Contacts of the helix formed by residues 286 - 290 (chain C) 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 PRO 286 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C HIS* 4.3 20.4 + - + +
48C GLY* 4.1 23.6 - - - +
49C TYR* 3.6 23.7 + - + -
50C SER 5.3 1.3 - - - +
229C VAL 5.8 1.1 - - - +
284C PRO 4.7 0.7 - - - +
285C SER* 1.3 87.8 - - - +
287C ALA* 1.3 63.6 + - + +
289C LEU* 3.2 20.1 + - + +
290C GLU* 3.5 9.4 + - - +
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Residues in contact with ALA 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ARG* 3.5 25.4 + - - +
49C TYR* 3.0 29.7 + - + +
277C LYS* 5.8 0.9 + - - -
285C SER* 3.0 9.0 + - - +
286C PRO* 1.3 82.1 - - - +
288C GLN* 1.3 63.9 + - + +
289C LEU 3.1 1.3 + - - -
290C GLU* 3.5 11.8 + - - +
72H ASN* 5.5 2.9 - - + +
74H VAL* 4.3 10.5 - - + -
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Residues in contact with GLN 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C THR* 4.9 0.9 - - - +
274C ALA* 3.2 27.6 + - - +
277C LYS* 3.0 56.3 + - + +
278C SER* 3.5 17.5 - - - +
283C LYS 4.2 1.2 - - - +
284C PRO* 4.4 5.4 - - + -
285C SER* 2.7 45.0 + - - +
287C ALA* 1.3 75.2 - - + +
289C LEU* 1.3 56.5 + - - -
290C GLU 3.4 2.8 + - - +
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Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C ALA* 4.0 14.6 - - + -
229C VAL* 3.7 24.9 - - + +
230C PHE* 3.8 28.0 - - + +
231C VAL 5.4 1.6 + - - +
270C THR* 3.5 11.1 - - + +
271C ILE* 4.1 15.0 - - + -
274C ALA* 3.5 14.4 - - + -
284C PRO* 3.5 38.6 - - + +
285C SER 2.9 15.2 + - - +
286C PRO* 3.2 11.2 + - + +
287C ALA 3.1 1.0 - - - -
288C GLN* 1.3 76.7 - - - +
290C GLU* 1.3 68.8 + - - +
291C LEU* 3.3 2.9 + - - +
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Residues in contact with GLU 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ARG* 3.9 12.9 - - - +
17C GLY* 3.2 25.0 - - - -
18C TYR* 2.8 27.7 + - + +
46C HIS* 3.7 15.3 - - - -
49C TYR* 2.9 39.8 + - - +
231C VAL 5.0 2.1 - - - +
270C THR* 3.2 9.9 - - - +
286C PRO 3.5 2.3 + - - +
287C ALA 3.5 11.4 - - - +
288C GLN 3.4 3.2 - - - +
289C LEU* 1.3 80.0 - - - +
291C LEU* 1.3 71.4 + - - +
292C ARG* 3.5 5.4 + - - +
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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