Contacts of the helix formed by residues 299 - 304 (chain B) in PDB entry 1FIC
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 PRO 299 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294B ASP* 3.4 20.4 - - - +
296B GLY 5.8 0.2 - - - +
298B ASP* 1.3 88.5 - - - +
300B SER* 1.3 57.3 + - - +
301B ASP 2.9 11.6 + - - -
302B LYS* 4.1 2.8 + - - +
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Residues in contact with SER 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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298B ASP* 2.7 21.4 + - - -
299B PRO* 1.3 71.2 - - - +
301B ASP* 1.3 62.2 + - - -
302B LYS 3.4 1.6 - - - -
303B PHE* 3.0 21.3 + - - +
304B PHE* 3.1 40.5 + - - -
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Residues in contact with ASP 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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293B PHE 3.3 13.0 - - - +
294B ASP* 3.9 4.9 - - - +
295B PHE* 3.1 21.2 + - + +
296B GLY 3.0 25.8 + - - -
297B ASP* 3.1 16.9 + - - +
298B ASP* 2.9 32.4 + - - +
299B PRO 2.9 2.8 + - - -
300B SER* 1.3 77.9 - - - +
302B LYS* 1.3 57.2 + - - +
304B PHE* 3.1 5.2 + - - +
305B THR* 2.9 36.9 + - - +
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Residues in contact with LYS 302 (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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291B ASP* 3.0 41.9 + - - +
292B GLY* 3.7 14.0 + - - +
293B PHE* 3.2 20.8 + - - +
294B ASP* 4.1 13.8 + - + +
299B PRO 4.1 3.5 + - - +
300B SER 3.4 0.4 - - - -
301B ASP* 1.3 79.3 - - - +
303B PHE* 1.3 60.9 + - - +
304B PHE 3.4 0.5 + - - -
306B SER* 3.6 20.1 + - - -
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Residues in contact with PHE 303 (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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300B SER* 3.0 16.5 + - - +
302B LYS* 1.3 79.2 - - - +
304B PHE* 1.3 97.0 + + - +
306B SER* 3.6 6.7 + - - -
310B MET* 5.5 0.2 - - - +
321B LYS* 6.2 3.6 - - + -
337B ASN* 2.9 16.2 + - - +
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Residues in contact with PHE 304 (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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298B ASP* 6.0 1.8 - - - -
300B SER* 3.1 39.6 + - - +
301B ASP* 3.1 6.7 + - - +
303B PHE* 1.3 104.2 - + - +
305B THR* 1.3 58.4 + - + +
321B LYS* 4.3 13.9 - - + -
337B ASN* 2.9 18.3 - - - +
338B LYS* 2.8 87.0 + - + +
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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