Contacts of the strand formed by residues 241 - 245 (chain C) in PDB entry 5AYR
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 VAL 241 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C LYS 3.0 9.6 + - - +
139C VAL* 3.2 7.2 - - + +
140C VAL 2.9 24.9 + - - -
240C LEU* 1.3 76.0 - - - +
242C PHE* 1.3 62.5 + - - +
243C LEU* 3.8 13.0 - - + -
262C HIS* 3.4 30.1 - - + +
264C LEU* 4.2 13.2 - - + -
287C THR* 3.5 36.1 - - + +
290C LEU* 4.0 13.0 - - + -
291C LEU* 4.0 22.0 - - + -
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Residues in contact with PHE 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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140C VAL* 3.4 35.7 - - + +
142C LEU* 5.1 3.4 - - + -
230C VAL* 4.3 15.9 - - + -
233C LEU* 4.8 9.0 - - + -
234C ASN 5.0 6.1 - - - -
240C LEU* 3.7 34.1 - - + -
241C VAL* 1.3 75.1 - - - +
243C LEU* 1.3 63.3 + - - +
244C LEU* 3.8 11.6 + - + -
256C ILE* 3.2 54.5 - - + -
261C HIS* 4.0 9.4 - + + -
262C HIS 2.8 20.7 + - - +
263C VAL* 3.5 5.6 - - + +
264C LEU 3.0 26.9 + - - +
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Residues in contact with LEU 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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139C VAL* 4.1 12.3 - - + -
140C VAL 2.8 16.0 + - - +
141C ILE* 3.9 25.9 - - + +
142C LEU 3.7 21.3 + - - +
241C VAL* 3.8 8.5 - - + -
242C PHE* 1.3 79.3 - - - +
244C LEU* 1.3 61.7 + - - +
245C TRP* 3.6 36.9 + - + +
264C LEU* 3.7 11.2 - - + -
283C HIS* 4.0 23.1 - - + +
284C PHE* 5.0 3.8 - - + -
287C THR* 3.5 26.0 - - - +
301C TRP* 4.7 9.0 - - + -
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Residues in contact with LEU 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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142C LEU* 3.6 28.0 - - + -
242C PHE* 4.5 12.6 - - + -
243C LEU* 1.3 74.1 - - - +
245C TRP* 1.3 61.2 + - - +
246C GLY 4.0 0.2 - - - -
249C ALA* 3.5 20.6 - - - +
250C GLN* 3.3 28.0 + - + +
253C GLY* 3.8 26.2 - - - +
254C SER* 5.8 0.2 - - - -
256C ILE* 4.7 2.9 - - + -
258C ARG* 5.0 0.4 - - - +
263C VAL* 3.5 30.5 - - + -
264C LEU 2.9 13.1 + - - +
265C GLN* 3.4 13.4 - - + +
266C THR 3.3 22.2 + - - -
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Residues in contact with TRP 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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141C ILE* 4.0 22.4 - - + -
142C LEU 5.1 3.8 + - - +
144C GLN* 5.4 1.0 + - - -
158C PHE* 3.9 28.7 - + + -
173C ILE* 3.5 31.0 - - + -
195C TRP* 6.2 0.9 - + - -
243C LEU* 3.6 34.0 + - + +
244C LEU* 1.3 80.2 - - - +
246C GLY* 1.3 63.8 + - - +
249C ALA* 3.4 16.5 + - - +
266C THR* 3.5 21.1 - - + -
267C ALA 3.7 11.4 - - - +
268C HIS* 3.6 17.3 - - + -
269C PRO* 3.7 17.7 - - + -
278C PHE* 3.7 16.1 - + - -
283C HIS* 3.2 25.2 + - + -
284C PHE* 4.2 21.5 - + - -
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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