Contacts of the helix formed by residues 273 - 282 (chain A) in PDB entry 5VZH
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 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A LYS 5.5 0.4 - - - +
272A LEU* 1.3 75.6 - - - +
274A GLN* 1.3 60.5 + - - +
275A GLN* 3.6 10.1 + - - +
276A GLN* 3.0 43.0 + - - +
277A LYS* 2.8 28.4 + - - +
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Residues in contact with GLN 274 (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 LEU 4.0 0.4 + - - -
273A THR* 1.3 74.0 - - - +
275A GLN* 1.3 58.7 + - - +
277A LYS* 3.3 10.8 + - - +
278A ALA* 2.9 28.6 + - - +
362A TYR* 4.3 9.3 - - + -
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Residues in contact with GLN 275 (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 PHE* 3.5 37.7 - - + +
245A GLY* 3.4 26.4 - - - +
273A THR* 3.2 8.5 + - - +
274A GLN* 1.3 79.0 - - - +
276A GLN* 1.3 55.8 + - - +
278A ALA* 3.2 3.8 + - - +
279A GLY 2.9 23.2 + - - -
362A TYR* 3.3 29.8 + - - +
389A PHE* 5.2 7.3 + - - -
2P G 3.8 20.7 + - - +
3P T 4.5 7.9 + - - -
9T G 5.8 0.2 + - - -
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Residues in contact with GLN 276 (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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243A ILE* 4.5 3.5 - - - +
244A PHE 3.9 6.7 - - - -
245A GLY* 2.9 35.1 + - - +
246A VAL* 3.9 8.5 - - + +
250A THR* 4.0 23.2 + - - +
254A TRP* 3.9 16.4 - - - -
271A LYS 4.1 1.9 - - - +
272A LEU* 3.5 20.3 - - + +
273A THR* 3.0 43.2 + - - +
275A GLN* 1.3 71.5 - - - +
277A LYS* 1.3 60.7 + - - +
279A GLY 3.7 0.5 - - - -
280A LEU* 2.8 32.5 + - - +
2P G 4.6 3.2 - - - -
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Residues in contact with LYS 277 (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 PRO* 5.0 6.7 - - + +
272A LEU* 3.8 25.8 - - + +
273A THR 2.8 22.3 + - - +
274A GLN* 3.5 11.2 - - - +
276A GLN* 1.3 76.5 - - - +
278A ALA* 1.3 56.6 + - - +
280A LEU* 3.8 4.7 - - - +
281A GLN* 2.8 43.6 + - - +
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Residues in contact with ALA 278 (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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274A GLN 2.9 9.3 + - - +
275A GLN 3.4 9.0 - - - +
277A LYS* 1.3 77.4 - - - +
279A GLY* 1.3 61.7 + - - +
281A GLN* 4.6 4.0 - - - -
282A HIS* 3.0 37.8 + - + +
362A TYR* 3.6 42.2 - - + -
391A ILE* 4.2 8.3 - - + -
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Residues in contact with GLY 279 (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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243A ILE* 3.9 10.0 - - - +
244A PHE* 3.6 36.4 + - - -
275A GLN 2.9 12.1 + - - -
276A GLN 3.3 0.9 + - - -
278A ALA* 1.3 75.2 - - - +
280A LEU* 1.3 57.3 + - - +
282A HIS 3.7 0.5 - - - -
283A HIS* 3.1 29.1 + - - +
286A LEU* 4.6 8.3 - - - +
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Residues in contact with LEU 280 (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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243A ILE* 4.1 9.2 - - + +
262A LEU* 4.1 39.7 - - + +
265A LEU* 3.8 21.3 - - + -
266A ARG* 3.2 56.7 + - + +
272A LEU* 3.8 27.6 - - + -
276A GLN 2.8 17.1 + - - +
277A LYS* 3.8 3.8 - - - +
279A GLY* 1.3 75.7 - - - +
281A GLN* 1.3 66.5 + - - +
283A HIS* 3.3 10.5 + - + +
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Residues in contact with GLN 281 (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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266A ARG* 4.9 5.7 + - - +
277A LYS* 2.8 32.6 + - - +
278A ALA* 3.9 5.4 - - - +
280A LEU* 1.3 75.2 - - + +
282A HIS* 1.3 72.3 + - + +
283A HIS 3.5 0.5 + - - -
284A GLN* 4.9 1.9 + - - +
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Residues in contact with HIS 282 (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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278A ALA* 3.0 29.8 + - + +
279A GLY 3.7 2.2 - - - -
281A GLN* 1.3 84.8 + - + +
283A HIS* 1.3 64.0 + - - +
284A GLN 3.2 3.4 + - - -
285A ASP* 3.2 9.2 + - - +
286A LEU* 2.9 36.1 + - + +
361A LEU* 3.8 41.5 + - + +
391A ILE* 4.1 16.2 - - + -
412A TRP* 5.0 8.0 - + - -
414A ALA* 3.5 20.9 - - + +
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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