Contacts of the helix formed by residues 295 - 301 (chain B) in PDB entry 6BFN
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 295 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294B GLY* 1.3 74.8 - - - -
296B LEU* 1.3 64.5 + - - +
297B GLU* 3.7 10.1 + - - +
298B ASP* 3.1 46.3 + - - +
299B ARG* 3.1 13.7 + - - +
344B SER* 3.3 28.4 - - - -
346B VAL 3.3 6.3 - - - -
347B LEU* 4.2 7.3 - - - +
348B LEU* 4.4 1.8 - - - -
601B DL1 4.5 8.6 - - - -
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Residues in contact with LEU 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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294B GLY 4.0 0.4 + - - -
295B SER* 1.3 72.0 - - - +
297B GLU* 1.3 56.9 + - - +
299B ARG* 3.3 0.8 + - - -
300B LEU* 2.9 45.6 + - + +
310B LEU* 3.8 27.1 - - + -
318B ILE* 4.1 31.6 - - + -
319B LEU* 5.3 1.1 - - + -
322B THR* 5.7 0.4 - - - +
343B SER* 3.6 11.4 - - - +
346B VAL* 2.7 33.2 + - + +
348B LEU* 4.2 10.3 - - + +
413B VAL* 4.3 17.7 - - + -
417B THR* 3.9 21.8 - - + +
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Residues in contact with GLU 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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295B SER* 3.0 6.6 + - - +
296B LEU* 1.3 76.9 - - - +
298B ASP* 1.3 65.8 + - - +
300B LEU* 4.7 0.9 - - - -
301B HIS* 3.1 42.1 + - + +
343B SER* 3.1 38.1 + - - +
344B SER* 3.7 19.9 - - - -
390B TYR* 5.5 1.0 + - - -
416B GLU* 5.3 0.2 - - - +
422B ARG* 3.2 36.0 + - - +
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Residues in contact with ASP 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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218B ILE 5.0 1.0 - - - +
293B ASN 5.9 0.7 - - - +
294B GLY* 5.5 0.6 - - - -
295B SER* 3.1 26.4 + - - +
297B GLU* 1.3 86.1 - - - +
299B ARG* 1.3 66.6 + - - +
302B CYS* 3.2 21.9 + - + +
303B GLN* 3.2 36.8 + - - +
422B ARG* 5.1 3.0 + - - +
601B DL1 4.1 30.8 - - - +
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Residues in contact with ARG 299 (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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293B ASN* 3.7 35.9 + - - +
295B SER 3.1 7.4 + - - +
296B LEU 3.3 6.3 + - - +
298B ASP* 1.3 77.6 - - - +
300B LEU* 1.3 62.8 + - - +
303B GLN* 3.4 38.1 + - - +
307B CYS* 4.0 16.8 - - - -
308B PRO 3.7 20.4 + - - -
309B PRO* 4.7 5.4 + - - +
310B LEU* 3.4 54.9 + - + +
348B LEU* 3.8 23.1 - - + -
352B LEU* 3.9 19.4 - - - +
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Residues in contact with LEU 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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296B LEU* 2.9 38.7 + - + +
297B GLU* 3.9 3.8 - - - +
299B ARG* 1.3 79.5 - - - +
301B HIS* 1.3 66.4 + - + +
303B GLN 5.2 2.1 + - - -
310B LEU* 4.1 14.1 - - + -
315B ARG* 3.7 35.2 - - - +
343B SER* 5.2 0.2 - - - -
413B VAL 5.4 0.2 - - - +
416B GLU* 3.8 37.5 - - + +
417B THR* 3.8 20.9 - - + +
420B GLY* 5.1 3.1 - - - -
481B ARG* 2.3 35.6 + - - +
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Residues in contact with HIS 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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297B GLU* 3.1 23.0 + - + +
300B LEU* 1.3 90.1 - - + +
302B CYS* 1.3 67.8 + - - +
303B GLN 3.4 4.8 + - - +
416B GLU* 2.7 31.7 + - + +
420B GLY 3.3 21.9 + - - -
421B GLN* 3.3 33.9 - - - -
422B ARG* 3.4 47.2 + - + +
481B ARG* 4.4 6.3 + - - +
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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