Contacts of the helix formed by residues 258 - 263 (chain C) in PDB entry 1F9E
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 ILE 258 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C GLY* 2.9 22.1 + - - +
242C ILE 4.2 1.6 - - - -
243C ILE* 3.8 22.9 - - + -
256C ALA 4.5 0.4 - - - +
257C PRO* 1.3 72.7 - - - +
259C TYR* 1.3 62.0 + - - +
261C LEU* 3.1 10.2 + - + +
262C THR* 3.1 27.5 + - + +
282C ILE* 3.3 32.1 - - + -
286C GLN* 3.9 9.9 - - - +
329D LEU* 4.1 20.2 - - + -
331D MET* 3.4 32.5 - - + -
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Residues in contact with TYR 259 (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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335B ASN* 5.3 5.5 + - + -
336B ASN* 5.0 13.0 + - - +
241C GLY 4.7 0.2 + - - -
257C PRO* 2.9 6.9 - - + +
258C ILE* 1.3 79.7 - - - +
260C GLU* 1.3 70.3 + - + +
262C THR* 3.5 9.5 + - - -
263C SER* 2.9 48.1 + - - -
324D GLU* 3.8 28.3 + - - -
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Residues in contact with GLU 260 (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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212C TYR* 3.6 26.8 + - + +
257C PRO* 2.9 38.1 + - + +
259C TYR* 1.3 84.0 - - + +
261C LEU* 1.3 64.8 + - - +
263C SER* 3.4 13.3 + - - -
264C GLN* 3.2 19.8 - - - +
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Residues in contact with LEU 261 (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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211C ILE* 4.4 8.5 - - + -
212C TYR* 3.6 28.7 - - + -
215C LEU* 3.7 23.9 - - + +
234C ILE* 3.5 29.4 - - + -
243C ILE* 4.5 22.0 - - + -
256C ALA* 4.3 9.9 - - + -
257C PRO 3.5 13.2 - - - +
258C ILE* 3.5 13.7 - - + +
259C TYR 3.1 0.8 - - - -
260C GLU* 1.3 77.6 - - - +
262C THR* 1.3 66.3 + - + +
264C GLN* 3.1 22.9 - - - +
265C PHE* 3.8 7.3 - - - -
280C PHE* 4.3 8.1 - - + -
282C ILE* 5.3 3.1 - - + -
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Residues in contact with THR 262 (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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258C ILE* 3.1 25.5 + - + +
259C TYR* 3.5 16.1 + - - -
261C LEU* 1.3 71.2 - - + +
263C SER* 1.3 62.0 + - - +
264C GLN 3.0 9.4 + - - -
265C PHE* 3.2 8.1 + - - -
280C PHE* 3.7 37.5 - - + -
327D PHE* 3.2 36.9 - - + -
329D LEU* 4.9 11.4 - - + -
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Residues in contact with SER 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C TYR* 2.9 44.1 + - - -
260C GLU* 3.4 15.1 + - - -
262C THR* 1.3 76.7 + - - +
264C GLN* 1.3 61.7 + - - +
265C PHE 3.1 0.9 - - - -
266C THR* 2.9 33.0 - - - +
269C LYS* 3.5 12.5 - - - +
327D PHE* 5.2 0.4 - - - -
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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