Contacts of the helix formed by residues 297 - 302 (chain B) in PDB entry 4Y5U
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 LEU 297 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B CYS* 3.7 11.0 - - + +
229B GLU* 3.7 28.9 - - + +
232B VAL* 3.6 35.4 - - + -
265B LEU* 5.4 0.2 - - + -
268B LEU* 4.0 15.5 - - + -
269B VAL* 4.3 15.5 - - + -
272B CYS* 3.7 22.9 - - - -
295B PHE* 3.3 15.0 - - + -
296B LEU* 1.3 77.1 - - - +
298B GLY* 1.3 54.2 + - - +
299B LEU 3.1 6.5 - - - -
300B ARG* 2.9 27.4 + - + +
301B PHE* 3.3 22.9 + - + -
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Residues in contact with GLY 298 (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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295B PHE* 3.3 27.7 + - - -
296B LEU 3.4 3.0 - - - -
297B LEU* 1.3 76.0 - - - +
299B LEU* 1.3 56.1 + - - +
300B ARG 3.1 1.1 - - - -
301B PHE 3.9 1.8 - - - -
302B LEU* 3.2 24.4 + - - +
349B ASN* 3.3 20.9 + - - +
356B CYS* 3.7 15.5 - - - -
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B GLN* 4.1 8.1 - - - +
229B GLU* 3.8 14.3 + - - +
296B LEU 4.6 0.8 + - - -
297B LEU* 3.1 2.0 - - - +
298B GLY* 1.3 76.4 - - - +
300B ARG* 1.3 74.4 + - - +
302B LEU 5.2 2.0 - - - -
349B ASN* 3.6 28.0 - - + +
350B SER 4.1 7.9 - - - +
351B ILE* 4.6 16.2 - - + -
354B ASN* 3.4 41.5 - - - +
355B CYS 3.5 26.7 - - - +
356B CYS* 4.6 0.8 - - - +
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Residues in contact with ARG 300 (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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229B GLU* 3.6 51.1 + - + +
232B VAL* 4.7 8.4 - - + +
233B ASP* 3.1 36.1 + - - -
297B LEU* 2.9 16.6 + - + +
299B LEU* 1.3 84.7 + - - +
301B PHE* 1.3 85.7 + - + +
302B LEU 3.8 2.9 - - - -
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Residues in contact with PHE 301 (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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232B VAL* 3.9 19.5 - - + -
235B TYR* 6.0 1.1 - + - -
265B LEU* 3.9 32.3 - - + -
269B VAL* 4.5 7.6 - - + -
295B PHE* 5.0 1.8 - + + -
297B LEU* 3.3 33.1 + - + +
300B ARG* 1.3 97.5 - - + +
302B LEU* 1.3 70.2 + - + +
306B ALA* 6.1 0.5 - - - +
392B PHE* 3.7 31.1 - + + -
394B LEU* 4.2 26.8 - - + -
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B PHE* 4.4 15.3 - - + -
298B GLY* 3.2 13.8 + - - +
299B LEU 5.2 1.2 - - - -
300B ARG 4.7 2.1 + - - -
301B PHE* 1.3 91.6 + - + +
303B GLY* 1.3 61.1 + - - +
306B ALA* 5.5 10.3 - - + +
307B LYS 5.3 2.2 - - - +
308B PRO* 5.6 2.0 - - + -
309B PRO* 3.7 38.4 - - + -
347B LEU* 4.0 22.4 - - + +
349B ASN* 3.6 14.5 + - - +
356B CYS* 4.4 7.6 - - - -
392B PHE* 3.5 26.7 - - + -
393B THR 5.4 0.7 - - - +
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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