Contacts of the helix formed by residues 296 - 302 (chain F) in PDB entry 1RFU
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 296 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266F VAL* 3.6 29.0 - - - +
269F ARG* 2.7 31.7 + - - +
292F ARG 2.4 22.7 + - - -
293F MET 2.5 18.8 + - - -
295F GLN* 1.3 71.0 - - - +
297F LYS* 1.3 66.2 + - - +
298F LYS 3.3 2.2 - - - -
299F ASP* 3.0 6.9 + - - +
300F ILE* 2.9 22.0 + - - +
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Residues in contact with LYS 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL* 3.3 34.9 + - + +
297B LYS* 5.1 0.9 - - + -
301B GLU* 2.6 39.1 + - - +
26F PHE* 3.8 25.6 - - + -
30F VAL* 4.2 8.7 - - + +
293F MET 3.3 1.8 + - - -
294F VAL 2.9 17.1 + - - +
295F GLN 3.3 1.2 + - - -
296F SER* 1.3 80.1 - - - +
298F LYS* 1.3 83.1 + - + +
300F ILE* 3.1 6.1 + - - +
301F GLU* 3.0 39.9 + - - +
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Residues in contact with LYS 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B LYS* 3.0 31.7 - - - +
301B GLU* 4.2 6.7 + - - -
295F GLN 5.0 1.2 + - - -
296F SER 3.3 0.6 - - - -
297F LYS* 1.3 96.6 - - + +
299F ASP* 1.3 67.8 + - - +
301F GLU* 3.1 22.5 + - - +
302F SER* 3.0 23.7 + - - +
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Residues in contact with ASP 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262F ALA* 4.2 3.1 - - - +
265F HIS* 3.5 35.1 + - + +
266F VAL* 5.2 0.9 - - + +
269F ARG* 2.6 36.7 + - - +
296F SER* 3.0 12.3 + - - +
298F LYS* 1.3 80.4 - - - +
300F ILE* 1.3 57.7 + - + +
302F SER 4.3 5.9 - - - +
303F PRO* 2.9 36.8 - - - +
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Residues in contact with ILE 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F PHE* 4.6 9.9 - - + -
27F PRO* 4.1 22.7 - - + -
30F VAL* 3.8 19.3 - - + -
31F LEU* 4.1 15.8 - - + +
236F LEU* 4.7 3.8 - - + -
240F MET* 4.3 20.8 - - - +
244F TRP* 4.1 4.2 - - - -
262F ALA* 4.6 6.5 - - + -
266F VAL* 4.3 17.0 - - + -
293F MET* 3.7 29.4 - - - +
296F SER* 2.9 25.1 + - - +
297F LYS* 3.4 7.0 - - - +
299F ASP* 1.3 78.7 - - - +
301F GLU* 1.3 64.2 + - - +
302F SER 3.4 0.2 + - - -
303F PRO* 3.5 9.0 - - - +
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Residues in contact with GLU 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B LYS* 2.6 36.2 + - - +
298B LYS* 4.2 4.5 + - - -
30F VAL* 4.0 16.5 - - + +
31F LEU* 4.2 12.4 - - - +
244F TRP* 4.0 15.8 - - - -
297F LYS* 3.0 33.2 + - - +
298F LYS* 3.2 36.7 + - - +
300F ILE* 1.3 79.0 - - - +
302F SER* 1.3 64.9 + - - +
303F PRO* 4.0 0.2 - - - -
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Residues in contact with SER 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244F TRP* 5.4 1.3 - - - -
298F LYS 3.0 11.5 + - - +
299F ASP* 3.3 6.7 - - - +
301F GLU* 1.3 81.0 + - - +
303F PRO* 1.3 67.9 - - - +
304F GLU 3.6 2.4 + - - -
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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