Contacts of the strand formed by residues 240 - 243 (chain C) in PDB entry 1FIU
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 CYS 240 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211B GLY* 5.3 3.1 - - - +
217C VAL* 3.5 10.4 - - - +
218C VAL 3.4 18.9 + - - -
238C ILE* 3.3 5.2 - - - +
239C ASP* 1.3 85.7 - - + +
241C VAL* 1.3 83.1 + - - +
242C TYR* 3.7 17.7 - - + +
272C LYS 4.0 8.1 - - - +
273C ARG* 3.7 23.8 - - - +
275C LYS* 3.8 34.8 - - - -
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Residues in contact with VAL 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C VAL* 3.3 21.1 - - + +
220C THR* 4.1 22.0 - - + -
228C ILE* 4.6 6.5 - - + -
231C ILE* 4.2 12.6 - - + +
232C ALA* 3.6 33.7 - - + +
238C ILE* 4.1 13.0 - - + -
240C CYS* 1.3 80.2 - - - +
242C TYR* 1.3 67.9 + - - +
273C ARG 3.0 12.7 + - - +
274C LEU* 3.2 17.8 - - + -
275C LYS 2.9 23.2 + - - -
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Residues in contact with TYR 242 (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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217C VAL* 3.7 32.1 - - + +
218C VAL 2.8 18.1 + - - +
219C VAL* 3.2 14.7 - - + +
220C THR* 3.0 26.2 + - - +
240C CYS* 3.7 26.2 - - + +
241C VAL* 1.3 79.1 - - - +
243C HIS* 1.3 60.7 + - - +
275C LYS* 3.5 21.1 - - + -
276C ASP 3.3 24.7 - - - +
277C ILE* 4.3 6.7 - - - -
279C ASP* 3.9 0.2 - - + -
280C LEU* 3.6 38.6 - - + +
283C ASP* 2.6 38.1 + - - +
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Residues in contact with HIS 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ILE* 4.3 6.7 - - + -
219C VAL* 5.4 0.2 - - - -
220C THR* 3.5 14.4 - - + -
221C ALA 4.2 0.2 - - - -
222C GLU 2.7 30.8 + - - -
223C PRO* 4.3 0.8 - - - +
228C ILE* 3.6 17.9 - - + -
242C TYR* 1.3 73.9 - - - +
244C PHE* 1.3 89.6 + + - +
245C ALA 3.1 33.1 + - - -
246C LEU* 3.5 15.9 + - + -
249C LEU* 3.9 22.1 - - + +
274C LEU* 4.1 8.2 - - + +
275C LYS 2.8 14.8 + - - +
276C ASP* 3.6 4.5 - - - +
277C ILE* 2.9 23.0 + - - -
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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