Contacts of the helix formed by residues 289 - 297 (chain B) in PDB entry 4HYY
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 GLY 289 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226B MET* 3.4 25.1 - - - +
242B ARG* 4.6 12.7 - - - +
246B LEU* 4.5 3.1 - - - +
288B ILE* 1.3 76.4 - - - +
290B GLY* 1.3 68.1 + - - +
292B ILE* 3.4 15.2 + - - +
293B LEU* 3.1 20.5 + - - +
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Residues in contact with GLY 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B LYS* 5.1 12.6 - - - -
287B PRO 4.7 3.2 + - - -
288B ILE 3.5 3.4 + - - -
289B GLY* 1.3 81.2 - - - +
291B HIS* 1.3 62.1 + - - -
292B ILE* 5.3 1.6 - - - -
293B LEU* 4.2 0.2 - - - +
294B ALA* 3.1 21.0 + - - +
300B ARG* 4.4 4.3 + - - +
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Residues in contact with HIS 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B GLY* 1.3 71.3 - - - -
292B ILE* 1.3 67.2 + - + +
294B ALA* 3.9 7.3 - - + +
295B HIS* 3.0 27.2 + - - +
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Residues in contact with ILE 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B GLN* 3.5 45.3 - - + +
246B LEU* 4.0 17.0 - - + -
247B ALA* 3.7 37.9 - - + +
250B LEU* 4.1 7.2 - - + -
289B GLY 3.7 12.8 - - - +
290B GLY* 3.2 1.6 - - - -
291B HIS* 1.3 84.2 - - + +
293B LEU* 1.3 62.3 + - - +
295B HIS* 3.9 4.0 + - - +
296B ALA* 3.4 19.2 + - - +
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 6.0 1.1 - - + -
123B GLU* 3.3 23.1 - - + +
225B ILE* 3.8 25.1 - - + -
226B MET* 3.9 15.3 - - + -
246B LEU* 5.2 1.6 - - + -
250B LEU* 3.8 29.4 - - + -
266B VAL* 5.2 3.1 - - + -
268B ASN* 3.5 25.4 - - - +
288B ILE 3.7 8.7 - - - +
289B GLY* 3.1 17.3 + - - +
290B GLY 4.2 0.2 - - - +
292B ILE* 1.3 78.5 - - - +
294B ALA* 1.3 67.2 + - - +
296B ALA* 3.3 8.1 + - + -
297B SER* 3.0 17.7 + - - +
300B ARG* 4.5 2.7 - - - +
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B GLY 3.1 16.0 + - - +
291B HIS* 3.9 8.7 - - + +
292B ILE 3.3 0.2 - - - -
293B LEU* 1.3 77.1 - - - +
295B HIS* 1.3 62.6 + - - +
297B SER* 3.2 18.4 + - - +
300B ARG* 3.1 35.4 + - - +
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Residues in contact with HIS 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B GLN* 3.9 21.9 + - - +
291B HIS 3.0 18.0 + - - +
292B ILE* 3.9 4.4 + - - +
294B ALA* 1.3 80.1 - - - +
296B ALA* 1.3 65.4 + - - +
297B SER 3.4 4.3 + - - +
298B THR* 5.6 0.7 - - - +
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Residues in contact with ALA 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 3.5 19.8 - - + +
250B LEU* 3.6 45.3 - - + -
254B GLN* 3.2 28.7 - - + +
292B ILE 3.4 4.6 + - - +
293B LEU* 3.3 5.2 + - + +
295B HIS* 1.3 82.9 - - - +
297B SER* 1.3 61.4 + - - +
298B THR* 3.7 5.8 + - - +
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Residues in contact with SER 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 3.6 22.9 - - - -
123B GLU* 3.1 36.1 + - - -
293B LEU* 3.0 18.8 + - - +
294B ALA 3.2 13.9 - - - +
295B HIS 3.3 4.1 - - - +
296B ALA* 1.3 78.7 - - - +
298B THR* 1.3 64.1 + - - +
299B THR* 4.1 4.3 - - - -
300B ARG* 3.2 14.9 - - - +
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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