + - + +
279O LEU* 3.6 9.6 + - + -
291O VAL 4.5 0.9 + - - -
292O THR 3.6 5.9 + - - +
293O SER* 1.3 70.6 - - - +
295O LEU* 1.3 54.0 + - - +
297O GLN* 3.6 3.3 - - - +
298O GLY* 2.6 36.4 + - - -
343O GLN* 3.4 25.1 + - + +
347O ALA* 6.4 0.7 - - + -
351O GLY 4.1 16.8 + - - +
353O THR* 4.8 3.6 + - - -
356O ASP* 2.8 40.8 + - - -
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Residues in contact with LEU 295 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279O LEU* 2.7 40.7 + - + +
293O SER* 4.4 0.2 - - - +
294O LYS* 1.3 76.8 - - - +
296O TYR* 1.3 67.7 + - - +
298O GLY* 2.8 3.5 + - - -
299O VAL* 2.8 22.2 + - + +
309O ALA* 4.5 11.7 - - + +
310O SER* 3.6 37.7 - - - +
311O ALA* 4.1 2.5 - - - +
324O PHE* 3.9 14.4 - - + -
340O ALA* 3.3 40.6 - - + +
343O GLN* 3.6 15.7 - - + +
344O LEU* 5.3 2.9 - - + -
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Residues in contact with TYR 296 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283O PRO* 4.4 14.6 - - + -
288O GLY 4.7 7.7 + - - -
289O SER* 4.3 19.1 - - - -
290O SER* 4.0 20.2 - - - +
293O SER* 2.7 25.8 + - - +
295O LEU* 1.3 80.6 - - - +
297O GLN* 1.3 68.8 + - - +
299O VAL* 2.7 16.3 + - - +
300O ALA* 3.2 11.4 + - + -
307O PHE* 3.6 33.1 + + - -
308O ASP* 3.8 21.0 + - - -
309O ALA 4.6 15.1 + - - +
52V ARG* 4.2 24.8 + - - +
56V SER* 3.9 22.2 - - - -
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Residues in contact with GLN 297 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289O SER* 2.8 24.9 + - - -
290O SER 2.8 23.1 + - - +
291O VAL* 3.0 37.5 - - + +
293O SER 2.9 19.3 + - - +
294O LYS* 3.6 3.8 - - - +
296O TYR* 1.3 79.4 - - - +
298O GLY* 1.3 66.9 + - - +
300O ALA* 3.0 19.9 + - - +
301O LYS* 3.3 33.0 + - - +
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Residues in contact with GLY 298 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294O LYS 2.6 15.0 + - - -
295O LEU 2.8 6.0 + - - -
297O GLN* 1.3 73.9 - - - +
299O VAL* 1.3 60.3 + - - +
301O LYS* 3.5 24.6 + - - +
302O ALA* 4.0 5.0 + - - +
339O ALA* 4.9 8.6 - - - +
343O GLN* 3.2 26.7 - - - -
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Residues in contact with VAL 299 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295O LEU* 2.8 20.0 + - + +
296O TYR 2.7 13.1 + - - +
298O GLY* 1.3 69.9 - - - -
300O ALA* 1.3 64.3 + - - +
302O ALA* 2.9 13.9 + - - +
303O THR* 3.1 19.6 + - + +
307O PHE* 3.6 26.7 - - + -
309O ALA* 4.2 19.3 - - + -
336O VAL* 3.9 38.1 - - + +
339O ALA* 4.8 7.4 - - + +
340O ALA* 4.4 14.8 - - + -
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Residues in contact with ALA 300 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296O TYR* 3.2 7.6 + - + +
297O GLN* 3.0 15.5 + - - +
299O VAL* 1.3 77.9 - - - +
301O LYS* 1.3 59.9 + - + +
302O ALA 2.9 3.3 + - - -
303O THR 2.8 23.2 - - - +
307O PHE* 3.5 24.8 - - + -
52V ARG* 4.7 9.0 + - - +
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Residues in contact with LYS 301 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297O GLN* 3.5 34.3 + - - +
298O GLY* 3.6 13.2 - - - +
299O VAL 3.2 1.0 - - - -
300O ALA* 1.3 76.3 - - + +
302O ALA* 1.3 57.7 + - - +
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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