Contacts of the helix formed by residues 295 - 302 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A GLY* 1.3 73.8 - - - -
296A LEU* 1.3 63.4 + - - +
297A GLU* 3.6 9.5 + - - +
298A ASP* 3.0 37.9 + - - +
299A ARG* 3.1 23.2 + - - +
343A SER 4.0 0.9 - - - -
344A SER* 3.4 28.2 - - - -
346A VAL 3.4 5.4 - - - -
347A LEU* 4.1 8.1 - - - +
348A LEU* 4.3 1.8 - - - -
601A DL1 4.5 8.4 - - - -
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Residues in contact with LEU 296 (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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294A GLY 4.0 0.2 + - - -
295A SER* 1.3 70.4 - - - +
297A GLU* 1.3 59.2 + - - +
299A ARG* 4.5 0.7 - - - -
300A LEU* 2.9 52.7 + - + +
310A LEU* 3.9 18.8 - - + -
318A ILE* 4.2 30.1 - - + -
319A LEU* 5.4 0.4 - - + -
322A THR* 5.8 0.2 - - - +
343A SER* 3.4 17.9 + - - +
346A VAL* 2.7 29.1 + - + +
348A LEU* 4.1 9.3 - - + +
413A VAL* 4.0 19.7 - - + -
416A GLU* 6.6 0.2 - - + -
417A THR* 4.0 23.1 - - + +
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Residues in contact with GLU 297 (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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295A SER* 3.7 7.6 + - - +
296A LEU* 1.3 76.9 - - - +
298A ASP* 1.3 64.9 + - - +
301A HIS* 2.9 52.0 + - + +
343A SER* 3.1 37.5 + - - +
344A SER* 3.6 21.7 - - - +
390A TYR* 5.1 2.3 + - - -
416A GLU* 5.2 0.3 - - - +
422A ARG* 4.1 16.7 + - - +
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Residues in contact with ASP 298 (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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218A ILE 4.9 1.6 - - - +
293A ASN 5.8 0.4 - - - +
294A GLY* 5.4 1.1 - - - -
295A SER* 3.0 29.1 + - - +
297A GLU* 1.3 82.6 - - - +
299A ARG* 1.3 68.2 + - + +
302A CYS* 2.9 42.9 + - + +
601A DL1 4.1 29.5 - - - +
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Residues in contact with ARG 299 (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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293A ASN* 3.7 27.0 + - - +
295A SER 3.1 16.8 + - - +
296A LEU 3.9 2.5 - - - +
298A ASP* 1.3 78.6 - - + +
300A LEU* 1.3 63.6 + - - +
302A CYS 4.7 3.5 + - - +
307A CYS* 3.5 38.5 + - - +
308A PRO* 3.1 24.5 + - - +
309A PRO* 4.7 4.2 + - - +
310A LEU* 3.7 49.7 + - + +
314A GLN* 5.4 1.0 + - - -
348A LEU* 3.7 20.0 - - + -
352A LEU* 4.5 14.1 - - - +
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Residues in contact with LEU 300 (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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296A LEU* 2.9 43.9 + - + +
297A GLU 4.0 2.0 - - - +
299A ARG* 1.3 79.5 - - - +
301A HIS* 1.3 73.1 + - + +
302A CYS 3.8 0.9 + - - +
310A LEU* 4.3 11.2 - - + -
315A ARG* 3.4 39.6 + - - +
416A GLU* 3.9 35.2 - - + +
417A THR* 3.9 17.5 - - + +
420A GLY* 5.0 1.8 - - - -
479A ASP* 4.9 3.2 - - - +
481A ARG* 3.4 27.1 + - - -
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Residues in contact with HIS 301 (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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297A GLU* 2.9 39.3 + - + +
300A LEU* 1.3 84.4 - - + +
302A CYS* 1.3 63.5 + - - +
303A GLN* 3.4 18.9 + - - +
416A GLU* 2.5 35.6 + - + +
420A GLY 3.9 10.8 + - - -
421A GLN 3.2 37.4 + - - -
422A ARG* 3.4 49.8 + - + +
481A ARG* 4.6 6.3 + - - +
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Residues in contact with CYS 302 (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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297A GLU 4.2 0.2 + - - -
298A ASP* 2.9 37.5 + - + +
299A ARG 4.9 3.6 - - - +
300A LEU 3.6 1.3 - - - +
301A HIS* 1.3 74.8 - - - +
303A GLN* 1.3 68.6 + - - +
305A GLN* 3.5 47.2 + - - +
422A ARG* 5.1 2.9 - - - +
481A ARG* 5.5 1.9 + - - -
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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