Contacts of the strand formed by residues 242 - 245 (chain C) in PDB entry 1JLH
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 PHE 242 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C LEU* 4.1 0.4 - - - +
205C PHE* 3.4 28.3 - + + -
207C ILE* 3.8 16.2 - - + -
221C ALA 4.1 5.4 - - - -
224C ALA* 3.8 9.9 - - + -
225C LYS* 3.5 32.1 - - + -
228C PHE* 3.7 26.9 - + + -
238C VAL* 2.8 36.7 + - + +
239C ALA 4.0 7.8 - - - +
240C LYS 3.8 0.8 - - - -
241C HIS* 1.3 89.6 - - + +
243C VAL* 1.3 66.4 + - - +
255C PHE* 3.3 26.7 - + - -
257C ILE* 3.2 27.8 - - + +
261C ASN* 5.1 0.3 - - - +
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Residues in contact with VAL 243 (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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131C PHE* 3.5 30.7 - - + -
140C TRP* 5.0 3.8 - - + -
204C LEU* 4.1 10.3 - - + -
205C PHE 2.9 8.8 + - - +
206C ILE* 3.6 33.7 - - + -
207C ILE* 3.0 23.7 + - - +
239C ALA 5.4 0.2 - - - +
242C PHE* 1.3 78.4 - - - +
244C ALA* 1.3 62.4 + - - +
245C LEU* 5.1 0.7 - - + -
257C ILE* 3.8 12.2 - - - +
261C ASN* 3.6 24.7 - - + +
263C PHE* 4.4 3.6 - - + -
281C LEU* 4.3 14.1 - - + -
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Residues in contact with ALA 244 (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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207C ILE 3.5 3.8 - - - -
212C PHE* 3.6 27.8 - - + -
243C VAL* 1.3 77.2 - - - +
245C LEU* 1.3 58.5 + - - +
246C SER* 3.7 2.7 - - - +
252C VAL* 3.8 21.3 - - + -
257C ILE* 3.8 12.0 - - + +
261C ASN 3.2 6.6 + - - +
262C MET* 3.2 5.7 - - + -
263C PHE* 2.8 34.3 + - - -
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Residues in contact with LEU 245 (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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153C ASN* 4.5 2.2 - - - +
206C ILE* 3.5 27.8 - - + -
207C ILE 3.0 8.3 + - - -
208C ALA* 3.8 18.6 - - + -
209C SER 3.1 21.1 + - - -
243C VAL* 5.1 0.7 - - + -
244C ALA* 1.3 77.9 - - - +
246C SER* 1.3 58.9 + - - +
263C PHE* 3.2 21.5 - - + +
265C PHE* 3.3 12.0 - - + -
278C ALA 3.2 28.0 - - - +
279C ILE* 3.5 27.6 - - + +
281C LEU* 3.9 27.1 - - + -
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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